Abstract1

FROM GENOMICS TO PLANT IMPROVEMENT
基因组学与植物改良

Proceedings of the 3rd International Conference
of Plant Molecular Breeding
第三届植物分子育种国际会议论文摘要

Beijing，September 5-9, 2010
北京，2010 年 9 月 5－9 日

Proceedings of the 3rd International Conference of Plant 第三届植物分子育种国际学术会议摘要
Molecular Breeding, Sept 5-9, 2010, Beijing, China 2010 年 9 月 5－9 日，中国，北京

ICPMB2010 Organization
Honorary Presidents
Dr. JM Ribaut, Generation Challenge Program, CGIAR
Dr. Huqu Zhai, Chinese Academy of Agricultural Sciences
Dr. Qifa Zhang, Huazhong Agricultural University
Dr. Jiayang Li, Chinese Academy of Sciences

President
Dr. Zhikang Li, Chinese Academy of Agricultural Sciences & International Rice Research Institute

Co-Presidents
Dr. Jianmin Wan, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
Dr. Aimin Zhang, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

International Organizing Committee

Chair : Zhikang Li, Chinese Academy of Agricultural Sciences & International Rice Research Institute

Co-Chair : JM Ribaut, Generation Challenge Program, CGIAR

Members:
Aimin Zhang, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Andrew H. Paterson, University of Georgia, USA
Christian Jung, Plant Breeding Institute, Christian-Albrechts-University of Kiel
David Mackill, International Rice Research Institute, Philippines
Jiayang Li, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Jinguo Hu, USDA-ARS, USA
John Z Yu, USDA-ARS, Crop Germplasm Research, Texas A&M University, USA
Lijun Luo, SAGC, Shanghai Academy of Agricultural Sciences
Mark J. van Haaren, Keygene N.V.
Masahiro Yano, National Institute of Agrobiological Sciences, Japan
Graham McLaren, The Generation Challenge Program, CGIAR
Henry T. Nguyen, University of Missouri, USA
Noel Ellis, John Innes Centre, UK
Peter Langridge, Australia National Center for Plant Functional Genomics, Adelaide, Australia
Qifa Zhang, Huazhong Agricultural University
Roberto Tuberosa, University of Bologna, Italy
Swapan Datta, Indian Council of Agricultural Research, India
Yunbi Xu, CIMMYT, Mexico
Xingwang Deng, Peking University, China; Yale University, USA

2


Zhonghu He, Chinese Academy of Agricultural Sciences & CIMMYT
Michael Thomson, International Rice Research Institute, Philippines

Local Organizing Committee

Chair : Jianmin Wan, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences

Co-Chairs :
Shuming Wang, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences

Members :
Daowen Wang, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Yuxian Zhu, Peking University, China
Zhen Zhu, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

Program Committee
Chair : Zhikang Li, Chinese Academy of Agricultural Sciences & International Rice Research Institute

Co-Chair: Jinguo Hu, USDA-ARS, USA

Members:
David Mackill, International Rice Research Institute, Ithaca, New York, USA
JM Ribaut, Generation Challenge Program, CGIAR
Masahiro Yano, National Institute of Agrobiological Sciences, Japan
Mark J. van Haaren, Keygene N.V.
Noel Ellis, John Innes Centre, UK
Peter Langridge, Australia Center for Plant Functional Genomics
Qifa Zhang, Huazhong Agricultural University, China
Roberto Tuberosa, University of Bologna, Italy
Swapan Datta, Indian Institute of Agricultural Research, India
Xingwang Deng, Peking University, China; Yale University, USA
Yongbiao Xue, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

3


Contents
LECTURES
Plenary Session I……………………………………………………………….……………..10-13
Molecular breeding in developing countries: not a dream anymore. Ribaut JM

Progress of rice functional genomics research and the implications in crop genetic improvement. Zhang QF

Towards molecular design of super rice. Li JY

Progress and challenges in molecular breeding for drought tolerance in crop plants. Nguyen HT

Plenary Session II…………………………………………………………….……………..14-18
Three genetic systems controlling rice growth and productivity–a reevaluation of the green revolution. Li ZK

Genomics-assisted germplasm enhancement and its integration to breeding in rice. Yano M

Molecular basis of heterosis in crop plants: From nonadditive gene expression to gene regulatory network.
Sun QX

Transgenic trait development and deployment circa 2010. Bedbrook J

Transgenic crop research in India-current status and perspectives. Datta S

Plenary Session III……………………………………………………………….…………..19-23
Fostering molecular breeding in developing countries: The GCP approach. Delannay X

The sorghum genome, the diversification of cereals, and the productivity of tropical grasses. Paterson AH

Polyploidy and epigenetics: direct application and impact on crop improvement. Chen ZJ

Identification of key regulators for flowering time control and their application in breeding of biennial crop
species. Jung C

Whole genome strategies for molecular plant breeding. Xu YB

Plenary Session IV…………………………………………………………….……………..24-28
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrid. Deng XW

Breeding seeds of innovation. Hervé PM

4


Breeding by design and innovations in molecular plant breeding. Sorensen A

Meeting the challenge of higher nutritional value in seeds: a novel way of increasing methionine content in
seeds of the model plant of tobacco. Amir R

Association mapping for enhancing maize genetic improvement. Yan JB

Concurrent session 1: Molecular breeding for abiotic stress tolerances……………….…29-35
Mapping QTLs for root morphology in relation to nutrient uptake in wheat. Tong YP
The research progress of drought tolerance and molecular breeding in maize. Wang GY

Towards molecular breeding for salt tolerance through modification of root System architecture. Li X

Mapping and validating QTLs for plant height developmental behaviours in bread wheat. Jing RL

Discovery of genes for drought resistance improvement of rice by systematic genetic and functional genomic
approaches. Xiong LZ

Heat stress transcriptome analysis and functional characterization of responsive genes in wheat. Ni ZF

Concurrent session 2: Gene discovery and function……………………………………….36-42
Identification and application of the rice broad-spectrum blast resistance gene Pigm. He ZH

Mutant resources for functional studies of genes related to fertility in rice. Wu CY

Gene discovery from common wild rice (Oryza rufipogon Griff). Sun CQ

Discovery of brown planthopper resistance gene in rice. He GC

Molecular basis of cytoplasmic male sterility in rice. Liu YG

Toward map-based cloning of a good eating-quality QTL derived from an elite Japanese rice cultivar
Koshihikari. Hori K

Map-based cloning of QTL genes for flowering time/maturity in soybean. Xia ZJ

Concurrent session 3: Molecular breeding for biotic stresses…………………….……….43-49
From QTLs for fungal disease resistance to marker-assisted selection in durum wheat. Maccaferri M

Genomic approaches to plant defense research and crop improvement for insect resistance. Huang YH

Improvement of maize resistance to head smut and stalk rot. Xu ML

Enhancing broad spectrum resistance to rice diseases. Wang SP

Molecular mapping of adult-plant resistance genes to stripe rust and powdery mildew and validation of allelic
5


specific markers for Lr34/Yr18/Pm38 in Chinese wheat cultivars. Xia XC

Infection character and rice resistance screening of Southern rice black-streaked dwarf virus, a new Fiji virus
threating rice production in Asia. Zhou GH

Concurrent session 4: New transgenic technologies, products and markets……………..50-58
New transgenic technologies. Broglie R

Simultaneously changing several quality traits of Brassica napus by one transgenic event. Liu CL

In situ Pistil Delivery: A High Throughput Method of Brassica Genetic Transformation. Guo XL

Wheat genetic transformation in China, current status, challenges and future perspectives. Xia LQ

A new effective selection marker for crop transformation. Xia M

Enhancing the lysine in wheat grain by genetic transformation of a lysine rich protein gene Cflr. Ma HX

Transgenic strategies for improving drought tolerance traits in chickpea. Bhatnagar-Mathur P

Identification of stress-inducible and tissue-specific promoters in rice. Zhou JL

Concurrent session 5: Molecular breeding for cotton, brassica and bio-energy crops…..59-65
Progress toward genome sequencing of upland cotton, Gossypium hirsutum. Yu SX

Maternal effects and genetic improvement of seed oil content in Brassica napus. Wang HZ

Towards establishing a molecular breeding platform in cotton: Progress and challenges. Kumpatla SP

Molecular breeding of apomixis hickory. Huang JQ

Mining of novel genes for cotton fiber improvement. Yu JZ

Rational design and molecular breeding of sorghum, a dedicated bioenergy crop. Huang YH

Molecular breeding for cottonseed quality improvement. Zhu SJ

Molecular focus in commercial plant breeding. Rossouw JD

Concurrent session 6: Maize molecular breeding……………………………………….....66-72
QTL fine mapping of leaf angle and leaf orientation value in maize. Chen YH

Application of molecular techniques in maize haploid breeding. Chang MT

Identification of gene marker sets for screening maize lines for resistance to aflatoxin contamination. Luo M

Maize disease resistance gene discovery and utilization through association and linkage mapping. Mahuku G

6


Forward to molecular breeding from genetics in high-oil maize. Li JS

Genome-wide association study identifies known as well as novel loci for maize kernel tocopherol content and
composition. Li Q

Concurrent session 7: Applied plant genomics: from genomics to field…………………..73-77
Molecular breeding in chickpea- still a dream or the reality now! Varshney RK

Single-base resolution DNA methylomes of rice and new regulatory roles of DNA methylation in plant gene
expression. Li X

Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted
selection in wheat. Paux E

Integrating technologies for genetic improvement of quantitative traits in sorghum. Mace E

Irradiation mutant mapping of wild beet translocation lines carrying resistance genes against the beet cyst
nematode. Capistrano G

Concurrent session 8: Rice molecular breeding…………………………………..………..78-85
Development of 384-plex SNP marker sets for diversity analysis, mapping, and marker-assisted selection in rice.
Thomson MJ

Epigenetic and genetic control of drought tolerance in rice – a merging story of Larmarkism and Mendelism.
Li ZK

Clustered QTLs for source leaf size and yield traits in rice (Oryza sativa L). Yu SB

Molecular breeding approaches for sustainable disease resistance in rice: Current and future strategies.
Vera Cruz CM

MAS pyramiding of disease and pest resistant genes into drought tolerant hybrid rice. Mei HW

Development of single nucleotide polymorphisms (SNPs) detection platforms for genetic analyses and
molecular breeding of rice. Chen HD

Identification of a new blast resistant gene from Dacca6, a useful donor to improve the wide spectrum resistance
of Jin23 against rice blast fungi (Magnaporthe grisea) in Southeast China. Shi BH

Concurrent session 9: Wheat molecular breeding…………………………………….……86-93
Towards systematic genetic and functional analyses of the complex gliadin gene family in common wheat.
Wang DW

Development and application of molecular markers for improving processing quality in common wheat.

7


He ZH

New insights into the organization, recombination, expression and functional mechanism of low molecular
weight glutenin subunit genes at the complex glu-3 loci in bread wheat. Ling HQ

QTL mapping and marker assisted selection for some quality traits in bread wheat. Gupta P

Application of MAS for resistance to Fusarium head blight in a wheat breeding program Fedak G

Genomic distribution of quantitative trait loci (QTL) for yield and yield-related traits in common wheat
(Triticum aestivum). Zhang LY

Gene function and modulation of DREB (dehydration-responsive element binding protein) genes from soybean.
Chen M

Concurrent session 10: Molecular breeding platform and new technologies…………...94-98
The integrated breeding platform: vision and practice. McLaren G

Optimization of NGS-based SNP discovery approaches for facilitating molecular breeding in orphan crop
species. Varshney R

ISMAB: A data visualization and decision support tool for crop improvement. Shah T

Bringing genomic data to breeding: what we expect from the IBP to help future breeding. Liang CZ

Development and optimization of the 50K infinium chip for maize diversity analysis. Ganal M

Concurrent session 11: Germplasm and genetic diversity…………………………..…..99-106
Core collection-based genomic stocks in wheat. Jia JZ

High-throughput SNP genotyping of a subset of lettuce landraces for genetic diversity assessment. Hu JG

The genetic diversity, structure and classification of rice germplasm in China Li ZC

Genetic Diversity Studies on Cool Season Legumes. Zong XX

Molecular diversity reveals narrow genetic base of local Ghanaian accessions. Quain MD

The strategy and potential utilization of temperate germplasm for tropical germplasm improvement—a case
study in maize (Zea mays. L). Wen WW

Concurrent session 12: Molecular breeding in legumes and trees crops…………….....107-110

Concentration of genetic diversity for gene discovery and broadening genetic base of modern cultivar in
soybean. Qiu LJ

8


Development and application of genomic resources for molecular breeding in groundnut (Arachis hypogaea L).
Pandey M

The genomics path from pre-breeding to marker-assisted selection in wheat and barley. Tuberosa R

Genomics tools to aid cassava breeding for drought tolerance Rabinowicz P

Genetic networks controlling zygomorphic development in legumes Luo D

POSTERS……………………………………………………………………………..….111-231

9


Plenary Session I

Molecular breeding in developing countries: not a dream anymore
Ribaut JM
Generation Challenge Programme (GCP), c/o CIMMYT, Int APDO Postal 6-641, 06600 Mexico, DF, Mexico.
Email: J.RIBAUT@cgiar.org

Molecular breeding (MB) is definitely an efficient approach, when the necessary minimum human
and operational resources are already in place.This is because MB increases genetic gain per crop
cycle, stacksfavourable alleles at target loci and reduces the number of selection cycles. In the last
decade, the private sector has benefitted immensely from MB, which demonstrates its efficacy. In
contrast, MB adoption is still limited in the public sector, and hardly used in developing countries.
Major bottlenecks in these countries include shortage of well-trained personnel, inadequate
high-throughput capacity, poor phenotyping infrastructure, lack of information systems or adapted
analysis tools, or simply resource-limited breeding programmes.The emerging virtual platforms
aided by the information and communication technology revolution will help to overcome some
of these limitations, by providing breeders with better access to genomic resources, advanced
laboratory services, and robust analytical and data management tools. It is unrealistic to project
that large-scale MB breeding activities will be conducted in the near-term in developing countries.
However, the exponential development of genomic resources,the ever-decreasing cost of marker
technologiesand the emergence of platforms for accessing MB tools and support services, plus the
increasing public–private partnerships and needs-driven demand for improved varieties to counter
the global food crisis, are all grounds to predict that MB will have a significant impact on crop
breeding in developing countries.

10


Plenary Session I

Progress of rice functional genomics research and the implications in crop
genetic improvement
Zhang QF

National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong
Agricultural University, Wuhan 430070, China
Email: qifazh@mail.hzau.edu.cn

There has been a large global effort in rice functional genomics research aiming at
characterization of the full complement of the rice genes. The Chinese program on rice functional
genomic research is composed of the following components: (1) development of technological
platforms, (2) functional genomics of agriculturally important traits, (3) molecular cloning of
important genes and, (4) gene discovery by resequencing natural diversity of the rice species. The
traits targeted for functional genomic studies include yield, grain quality, stress tolerance, disease
and insect resistances, and nutrient use efficiency. Major progress has been made in a number of
fronts. Totally 270,000 independent transformants have been generated for the T-DNA insertion
mutant library and are now being screened for mutations of important traits. Over 50000 flanking
sequences have been isolated, and their analyses identified a number of interesting features of
nonrandom distributions of the T-DNA insertions in the rice genome. A large number of mutants
have now been targeted for gene isolation. For genome-wide expression profiling, data have been
generated from a large number of tissues covering the whole life cycle of the rice plants grown
under various conditions. Map-based cloning has been applied to isolate genes of agronomic
importance, including dozens of genes for yield, grain quality, fertility restoration, resistances to
biotic and abiotic stresses. Hundreds of accessions of rice germplasm have been resequenced
using new sequencing technologies. The implications of these developments in crop genetic
improvement will be discussed in the presentation.

11


Plenary Session I

Towards Molecular Design of Super Rice

Li JY, Wang YH
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
Email: jyli@genetics.ac.cn

Rice (Oryza sativa. L) is one of the most important staple crop, feeding more than half of the
world’s population. To achieve super rice varieties, we focus on the improvement of the grain
yield, grain quality, disease and insect resistance. Rice plant architecture, a collection of the
important agronomic traits that determine grain production, is mainly affected by factors
including tillering (tiller number and tiller angle), plant height, and panicle morphology. To
elucidate molecular mechanisms that control rice plant architecture, we have identified several
key genes that contribute greatly to the plant architecture of rice. Among them, the
MONOCULM1 (MOC1) gene was characterized as an essential regulator involved in tiller bud
initiation and outgrowth; the DWARF27 (D27) gene acts as a new component involved in the
biosynthesis of strigolactones and controls rice tiller number by regulating the outgrowth of tiller
buds; the LA1 gene plays an important role in determining tiller angle by negatively regulating
polar auxin transport (PAT); the SHORT PANICLE1 (SP1) gene encodes a transporter that
regulates the panicle size. The quantitative trait locus (QTL) gene, Ideal Plant Architecture 1
(IPA1), profoundly affects rice plant architecture and substantially enhances rice grain yield. Our
studies demonstrate that the application of these genes will facilitate to breed new elite varieties
by modifying tiller number, tiller angle, plant height, panicle morphology and lodging resistance.
To improve the rice grain quality, we carried out a systematic examination of genetic
determinations of rice grain ECQ through a comprehensive association analysis, the results of
which were then further have been confirmed by gene transformation. A series of molecular
markers have been developed for MAS. Our research findings provided a much clearer picture of
how starch synthesis system regulates grain quality. Also, we engage in cloning insect resistance
genes and developing molecular markers that are linked to quantitative trait loci for rice insect
resistance. Our studies will provide a molecular basis for developing super rice varieties in the
future.

12


Plenary Session I

Progress and challenges in molecular breeding for drought tolerance in crop
plants

Nguyen HT, Valliyodan B, Manavalan L
Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia,
MO 65211
Email: nguyenhenry@missouri.edu

Production of sufficient food for the growing world population during the verge of global climate
changes will be one of the major challenges for the future. This demands the requirement of
directed adaptation of crop species on an unprecedented magnitude. The global grain demand is
expected to be double by 2050. Much effort is being made by agricultural researchers worldwide
to reduce water use by crops to address the challenge which especially affect farmers in
drought-prone environments across the developing world. Understanding the concept and
components of drought resistance is a key factor for improving drought tolerance of crops.
Research to date has shown that improvements in crop drought resistance are from the increasing
dehydration avoidance, specifically increasing water availability for plant functions through
changes such as earlier development, smaller leaves, and deeper roots. In addition, plasticity
response of root growth under water deficit conditions, and dehydration tolerance traits such as;
osmotic adjustment, cell membrane stability, and mobilization of stem carbohydrate reserves in
crops also play specific roles in drought resistance mechanisms.
Molecular breeding approaches through identification of quantitative trait loci (QTL) and
marker-assisted selection offers an opportunity for significant improvements in the drought
tolerance of crops; however the successful application of marker assisted selection to crop
breeding is still in the preliminary stage. Past studies aimed at osmo-protection did not result in
field performance for drought tolerance in crops. Recent work on engineering candidate genes
including transcription factors and cold shock responsive proteins to enhance drought tolerance
showed promising results in field conditions. Transgenic maize plants with a transcription factor
show tolerance to drought based on the responses of a number of stress-related parameters,
including; stomatal conductance, leaf temperature, reduced wilting, and maintenance of
photosynthesis. Another example is engineering farnesylation machinery for plant drought
tolerance and yield protection-through stomatal closure, and these transgenic plants showed
promising field performance. Enhanced drought tolerance has also been observed in transgenic
plants expressing a cold shock protein under field conditions. Research advances in the area of
integrated functional genomics will certainly be helpful to improve the molecular breeding and
plant transformation approaches to achieve a significant progress in the generation of crop plants
with enhanced drought resistance.

13


Plenary Session II

Three Genetic systems Controlling Rice Growth and productivity – A
Reevaluation of the Green Revolution

Zhang F1, Xu JL1, Gao YM1, Yu SB2, Fu BY1, Ali J2 and Li ZK1,2 , *
1
Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese
Academy of Agricultural Sciences, Beijing 100081, China; 2 IRRI, DAPO Box 7777, Metro Manila, The
Philippines.
*Email: zhkli@yahoo.com.cn

The well-known Green Revolution (GR) since 1960s has more than doubled the productivity of rice, which
results from loss of function alleles at the GAox-2 locus encoding gibberellin 20-oxidase. Over 95% of the
current worldwide rice breeding programs are carried out in the mutant sd1 genetic backgrounds without
functional gibberellin acids (GA). To better understand the effects of sd1 on rice yield and related traits, the
phenotypic data of the IR64/Azucena DH population across 11 diverse environments were reanalyzed
using a new molecular-quantitative genetics model. Three genetic systems controlling rice growth and
productivity in rice were revealed, resulting in the discovery of 157 functional genetic units (FGUs)
affecting 9 traits related to rice growth, development and productivity. The first one was the GA-mediated
pathways controlled by SD1 and its 43 downstream FGUs for increased plant height (PH), increased
biomass, reduced spikelet fertility (SF), delayed heading (HD), reduced harvest index (HI), reduced panicle
number (PN), increased grain weight (GW) and reduced yield. Their effects gain yield (GY) and spikelet
number per panicle (SN) varied depending on the environments. Of these downstream FGUs, 3 PH QTLs
(QPh2b, QPh3b and QPh4a) had effects highly correlated with the mean PH values of the SD1
subpopulation, suggesting their positive responses to the overall soil fertility levels of the test environments.
Together, the GA-mediated pathways explained 38.6%, ranging from 16.0% for SF to 54.8% for PH. The
second system was the GA-repressed pathways that were expressed only in the mutant (sd1) background,
which comprised of 39 FGUs for PH, SF, biomass, HD, SN, PN, HI, GW, and yield. The effect directions
of most these pathways could not be determined based on available QTL information. The GA-repressed
pathways collectively explained 32.3% of the total genotypic variation of the 9 traits in the DH population,
ranging from 14.7% for PN to 59.3% for SN. The third one was the GA independent pathways controlled
by 75 FGUs that affected all measured traits. Together, the GA-independent pathways explained 29.2% of
the total genotypic variation of the 9 traits in the DH population, ranging from 6.0% for PH to 55.8% for
PN. Because the overall effects of the GR are reflected by the differences between the GA-mediated and
GA-repressed pathways, detailed Comparison between them indicated that the former had larger effects on
PH, HD, PN, HI and GY, whereas the latter influenced more SN and SF. Based on these results, the
advantages and potential consequences of the GR gene, sd1, were discussed in the context of the global
rice improvement and its challenges. Alternative breeding strategies for developing “Green Super Rice”
cultivars that have high yield potential with less input are proposed based on our discoveries.

14


Plenary Session II

Genomics-assisted germplasm enhancement and its integration to breeding in
rice

Yano M*, Hori K, Uga Y, Fukuoka S, Ebana K, Yonemaru J and Yamamoto T
QTL Genomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Japan.
*E-mail: myano@nias.affrc.go.jp

Progresses on recent genomics in rice have provided a new tools and opportunities to enhance
activity in crop improvement. Elucidation of the association between nucleotide and phenotypic
changes is inevitable to this end and has been a big challenge in molecular genetics and breeding
of rice. Toward this goal, we have been involved in the genetic dissection of natural phenotypic
variations in rice and have identified several genes involved in complex traits, including heading
date, shattering habit, pre-harvest sprouting, root morphology, disease resistance, seed size and
eating quality. To enhance the power of genetic dissection of complex phenotypes, we are
developing several mapping populations, such as recombinant inbred lines and chromosome
segment substitution lines, which will allow us to extract the useful alleles from natural variants.
Recently, QTL for durable resistance to rice blast has been cloned from Japanese upland rice. This
finding has opened new opportunity to introduction of the unique blast resistance gene without a
linkage drag of low eating quality. We have also detected a major QTL for deeper rooting on
chromosome 9. This finding has open new opportunity to enhance drought avoidance in rice. To
facilitate allele mining using novel plant materials, we have also embarked on the genome-wide
discovery of single nucleotide polymorphisms (SNPs). In particular, to overcome a shortage of
SNPs among temperate japonica cultivars, we have attempted whole-genome sequencing of
several Japanese cultivars using next-generation sequencing approaches. This SNP discovery has
led to the development of an array-based SNP genotyping system in Japanese rice cultivars.
Large-scale genotyping of these SNPs has made it possible to visualize pedigree haplotypes of
particular chromosome segments in the Japanese landraces and modern cultivars. These efforts in
genomics have opened up new opportunities to accelerate not only the genetic dissection of
complex traits, but also integration of genomics to breeding in rice.

15


Plenary Session II

Molecular basis of heterosis in crop plants: From nonadditive gene expression
to gene regulatory network

Sun QX, Ni ZF, Yao YY, Peng HR, Du JK
China Agricultural University, Beijing 100183, China.
*Email: qxsun@cau.edu.cn

Whole genome expression analysis in hybrid and its parental inbreds provides a platform to identify
nonadditively expressed genes in hybrids, which have given some insights into the understanding of
mechanisms of heterosis. In this study, two wheat (Triticum aesticum L.) hybrid F1 derived from same female
parent but displaying contrasting heterosis in primary root are used for expression analysis by using wheat
genome array. The expression polymorphism analysis between the parental inbreds indicates that up to 4%
genes display expression difference, but more than 3 times more present-absent genes between the two parental
inbreds are detected in highly heterotic Hybrid A than in nonheterotic Hybrid B. Differential expression (DE)
analysis in hybrids and their parental inbreds identify 1019 (4.94%) and 698 (3.23%) DE genes in Hybrid A and
B, respectively. It is interesting to note that heterotic Hybrid A tends to have more DE genes of dominance and
partial dominance expression modes than nonheterotic Hybrid B which, however, tends to have more DE genes
of negative partial dominance expression mode. By adopting the “Wooden Barrel Principle”, we propose that
accumulation of dominance and partial dominance expression in wheat hybrid could be a major determinant of
root heterosis. We also find that a substantial number of stress-related genes as well as retrotransposon-like and
transposon-like genes are also included in the DE genes. We propose that as compared to the interspecific
hybridization which can be a source of genomic shock as described by Barbara McClintock, hybrids derived
from less distantly-related two inbreds can be a source of “mild genomic shock” or “intrinsic stress” in the
hybrid genome, which, in turn, could cause expression changes of genes, especially stress-related genes and
retrotransposon. Heterosis in internode elongation and plant height are commonly observed in hybrid plants, and
higher GAs contents were found to be correlated with the heterosis in plant height. By using the uppermost
internode tissues of wheat, we examined expression patterns of genes participating in both GA biosynthesis and
GA response pathways between a hybrid and its parental inbreds. Our results indicated that among the 18 genes
analyzed, genes encoding enzymes that promote synthesis of bioactive GAs, and genes that act as positive
components in the GA response pathways were up-regulated in hybrid, whereas genes encoding enzymes that
deactivate bioactive GAs, and genes that act as negative components of GA response pathways were
down-regulated in hybrid. Moreover, the putative wheat GA receptor gene TaGID1, and two GA responsive
genes participating in internode elongation, GIP and XET, were also up-regulated in hybrid. A model for GA
and heterosis in wheat plant height was proposed. This model is also validated by using 16 wheat hybrids with
different level of heterosis in plant height. Our results provided molecular evidences not only for the higher GA
levels and more active GA biosynthesis in hybrid, but also for the heterosis in plant height of wheat and possibly
other cereal crops. Moreover, overexpression of 6 differentially expressed genes suggested that up-regulated
genes in hybrids could enhance the trait performance but the down-regulated genes in hybrids can have negative
effects on the trait performance.
16


Plenary Session II

Transgenic Trait Development and Deployment Circa 2010
Bedbrook J
Vice President, DuPont Agricultural Biotechnology

Transgenic traits providing weed and insect pest control solutions, first introduced in the mid
1990’s have been rapidly adopted globally in corn, soybean and cotton. Next generation
transgenic traits providing new functionalities, including; grain quality attributes, abiotic stress
tolerance, disease resistance and seed production systems are close to commercialization. In this
paper I describe DuPont’s approaches to genetic based gene discovery, event selection, trait
development and commercial deployment for these next generation traits.

17


Plenary Session II

Transgenic Crop Research in India-Current status and perspectives

Datta SK
Crop Science Division, ICAR, Krishi Bhavan, New Delhi-110114, India
Email: swpndatta@yahoo.com

Functional genomics provides powerful tool for the identification of desirable genes and their
introduction into crops for the trait improvement. The ability to introduce beneficial genes under
the control of specific promoters through transgenic approaches is the path towards targeted crop
improvement. Development and commercialization of transgenic crops expressing a wide range of
agronomic traits during mid-nineties has virtually revolutionized the face of global agriculture.
Safety of transgenic crops, especially GM food crops is a major concern. To address all the issues
related to biosafety, environmental safety, risk assessment, biodiversity and socio-economic
impact the GM crops, Government of India has entrusted the task to the Ministry of Science and
Technology to develop one window regulatory mechanism to approve and release the GM in the
field through NBRA (National Biotechnology Regulatory Authority). The environmental release
of transgenic cotton with insect-pest resistance in 2002 is a landmark in Indian agriculture. It has
placed India at the forefront of global cotton production and trade. At the global level, cultivation
of transgenic crops in the past twelve years has conferred significant social, economic and
environmental benefits to mankind. Such a sea change in the production of major food crops is the
need of the hour. Bt cotton, which confers resistance to important insect pests of cotton, was first
adopted in India as hybrids in 2002. The number of events, as well as the number of Bt cotton
hybrids and companies marketing approved hybrids increased from one event and 20 hybrids in
2005 by more than three-fold in 2009 to six events and 282 hybrids. India currently produces >30
million bales of cotton per year and occupies # 2 position in terms of global cotton production
and now #1 in Bt cotton areas. Other Crops such as Bt rice, Bt brinjal, transgenic tomato,
Sorghum, Brassica, Groundnut etc are at the different stages of development.

18


Plenary Session III

Fostering Molecular Breeding in Developing Countries -the GCP approach

Xavier Delannay
Generation Challenge Program, CGIAR
Email：x.delannay@cgiar.org

An important focus of the Generation Challenge Programme (GCP) since its inception has been to
promote an increased use of molecular marker technologies in developing country breeding
programmes. This started with the implementation in applied breeding programmes of
marker-assisted selection for new important traits that had been mapped with funding assistance
from the GCP. More recently, the GCP has focused on the implementation of new integrated
breeding programmes in developing country crops through the use of molecular breeding
technologies such as marker-assisted recurrent selection (MARS). The use of MARS should help
accelerate the improvement of crops growing under suboptimal conditions of Africa and Asia,
which is also a focus of the GCP. This development will be greatly facilitated by the Integrated
Breeding Platform that is concurrently being developed by the GCP. Examples will be shown of
practical applications of molecular breeding being used or being put in place in developing
countries for crops such as rice, cassava, sorghum, cowpea and chickpea.

19


Plenary Session III

The sorghum genome, the diversification of cereals, and the productivity of
tropical grasses
Paterson AH

Plant Genome Mapping Laboratory, University of Georgia 111 Riverbend Road, Rm 228, Athens, GA 30602

Email: paterson@plantbio.uga.edu

Sorghum, an African grass related to sugarcane and maize, is grown for food, feed, fiber, and fuel,
is representative of tropical grasses that are among the most efficient biomass accumulators thanks
to ‘C4’ photosynthesis. An initial analysis of the sorghum genome placed ~98% of genes in their
chromosomal context using whole genome shotgun sequence validated by genetic, physical, and
synteny information. Genetic recombination is largely confined to about one-third of the sorghum
genome with gene order and density similar to those of rice. Retrotransposon accumulation in
recombinationally-recalcitrant heterochromatin explains the ~75% larger genome size of sorghum
than rice. While gene and repetitive DNA distributions have been preserved since
paleopolyploidization ~70 million years ago, most duplicated gene sets lost one member before
sorghum/rice divergence. Concerted evolution makes one duplicated chromosomal segment
appear only a few million years old. About 24% of genes are grass-specific and 7% are
sorghum-specific. Recent gene and miRNA duplications may contribute to sorghum’s drought
tolerance. The sorghum sequence offers new means to improve sorghum itself and new or existing
biofuel crops, and to try to control weedy and invasive plants.

20


Plenary Session III

Polyploidy and epigenetics: direct application and impact on crop
improvement

Chen ZJ
Institute for Cellular and Molecular Biology, The University of Texas at Austin, Texas 78712, USA.
Email: zjchen@mail.utexas.edu

Polyploidy, or whole-genome duplication (WGD), is common in some animals and many plants,
including important crops such as wheat, cotton, canola, sugar cane, and switchgrass. The
common occurrence of polyploidy suggests an evolutionary advantage of having multiple sets of
genetic material for adaptive evolution and crop domestication. However, increased gene and
genome dosages in autopolyploids (duplications within species) and allopolyploids (combination
of two or more divergent genomes among species) often cause genome instabilities, chromosome
imbalances, regulatory incompatibilities, and reproductive failures. Therefore, new allopolyploids
must establish a compatible relationship between alien cytoplasm and nuclei and between two
divergent genomes, leading to rapid changes in genome structure, gene expression, and
developmental traits such as fertility, inbreeding, apomixis, flowering time, and hybrid vigor.
Although the underlying mechanisms for these changes are poorly understood, some themes are
emerging. There is compelling evidence for epigenetic changes during early stages of polyploid
formation. Using Arabidopsis allopolyploids and hybrids as model systems, we found that
changes in cis- and trans-acting effects, chromatin modifications, RNA-mediated pathways, and
regulatory networks modulate differential expression of homoeologous genes and phenotypic
variation such as flowering time. We have shown that nonadditive gene expression, small RNAs,
and epigenetic regulation of circadian-mediated metabolic pathways, play central roles in growth
vigor in hybrids and allopolyploids. Understanding epigenetic mechanisms for polyploidy and
hybrid vigor will facilitate the use and exploitation of the increased biomass and yield in hybrids
and allopolyploids for food, feed, and fuels.

21


Plenary Session III

Identification of key regulators for flowering time control and their application
in breeding of biennial crop species

Jung C*, Wafa SAE, Büttner B, Schulze-Buxloh G, Müller A
Plant Breeding Institute, Christian-Albrechts-University of Kiel
*Email: c.jung@plantbreeding.uni-kiel.de

Floral transition is a major developmental switch that is tightly controlled by regulatory pathways
that integrate endogenous and environmental cues to ensure flowering under favourable
conditions. Sugar beet (Beta vulgaris) is a biennial crop which bolts and flowers after a period of
cold temperatures over winter, however annual types without vernalization requirement exist. We
have identified >30 flowering time regulators from the beet genome by different approaches. The
existence of an FLC-like gene in beet suggests similar regulatory pathways as in Arabidopsis. In a
complementary approach additional components of the floral transition gene network in sugar
beet are being identified by homology to genes from model species and genome-wide transcript
profiling. We found a number of ESTs with homology to Arabidopsis genes. Using RACE and
BAC cloning we identified full length cDNA and genomic sequences. We functionally
characterized these sequences by expression analysis and transformation into Arabidopsis. We
found evidence for the existence of autonomous and vernalization pathways in beet similar to
Arabidopsis, however substantial differences between both species exist. Annuality is controlled
by the bolting locus B. We have identified by map based cloning sequences from the B locus with
homology to floral transition genes from other species that suggest that they mediate bolting time
control in response to environmental cues. Another QTL for early bolting was mapped with
molecular markers demonstrating for the first time that at least two loci cause early bolting in
beets. A beet TILLING platform now also enables the identification of mutants and functional
characterization of candidate genes. New beet prototypes with altered vernalization requirement
have been produced either by EMS mutagenesis or transformation. These mutants in combination
with transgenic beets with altered bolting behaviors are needed for the breeding of winter beets
which are sown before winter. Apart from winter hardiness these beets must be completely bolting
resistant to prevent bolting after winter. Different approaches to establish fully bolting resistant
beet prototypes are presented.

22


Plenary Session III

Whole Genome Strategies for Molecular Plant Breeding

Xu YB1*, Lu YL2 and Gao SB2
1
Institute of Crop Science and CIMMYT, Chinese Academy of Agricultural Sciences, National Key Facilities
for Crop Genetic Resources and Improvement, 12 Zhongguancun South St., Beijing 100081, China. 2Maize
Research Institute, Sichuan Agricultural University, Ya’an, Sichuan 625014, China.

*Email: y.xu@cgiar.org

Molecular breeding for complex traits in plants needs to understand and manipulate many factors
influencing plant growth and development including genotypes, environments and their
interaction. Molecular breeding procedures can be facilitated and revolutionized through whole
genome strategies, which are featured by utilizing full genome sequence and genome-wide
molecular markers to address all genomic and environmental factors through a representative or
complete set of genetics and breeding germplasm. The strategies should be developed for
understanding specific genomic region, genes, haplotypes, linkage disequilibrium block or alleles
and their contribution to specific phenotypes and breeding products. Genotyping-by-sequencing
and genomewide selection are two important components of the strategies. These strategies need
to be integrated with precision phenotyping and powerful population management systems.
Examples of such integrated systems include joint linkage-linkage-disequilibrium mapping for
marker development and gene discovery, breeding-to-genetics approaches by using existing
genetic and breeding materials, and simultaneous genomewide improvement for multiple traits.
As components of whole genome strategies, molecular breeding platforms and methodologies
should be backed up with strong supporting systems such as breeding informatics and decision
support tools. Some basic strategies will be discussed using maize as an example, including (1)
seed DNA-based genotyping for simplifying marker-assisted selection, reducing breeding cost and
increasing scale and efficiency, (2) selective genotyping and phenotyping for capturing most
important contributing factors with optimized breeding design, (3) flexible genotyping systems
refined for different selection methods including marker assisted selection, marker assisted
recurrent selection and genomic selection, and (4) sequence-based strategies for marker
development, allele mining, gene discovery and molecular breeding.

23


Plenary Session IV

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and
Their Reciprocal Hybrids

He GM, Zhu XP, Elling AA, Chen LB, Chen RS and Deng XW*
Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking
University, Beijing 100871, China. Department of Molecular, Cellular and Developmental Biology, Yale
University, New Haven, CT 06520, USA. Institute of Biophysics, Chinese Academy of Sciences, 15 Datun
Road, Beijing 100101, China
*Email: xingwang.deng@yale.edu

The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental
interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA
transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity
was correlated with DNA methylation and both active and repressive histone modifications in
transcribed regions. Differential epigenetic modifications correlated with changes in transcript
levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic
modifications in reciprocal hybrids were observed. Through analyses of single nucleotide
polymorphisms from our sequence data, we observed a high correlation of allelic bias of
epigenetic modifications or gene expression in reciprocal hybrids with their differences in the
parental lines. The abundance of distinct small RNA size classes differed between the parents and
more small RNAs were down-regulated than up-regulated in the reciprocal hybrids. Together, our
data reveal a comprehensive overview of transcriptional and epigenetic trends in heterotic rice
crosses, and provides a very useful resource for the rice community.

24


Plenary Session IV

Breeding Seeds of Innovation
Hervé PM
Bayer Cropscience, Bioscience NV Belgium

At Bayer Cropscience, we help farmers worldwide meet the ever-increasing demand for
affordable and high quality food, feed, fiber and energy crops. We aim at providing sustainable
crop solutions from seed to harvest, with outstanding seeds and modern crop protection products.
Major technology platforms based on the complementary of modern breeding methods and plant
biotechnology are used to develop new seeds and innovative traits solutions. An update of our
Seeds & Traits Pipeline and key examples of successful molecular breeding solutions for our core
crops will be presented.

25


Plenary Session IV

Breeding by design and innovation in molecular plant breeding
Sørensen AP, van Schriek M, Hofstede R, Guerra J, Prins M and Buntjer JB
Keygene N.V., Agro Business Park 90, P.O. Box 216, 6700 AE Wageningen, the Netherlands

Since the concept of Breeding by Design (BBD) was launched by KeyGene in 2003, DNA
technologies have developed with a dramatic acceleration; especially high-throughput sequencing
technologies are revolutionizing the DNA research arena. The possibilities for genetic research to
elucidate the molecular mechanism of phenotypic expression have increased significantly. As a
consequence, implementing BBD or BBD like approaches for trait and variety improvement
programs is ongoing.
We will discuss here a selection of current genomic tools and applications. Whole genome
sequence scaffolds and whole genome BAC based physical maps of commercial crop species are
being developed, following the examples of model plant organisms. The discovery of total
germplasm variation at the genotypic level and at the gene haplotype level is practically feasible
for many crop species. Phenotypic evaluation of germplasm variability is performed with high
precision digital imaging systems and supported by statistical tools for evaluation of
reproducibility, heritability and interrelatedness of phenotypic scores.
The current challenge for plant geneticists clearly lies in the ability to integrate and aggregate the
different and large data sources, in order to make firm and robust associations between the
phenotypic variability and the genotypic variability, after which these can immediately be
exploited by modern plant breeders. Furthermore novel technologies for generation of mutant
alleles of interesting plant genes are in development and will increase the genetic variability of
germplasm available for variety improvement programs. We will present some of the approaches
taken by Keygene to assist plant breeders in these novel opportunities.

26


Plenary Session IV

Meeting the challenge of higher nutritional value in seeds: a novel way of
increasing methionine content in seeds of the model plant of tobacco

Godo I, Matityahu I, Hacham Y, Amir R
Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel

The sulfur-containing amino acid, methionine, is an essential amino acid whose level limits the nutritional
value of crop plants. Yet, aside from its nutritional importance, methionine is also a fundamental
metabolite in plant cells because it indirectly regulates a variety of cellular processes as the precursor of
S-adenosyl methionine (SAM). This study describes the first modification of methionine biosynthesis in
seeds using the model plant, tobacco (Nicotiana tabacum). Overexpression of the unregulated form of
cystathionine gamma synthase (AtD-CGS), the first unique enzyme of methionine biosynthesis pathway
from Arabidopsis in tobacco plants, led to an over 10-fold increase in methionine content. However, in
these transgenic plants, the methionine level inside their seeds increased only by 15% compared to
wild-type seeds. Similar results were obtained when AtD-CGS was seed-specific expressed in tobacco
plants. This suggests that the CGS expression level does not limit methionine synthesis in tobacco seeds.
To further study the factors regulating methionine synthesis in seeds, the receptacle of developing pods
were fed with homoserine, the substrate of CGS. Seeds from these pods demonstrated three-fold higher
levels of methionine, suggesting that homoserine content limits methionine synthesis. To further test this
assumption, we next crossed between plants seed specific expressing AtD-CGS with those seed-specific
expressing the feedback-insensitive bacterial aspartate kinase (bAK), which evidence suggests their seeds
have a higher homoserine content. Seeds obtained from the progenies of this cross showed a three-fold
higher level of methionine compared to wild-type seeds. In addition, the level of threonine, an important
essential amino acid that limits the nutritional quality of cereals, accumulated significantly in these seeds.
Our next goal was to reveal if the developing transgenic seeds are tolerant to metabolic perturbations that
occur with changes in methionine and threonine levels. To this end, we performed metabolic profiling to
wild-type and transgenic seeds expressing AtD-CGS, bAK and AtD-CGS/bAK using GC-MS. A principal
component analysis of about 150 metabolites from each transgenic line shows that these lines differ
significantly from one another. Of these metabolites, only 12 compounds significantly changed and
contributed to this diversity. These include the main amino acids, glutamine and asparagine, and several
sugars, trehalose, galactose, glycerol and melbiose. A further study should be performed to reveal the
relationships between these metabolites and methionine metabolism. In general, this study demonstrates a
novel way of increasing methionine content in seeds, which consequently contributes to enhancing their
nutritional value.

27


Plenary Session IV

Association mapping for enhancing maize genetic improvement
Yan JB 1,2 *, Li JS 2
1
International Maize and Wheat Improvement Center, (CIMMYT), Apartado Postal 6-640, 06600 Mexico, DF,
Mexico China
2
National Maize Improvement Center of China, CAU, Beijing 100193, China
E-mail: j.yan@cgiar.org

Association mapping through linkage disequilibrium (LD) analysis is a powerful tool for the
dissection of complex agronomic traits and for the identification of alleles that can contribute to
the enhancement of a target trait. With the developments of high throughput genotyping
techniques and advanced statistical approaches as well as the assembling and characterization of
multiple association mapping panels, maize has become the model crop for association analysis.
In this talk, we summarize the progress in maize association mapping and the impacts of genetic
diversity, rate of LD decay, population size and population structure. We also report the use of
candidate genes and gene-based markers in maize association mapping studies which has
generated particularly promising results. In addition, we examine recent developments in
genome-wide genotyping techniques which promise to improve the power of association mapping
and significantly refine our understanding of the genetic architecture of complex quantitative traits.
Already these seem to be suggesting that the structure of agronomic traits in maize has more in
common with important traits in humans and animals than it does with similar traits in
Arabidopsis and rice. The new challenges and opportunities associated with genome-wide
analysis studies will be discussed.

28


Concurrent session 1: Molecular breeding for abiotic stress tolerances

Mapping QTLs for root morphology in relation to nutrient uptake in wheat

He X, Li JJ, Ren YZ, Zhao XQ, Li B, Li ZS and Tong YP*
State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental
Sciences, Chinese Academy of Sciences, Beijing 100101.
*Email: yptong@genetics.ac.cn

Nitrogen (N) and phosphorus (P) fertilizers are required to maximize crop yields in many
agricultural systems. However, the recovery rates of fertilizer N and P were low. To increase N
and P recovery rates, systematic approaches are required, including optimizing management
practices and breeding crops with improved N and P use efficiency.
Previous studies have shown that vigorous early root growth is a major factor influencing N and P
uptake in wheat. However, roots, the ‘unseen half’ of wheat plants, are difficult to be selected
directly by wheat breeders. Therefore, identifying QTLs/genes regulating root traits can help
wheat breeders to develop wheat varieties with ideal root system for efficient use of nutrients
through MAS approach.
A RIL population of derived from two Chinese wheat varieties Xiaoyan 54 and Jing 411 was used
to map QTLs for root traits in relation to N and P uptake. A hydroponic culture and a soil column
experiment were carried to phenotype the RIL population at seedling stage. For the hydroponic
culture, the maximal root length (MRL), root dry weight (RDW), shoot dry weight (SDW), N
(NUP) and P (PUP) uptake of this RIL population were investigated under sufficient nutrient
supply, low N and low P conditions. Phenotype variation explained by individual QTL varied
from 4.6% to 32.7%. For the soil column experiment, root distribution in the soil profiles, SDW,
NUP and PUP were investigated under sufficient nutrient condition. Phenotype variation
explained by individual QTL varied from 5.2% to 22.5%. To develop MAS for breeding wheat
root traits, we analyzed the effects of pyramiding multi-QTLs on RDW, as well as SDW, NUP and
PUP investigated in these tow experiments. The results showed that pyramiding the three QTLs
linked with Xgwm157-2D, Xgwm533.2-3B and Xbarc90-4B, respectively, significantly increased
RDW, SDW, NUP and PUP under different N and P supply levels in the hydroponic culture. The
RILs harboring the positive alleles at these three loci had, averagely, 33%-69% higher SDW,
RDW, NUP and PUP than those with the negative alleles under different N and P conditions. In
the soil column experiment, pyramiding the three QTLs linked with Xgwm157-2D,
Xgwm533.2-3B and Xbarc70.1-4A, respectively, significantly increased SDW, RDW, NUP and
PUP. The RILs harboring all the three positive alleles had, averagely, 30% higher SDW, 25%
higher RDW in the 0-30 cm soil layer, 48% higher RDW in the 30-60 cm soil layer, 43% higher
RDW in the 60-90 cm soil layer, 31% higher total RDW, 31% higher NUP and 30% higher PUP
than those with the negative alleles.

29



The research progress of drought tolerance and molecular breeding in maize
＊
Zheng J, Fu JJ, Liu YJ, Jian M, Wang GY

Institute of Crop Sciences and National Center for Plant Gene Research, Chinese Academy of Agricultural
Sciences, Beijing 100081, China.
＊
Email: gywang@caas.net.cn

Drought stress greatly affects maize growth and its yield potential. In order to understand the
molecular basis in response to drought stress, and further to improve the drought tolerance in
maize, transcriptome analysis, QTL mapping and transgenic approaches were performed in our
lab. Genome-wide gene expression profiling was analyzed between the drought-tolerant line
Han21 and drought-sensitive line Ye478. Our data identified a common set of ~2,600 regulated
genes under drought stress between the two lines, and showed that the drought tolerant line has
fewer genes with altered expression. The potential components of the abscisic acid signaling
pathway were significantly identified from the common set of genes. A total of 827 genes with
significantly differential expression between the two lines under drought stress were identified. A
F2 population of Han21×Ye478 was used to construct the genetic linkage map and QTL mapping.
Drought tolerant NILs (near-isogenic lines) were also screened out from the backcross population
of Han21×Ye478 under severe drought stress conditions. Additionally, the transgenic maize that
overexpressed HDG11, which encodes a homeodomain-START transcription factor, had
increased the drought tolerance with improved maize root system and reduced stomatal density.

30



Towards molecular breeding for salt tolerance through modification of root
System architecture

Zhao YK, Wang T, Wang ZJ and Li X*
Plant Cell & Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and
Developmental Biology, 286 Huaizhong Road, Shijiazhuang, Hebei, P.R. China.
*Email: xli@genetics.ac.cn

Salinity is a major constraint to crop growth and production. Root system architecture has been
considered as one of most important traits of crops in response to various abiotic stresses.
Research on root traits is a major breeding objective in genetic improvement in nutrient use
efficiency and drought tolerance. Some quantitative trait loci (QTLs) and genes conferring
superior root system architecture have been identified. However, the role of developmental
plasticity of root system architecture under salt stress is largely unknown, and the genes and QTLs
mediating this trait remains to be identified. To investigate the response of plant root system to
salt stress, we have conducted a systematic study using Arabidopsis plants. We found that the root
system architecture is highly sensitive to salt stress. The SOS (Salt Overly Sensitive) genes are
essential for root plastic development in response to salt stress. Loss of function in the SOS genes
are hypersensitive to salt, particularly the mutant plants exhibited developmental failure in lateral
root initiation and emergence. In contrast, the transgenic plants overexpressing the SOS genes
showed enhanced tolerance to salt stress and developed more root mass. Further, we have
identified the STS1 (Sensitive To Salt1) gene as an upstream regulator in the root traits mediated
by the SOS signaling pathway in response to salt stress. STS1 gene encodes a WD40 repeat
protein and is induced by salt stress. Interestingly, STS1 interacts with ABI2, a key regulator of
ABA signaling pathway, suggesting that ABA may play an important role in the root trait. The
SOS and STS1 genes are found to be conserved in Arabidopsis and winter wheat. The functions of
the genes and the SOS and ABA signaling in developmental plasticity of root system architecture
in various winter wheat with different salt tolerance are under investigation. These results will
further our understanding of the genetics of salt tolerance in crops and to provide novel insights
into improvement of their performance under salt stress conditions.

31



Mapping and validating QTLs for plant height developmental behaviours in
bread wheat
Wu XS, Wang ZH, Zhang JN, Wei TM, Shi W, Zhang B, Jing RL*
The National Key Facility for Crop Gene Resources and Genetic Improvement; Institute of Crop Science,
Chinese Academy of Agricultural Sciences, Beijing 100081, China.
* Email: jingrl@caas.net.cn

Plant height (PH), a crucial trait related to yield potential in crop plants, is known to be typically
quantitatively inherited. However, its full expression can be inhibited by a limited water supply.
As a trait easily measured, plant height is also a suitable model trait for exploring drought
tolerance from jointing stage to flowering time in wheat (Triticum aestivum L.). In this study, we
mapped and validated QTLs for plant height developmental behaviours in wheat by a doubled
haploid (DH) population, a recombinant inbred line (RIL) population, a collection of accessions
and backcross lines. The genetic basis of the developmental behaviour of PH was assessed in a
150-line doubled haploid population (Hanxuan 10 × Lumai 14) grown in 10 environments (year ×
site × water regime combinations) by unconditional and conditional quantitative trait locus (QTL)
analyses in a mixed linear model. QTLs with additive and epistatic effects that expressed
selectively during ontogeny were identified. Total of seven genomic regions covering PH QTL
clusters on different chromosomes identified from the DH population were used as the candidate
QTLs and extensively analyzed in a RIL population derived from the same cross as the DH. Five
additive QTLs and eight pairs of epistatic QTLs significantly affecting plant height development
were detected by unconditional QTL mapping method. Six additive QTLs and four pairs of
epistatic QTLs were validated using conditional mapping approach. Among them, three additive
QTLs and three pairs of epistatic QTLs were common QTLs detected by both methods. Three
QTLs were expressed under both drought and well-water conditions. Total of 270 historical winter
wheat accessions planted in northern China were genotyped using 60 PH candidate markers on six
chromosomes. A list of association was identified in the regions of gene Rht, indicating a
consistency of association analysis with linkage mapping. A total of 68 backcross lines of BC3F3-4
were used to validate the QTLs detected in the genetic populations and natural collection. The
results showed that some lines pyramiding multi-allele with effect of increasing or decreasing
plant height exhibited superiority over the opposite lines. This case, mapping and validating QTLs
for plant height developmental behaviours in wheat indicates the possibility of molecular breeding
for plant complex quantitative traits.

32



Discovery of genes for drought resistance improvement of rice by systematic
genetic and functional genomic approaches

Xiong LZ
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,
China
E-mail: lizhongx@mail.hzau.edu.cn

Drought resistance is a very complex trait with distinct molecular and physiological mechanisms
in different plant species. Irrigated rice has been domesticated in full irrigation ecosystem and it is
extreme sensitive to drought. With a long-term goal of improving drought resistance in irrigated
rice, we have adopted a strategy by integrating the approaches including germplasm exploitation,
genetic and functional genomics approaches to identify loci/genes effective for drought resistance
improvement of rice. In this paper, we described the approaches and the major progresses made to
discover genes for drought resistance improvement. On the basis of genetic dissection of drought
resistance of rice, more than 30 QTLs have been targeted for construction of near isogenic lines
and marker-assisted molecular breeding. Several drought resistance-associated genes were
identified through drought screening of T-DNA insertion mutants of rice. Hundreds of genes
differentially involved in drought responses and adaptation were identified through comparative
expression profiling analysis. More than 200 drought-responsive candidate genes were
transformed into rice for drought resistance testing, and a few genes (such as SNAC1, OsSKIPa,
and OsLEA3-1) showed significant effect in improving drought resistance of transgenic rice.
Finally, problems and perspectives of drought resistance improvement in rice will be discussed.

33



Heat stress transcriptome analysis and Functional Characterization of
Responsive Genes in wheat

Qin DD1, 2, Peng HR1, 2, Ni ZF1, 2, Yao YY 1, 2, Zhou CL1, 2, Sun QX 1, 2, *
1
Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology, China
Agricultural University, Beijing100193, China
2
Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genomics and Genetic
Improvement (MOA) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University,
Beijing100193, China
Email: qxsun@cau.edu.cn

Wheat (Triticum aestivum L.) is a major crop around the world, and heat stress during the late
stage affects its yield and quality badly. So, it’s urgent to elucidate the mechanisms of wheat heat
tolerance, and identify thermotolerance-related genes for future thermotolerant wheat breeding
programme.
In this study, using Affymetrix Genechip® Wheat Genome Array, we analyzed genome-wide
gene expression profiles of the leaves between two wheat genotypes with contrasting
thermotolerance under heat treatment, namely, heat susceptible ‘Chinese Spring’ and heat tolerant
‘TAM107’. A total of 6560 (~10.7%) probe sets were identified as heat responsive in our study.
Except for heat shock proteins and heat shock factors, these genes also included transcription
factors, components involved in hormone biosynthesis and signaling, calcium signal pathway,
RNA metabolism, primary and secondary metabolisms, as well as other stresses related proteins.
Further analysis showed that, 313 probe sets were differentially regulated between the two
genotypes, 1314 were between heat treatments with and without pre-acclimation, while 4533
between short and prolonged heat treatments. Furthermore, two genes, TaMBF1c (Multiprotein
bridging factor 1, MBF1) and TaGAST (Gibberellin stimulated transcript), which were strong
induced by heat stress in both genotypes were cloned and functionally characterized.
The complete ORF encoding TaMBF1c included 471bp, the deduced amino acid sequence
revealed existence of MBF1 and helix-turn-helix conserved domains at the N- and C-terminus,
respectively, and was highly homologous to rice ERETC and AtMBF1c. TaMBF1c contained no
intron in it. The 1074bp promoter region of it contained three heat shock elements (HSEs),
identifying it as a potential heat shock factor regulated gene. Northern blot analyses showed that
there was no detectable expression of TaMBF1c under control condition, and the expression of it
was rapidly and significantly induced by heat stress not only at seedling stage but also at
flowering stage, and was only slightly induced by drought and H2O2 stresses, ABA and ACC
application, however, not by rhythm, salt and MeJA treatments. In addition, ectopic
over-expression of TaMBF1c in yeast imparts high temperature stress tolerance to wild type yeast
cells. The most important is that thermotolerance was significantly increased in TaMBF1c
overexpressed transgenic rice.
34


Another heat-induced gene TaGAST was also gotten by in silico cloning and RT-PCR.
Bioinformatic analysis showed that the sequence of TaGAST encoded a protein with 99 amino
acids which had a GASA domain in the C-terminal. In addition, the promoter region of TaGAST
was cloned using BD Genome Walker method, and HSE and several cis-elements involving in
other abiotic stress response were found in this region．Consistently, the expression of TaGAST
was at low level in seedling leaves of the two wheat genotypes mentioned above, but strongly
induced by stress factors, such as PEG, high salinity, oxidation and high temperature, and also the
phytohormones such as ABA, ACC and MeJA treatment．The results suggested that this gene
might be involved in various abiotic stress respons．In order to investigate the role of TaGAST in
plant thermotolerance, it was over-expressed in Arabidopsis by Agrobacterium-mediated
transformation method. The transgenic lines overexpressing TaGAST showed no phenotypic
difference compared to wild type under normal growth condition, but showed
membrane-thermostabler than WT. And had significantly higher survival rate under heat stress．
All the above results indicate that these two genes have potential importance in improving
thermotolerance of wheat and other cereals, and the transgenic of wheat is underway.

35


Concurrent session 2: Gene discovery and function

Identification and application of the rice broad-spectrum blast resistance gene
Pigm

He ZH*, Deng YW
National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai
Institutes for biological Sciences, CAS, Shanghai 200032, China
*E-mail zhhe@sibs.ac.cn).

Rice blast is one of the most destructive diseases of rice. The identification and utilization of
broad-spectrum resistance genes has been the most effective and economical approach to control
the disease. A native Chinese variety, GM4, was identified with broad-spectrum and durable
resistance. Genetic and mapping analysis indicated that blast resistance to nine isolates of
different races in GM4 is controlled by the same dominant locus designated as Pigm, which was
identified resistance gene cluster including 13 NBS-LRR members on chromosome 6 by
map-based cloning strategy, allelic to two known blast resistance genes Pi2 and Pi9. Sequence
comparison of the orthologous and paralogous genes between the Pigm/Pi9/Pi2 loci showed that
the Pigm loci had undergone duplication result from LTR retrotransposon, unequal cross and
illegitimate recombination during the evolution of the resistance gene cluster. Furthermore, our
analysis showed that Pigm confers resistance to blast isolates from different cultivated regions
than Pi9/Pi2/Pizt/Piz. In the Pigm locus, Pigm-1 controls leaf blast resistance, Pigm-2 confers
neck blast which leads to large loss of grain yield. Genetic and transcriptional analysis suggested
that broad-spectrum resistance might be attributed to the different expression patterns of diverse R
genes. We have succeeded in developing elite hybrid rice lines with broad-spectrum blast
resistance with molecular markers-assisted selection for Pigm, indicating good potential of the
gene in rice molecular breeding. All the elite hybrid rice lines harboring the Pigm exhibited a high
resistance or immunity to blast in natural blast nurseries nationwide from 2008 to 2010.

36



Mutant resources for functional studies of genes related to fertility in rice

Wu CY
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong
Agricultural University, Wuhan 430070, China
Email: cywu@mail.hzau.edu.cn

T-DNA tagging strategy is a high throughput approach for function analysis the plant genome.
We have generated more than 100 thousand independent transgenic lines using the enhancer trap
construct, consisting of the GAL4/VP16-UAS elements with GUS (or GFP) as the reporter. The
system has three built-in strategies for functional analysis of the rice genome. First, T-DNA
insertions cause gene mutations, providing an efficient approach for gene identification and
isolation. Second, expression of the reporter gene indicates the presence of an enhancer element in
the neighboring genomic region, which can be used for isolation and characterization of the
enhancer. Third, the lines showing spatial- or temporal-specific expression of the reporter gene
can be used to drive ectopic expression of a transgene, thus useful for unveiling latent functions of
unknown or known genes.
Employing our rice T-DNA insertional mutant library, we identified two genes, designed PAIR3
and OsRPA1a, which play essential roles in DNA metabolism during meiosis process. Both pair3
and Osrpa1a mutants exhibit a phenotype of completely sterile compared with their wild types.
Genetic analysis of those mutants revealed that the T-DNA insertion tag co-segregated with the
sterility phenotype. During meiotic prophase I, the pair3 mutant fails in homologous chromosome
pairing and synapsis, resulting in no formation of bivalents and subsequent random segregation of
the univalents in anaphase I. PAIR3 encodes a protein that contains putative coiled-coil motifs, but
does not have any close homologs in other organisms. Primary results suggest that PAIR3 plays a
crucial role in homologous chromosome pairing and synapsis in meiosis. Another mutant osrpa1a
exhibits abnormal chromosomal fragmentation occurred in male meiocytes after anaphase I.
Further study identified that the leaves of Osrpa1a were hypersensitive to DNA mutagens.
Genetic complementation and RNAi results confirmed that OsRPA1a was responsible to the
mutant phenotypes in Osrpa1a. Our data suggest that OsRPA1a plays an essential role in DNA
repair but may not participate in, or at least is dispensable for, DNA replication and homologous
recombination in rice.

37



Gene discovery from common wild rice (Oryza rufipogon Griff.)
Sun CQ
State Key Laboratory of Plant Physilogy and Biochemistry, National Center for the Evaluation of Agricultural
Wild Plants (Rice), China Agricultural University, Beijing 100193, P R China.
Email: suncq@cau.edu.cn

Common wild rice (Oryza rufipogon Griff.), ancestor species of cultivated rice (O. sativa L.),
constitute an important gene pool for rice improvement. To discover favorable genes from wild
rice which have been lost or weakened in cultivated rice has become more and more important for
modern breeding strategy. In recent years, we have developed two sets of introgression lines (ILs)
derived from the cross between O. rufipogon from Jiangxi and Yunnan province of China, as the
donor, and elite cultivars, as the recipient. Several QTLs for yield-related traits, quality traits and
tolerence to abiotic stress were mapped using introgression lines. Some major QTLs were
fine-mapped and cloned. Two key genes, PROG1 and SHA1, controlling rice domestication were
identified. PROG1 controlling prostrate growth of wild rice on chromosome 7 encodes a single
Cys2-His2 zinc-finger protein. prog1 variants identified in O. sativa disrupt the prog1 function
and inactivate prog1 expression, leading to erect growth, greater grain number and higher grain
yield in cultivated rice. SHA1 controlling seed shattering of wild rice on chromosome 4 encodes a
member of the trihelix family of plant-specific transcription factors. The predicted amino acid
sequence of SHA1 in wild rice is distinguished from that in cultivated rice by only a single amino
acid substitution (K79N) caused by a single nucleotide change (g237t).

38



Discovery of brown planthopper resistance gene in rice
He GC
College of Life Sciences, Wuhan University, Wuhan 430072, China
Email: gche@whu.edu.cn

The brown planthopper (Nilaparvata lugens Stal; BPH) is an insect that feeds on the leaf sheath of
rice (Oryza sativa L.) plants, ingesting nutrients specifically from the rice phloem using its stylet
mouthparts. In the last decade, the BPH has frequently caused widespread destruction of rice
crops and heavy losses of yields. The most economic and efficient method for controlling the
BPH is to use the host resistance as part of IPM.
To date, more than 19 BPH resistance genes in rice have been reported. Resistance of Bph1, bph2
and Bph3 has been reported to be overcome by new biotypes of BPH. Wild rice germplasm is an
important gene pool for rice breeding. Two major loci for BPH resistance, Bph14 and Bph15,
were detected in the F2 population and RIL population of Minghui63 X B5. Bph14 was mapped
on the long arm of chromosome 3 and Bph15 on the short arm of chromosome 4. These loci were
also found to confer resistance to the white-backed planthopper.
Analysis of recombination events in the Bph14 region delimited the gene to genomic segment of
34-kb between SM1 and G1318. Two predicted genes encoding putative resistance proteins,
designated Ra and Rb respectively, were identified after sequencing this region. Transgenic
experiment showed that Ra confers the resistance phenotype and is the Bph14 gene. The Bph14
gene encodes a putative 1,323 amino acid protein containing a coiled-coil, nucleotide-binding and
leucine-rich repeat (CC-NB-LRR) motif. Comparison analysis showed that in the LRR domain 54
residues and two deletions of Bph14 were unique.
Electronic penetration graphs (EPG) revealed that BPH insects spent more time walking, but less
time ingesting phloem, on the plants carrying resistance genes Bph14 and Bph15 than they did on
susceptible plants. Tests with [14C]sucrose showed that insects ingested much less phloem sap on
the resistant plants than on susceptible plants. In the plants infested with the BPH, callose was
found deposited on the sieve plates of the target sieve tubes, where the stylets had been inserted.
Counts of the bright callose plugs revealed more callosic sieve plates in the resistant than in
susceptible plants. Moreover, with prolonged BPH feeding, the callose deposition decreased
quickly in susceptible plants. It was found that the genes encode for callose decomposing enzyme
β-1,3-glucanase were differetially regulated in the resistant and susceptible rice plants. In the
susceptible rice the β-1,3-glucanase gene Osg1 and Gns5 were enhanced, and thereby facilitated
the BPH’s continued feeding from the phloem in the susceptible plants, while in the resistant
plants, these genes expression unchanged. As a result, BPH feeding on the resistant rice plants
were suppresed.

39



Molecular basis of cytoplasmic male sterility in rice
Wang Z, Zou Y, Luo D, Liu Z, Xu H, Wu H, Guo J, Zhang Q, Ye S, Chen Y, Liu YG*
Key Laboratory of Plant Functional Genomics and Biotechnology of Education Department, Guangdong Province,
College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
*Email: ygliu@scau.edu.cn

The successful breeding and commercial cultivation of hybrid rice is one of the most important
achievements in agriculture. Hybrid rice has been developed and released in 1970s in China, which
has about 20% yield advantage over improved inbred varieties. Since the late of 1980’s, hybrid rice
has occupied ~55% (~15-17 million hectares) of the total rice planting area each year in China.
Therefore, hybrid rice has contributed tremendously to the food security in China, and given a great
impact to agriculture. The successful development of hybrid rice is mainly due to the development
and utilization of cytoplasmic male sterility (CMS) systems. Three types of CMS systems,
Wild-abotive (WA), Boro II (BT), and Hong-Lian (HL), have been used for the hybrid breeding.
To reveal the molecular basis of the cytoplasmic male sterility systems in rice, we have identified
and functionally studied the genes conferring the CMS and restoration. We found that a
mitochondrial open reading frame of previously unknown function in Boro II cytoplasm, orf79,
encodes a cytotoxic peptide that causes the male sterility. Furthermore, we isolated two restorer
genes, Rf1a and Rf1b, at the previously reported single locus Rf1, revealing that Rf1 is a complex
locus. Rf1a and Rf1b encode PPR (Pentatrico Peptide Repeat) proteins, and they target to
mitochondria to cleave and degrade the orf79 mRNA, respectively, thus silence orf79 and restore
the mal fertility. When both restorers are present in the hybrids, Rf1a preferentially cleave the orf79
mRNA, showing an epistatic effect over Rf1b. The study further revealed that Rf1a has a role to
promote the editing of the mitochondrial atp6 mRNA, suggesting that this may be its primary
function, while the action as the fertility restorer be a new function.
CMS-WA is the most widely used system for hybrid rice. We identified a novel mitochondrial gene
conferring CMS-WA. Transformation of rice and Arabidopsis with this gene caused male sterility.
CMS-WA is restored by Rf loci, Rf3 and Rf4, via suppressing the function of this CMS gene with
different mechanisms. Evolutionary analysis revealed that this CMS gene was generated through
rearrangement of multiple fragments of the mitochondrial genomes and unknown sources in this
locus during the evolution of wild rice species. Further, we studied the molecular mechanism of the
CMS induction involving in the cytoplasmic-nuclear interaction.

40



Toward map-based cloning of a good eating-quality QTL derived from an elite
Japanese rice cultivar Koshihikari

Hori K1*, Takeuchi Y2, Nagasaki H1, Ando I2, Yano M1
1
National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
2
National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
*E-mail: horikiyo@affrc.go.jp

Eating quality is an important trait to consider in rice breeding, because it determines consumer
preference and the rice price. The eating quality of cooked rice is a complex trait determined by
multiple genes and is largely affected by environmental factors. Although several physicochemical
properties of the rice grain, such as amylose and protein contents, pasting properties and gel
consistency are used to evaluate eating quality, a sensory test of cooked rice is still required for
the final selection procedure in rice breeding. The sensory test is time-consuming and
labor-intensive because trained panels evaluate each breeding line for appearance, taste, and
texture of the cooked rice by eating it. A japonica rice cultivar Koshihikari has a good eating
quality including high glossiness, a high level of stickiness, good taste, and low hardness of
cooked rice. We evaluated the eating quality of cooked rice using the sensory test in a set of
reciprocal backcrossed inbred lines (BILs) from crosses between Nipponbare and Koshihikari in
2006 and 2007. The major quantitative trait loci (QTL) for eating quality were detected on the
short arm of chromosome 3 in the two BILs. The Koshihikari allele of the QTL increased eating
quality. To validate the eating quality QTL, we developed a substitution line with a Koshihikari
segment on the short arm of chromosome 3 in a Nipponbare genetic background, and evaluated
the eating quality of the substitution line using sensory tests in 2008 and 2009. The eating quality
of the substitution line was improved as compared with Nipponbare in both seasons. In order to
screen for putative candidate genes of the eating quality QTL, a large chromosome segment (11.3
Mbp) of the genome was sequenced. Sequence comparison between Nipponbare and Koshihikari
revealed insertion/deletion polymorphisms and single nucleotide polymorphisms in the sequences
of 13 predicted genes in the candidate region of the QTL. RT-PCR revealed that nine of the 13
genes were expressed in the endosperm during the ripening period after pollination. For
fine-mapping of the eating quality QTL, we developed additional substitution lines to replace
different Koshihikari segments on the short arm of chromosome 3 in the Nipponbare background.
Sensory tests of these substitution lines are now underway to narrow down the candidate region
for the eating quality QTL.

41

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