Whole genome sequencing of Napier grass (C. purpureus) accessions from sub-Saharan Africa
1. Better lives through livestock
Whole genome sequencing of Napier grass (C. purpureus)
accessions from sub-Saharan Africa
Abel Teshome (PhD), FLAIR research fellow
Feeds and Forages Program, ILRI
December 2021
Addis Ababa
2. 2
Small-scale dairy
farmer milk yield/day
Diary farms in Ethiopia
2% of the total cattle population
Dairy farms in EU/UK Carcass average/head
Ethiopia:110 kg
UK: 346 kg
Ethiopia boasts the largest livestock inventory in Africa. However, below-par productivity in the
dairy sector forces the country to spend hard currency on importing dairy products from abroad
30L
15L
5L
3. 3
Improving livestock productivity requires:
• Access to feed/ fodder/ grazing resources (improved)
• Access to water
• Breeding stock
• Animal health services
• Access to markets
• Access to finance (incl. insurance)
• Access to knowledge
• Security
Health &
management
Breed
Forage &
feed
5. 5
Why Napier grass?
• High yield per unit area,
• Perennial,
• Can withstand repeated cuttings,
• Energy crop,
• Tolerance to intermittent drought,
• Cut and carry feeding,
• Pests & disease tolerant,
• Salt tolerance,
• Soil and water conservation, &
• Ease of propagation Kingdom: Plantae
Clade: Tracheophytes
Clade: Angiosperms
Clade: Monocots
Clade: Commelinids
Order: Poales
Family: Poaceae
Subfamily: Panicoideae
Genus: Cenchrus
Species: C. purpureum
6. 6
• Morphological traits
• Height
• No of tillers per plant
• Leaf hairiness
• Agronomic traits
• Number of plants surviving
• Plant vigour
• Yield traits
• Total fresh weight (g)
• Leaf dry matter (g)
• stem dry matter (g)
• Leaf/Stem ratio
Drought tolerance trial established in Bishoftu, Ethiopia (2017 - 2021)
7. 7
• MINING GENEBANKS: Quantify genome variation in a large and
representative sample of accessions from Africa (500)
• POPULATION ANALYSIS: Identify features that make specific geographic or
genetic subsets particularly well suited for forward genetics, field experiments
and select
• ASSOCIATION MAPPING: GWAS analysis for traits of interest such as water
use efficiency, nutritional quality, anthocyanin content, and dry matter yield etc.
• FUNCTIONAL GENETICS: Conduct comparative genomic analysis through
the use of genes that are known to contribute to the regulation of traits of interest
in Arabidopsis and identify their homologues in C. purpureus.
Research objectives
8. 8
0.0e+00
5.0e+07
1.0e+08
1.5e+08
2.0e+08
A01 B01 A02 B02 A03 B03 A04 B04 A05 B05 A06 B06 A07 B07
Chromosome
Position
chr
A01
B01
A02
B02
A03
B03
A04
B04
A05
B05
A06
B06
A07
B07
More than a million polymorphic and bi-allelic SNPs identified from 350
Napier grass accessions
12. 12
Association mapping for agronomic traits
4 of 17 TIBBS CORTES ET AL.
The Plant Genome
F I G U R E 1 Genome-wide association study methods for improving computational speed and statistical power. Different methods are grouped by
general strategy, and the position of each method shows the general trend of improved statistical power (shown on the x axis) and computational speed
(shown on the y axis). CMLM, compressed mixed linear model; ECMLM, enriched compressed mixed linear model; EMMA, efficient mixed-model
Cortes et al 2021
rMVP (R )
GAPIT (R )
Tassel (GUI)
13. 13
Correlation between six agronomic traits
Traits Acronym
Plant height PH
Leaf length LL
Leaf width LW
Tiller number TN
Total fresh weight TFW
Total dry weight TDW
16. 16
SNPs significantly associated (FarmCPU method) with
plant height (PH) under wet seasons
0 1 2 3 4
0
2
4
6
8
1
0
FarmCPU.PH_wet_sws_sqrt
Expected −log10(p)
O
b
s
e
r
v
e
d
−
l
o
g
1
0
(
p
)
0 1 2 3 4
0
2
4
6
8
10
FarmCPU.PH_wet_MWS_sqrt
Expected −log10(p)
Observed
−
log
10
(
p
)
20. 20
4 of 17 TIBBS CORTES ET AL.
The Plant Genome
F I G U R E 1 Genome-wide association study methods for improving computational speed and statistical power. Different methods are grouped by
general strategy, and the position of each method shows the general trend of improved statistical power (shown on the x axis) and computational speed
(shown on the y axis). CMLM, compressed mixed linear model; ECMLM, enriched compressed mixed linear model; EMMA, efficient mixed-model
association; EMMAX, efficient mixed-model association expedited; FarmCPU, fixed and random model circulating probability unification; FaST-
Cortes et al 2021
rMVP (R )
GAPIT (R )
Tassel (GUI)
Association mapping for nutritional traits
21. 21
Traits Acronym
Acid detergent fibre ADF
Acid detergent lignin ADL
neutral detergent fiber NDF
crude protein CP
Organic matter OM
in vitro organic matter digestibility IVOMD
Metabolizable energy ME
Correlation among seven nutritional traits
24. 24
Upcoming project activities
Repeat SNP calling with more than 450 bam files
• There are additional accessions currently being squenced
Develop molecular markers (SNPs/SSRs) for all Napier grass
genebank accessions
Paternal analysis for progenies
Plan crosses based on the field trial results and genomic tools
developed in this project
• Crosses between hetrotic groups
Comparative genomics
• Correlate identified SNPs with genes in other
forage/food species such as pearl millet
Publish the Linux/R scripts in CGspace
Manuscript development