Shoot fly is one of the most destructive pest in sorghum causing up to 80% grain and 68% fodder losses. Management of shoot fly with host plant resistance is the most effective means to reduce shoot fly damage as compared to other management practices. In this study, the shoot fly QTL introgressed lines were validated using singlenucleotide polymorphism (SNP) markers tightly linked to shoot fly resistant QTLs.

1. Sunita G1, Jayakumar J1, Anil G1, Santosh P Deshpande1, Rajaguru B1, Jagdish J1, Sharma H C2, Ashok Kumar A1*
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India.
2Dr. Y S Parmar University of Horticulture & Forestry, Nauni, Himachal Pradesh
*Corresponding author email: a.ashokkumar@cgiar.org
Introduction
Shoot fly is one of the most destructive pest in sorghum causing up to 80% grain and
68% fodder losses. Management of shoot fly with host plant resistanceis the most
effective means to reduce shoot fly damage as compared to other management
practices. In this study, the shoot fly QTL introgressed lines werevalidated using single-
nucleotide polymorphism (SNP) markers tightly linked to shoot fly resistant QTLs.
Materials and Methods
 Two elite sorghum genotypes viz., SPV1411 (Parbhani Moti) and ICSB 29004 were
used as recurrent parents. J2658-6, J2714 and J2614 (ILs of BTx623, an elite
sorghum line) were used as donor parents. Using these parents three crosses
were made ICSB 29004×J 2658, ICSB29004×J2714 and SPV 1411×J2614.
 The four validated QTLs imparting shoot fly resistance on chromosome SBI-01,
SBI-07 and SBI-10 used in this study govern different component traits, such as
chromosome SBI-01 Ovipositional non-preference and Seedling vigor; SBI-07
Glossiness and Ovipositional Nonpreference, and SBI-10 Glossiness, Oviposition
Non-preference, Dead hearts, and Leaf Trichomes.
 SSR molecular markers were used for foreground selection (FGS) as well as for
background selection.
 Field Evaluation was done by collecting the data on five component traits
contributing to shoot fly resistance were recorded for two seasons viz., 2014 post-
rainy and 2015 rainy, at ICRISAT-Patancheru, Hyderabad, India along with checks
(shoot fly resistant check IS18551 and susceptible checks Swarna and 296B).
 Ten identified SNPs linked to shoot fly resistant component traits, glossiness and
trichome density on SBI-10 and SBI-05 were used for validation.
Acknowledgements:
 Department of Science and Technology, Govt. of India
Conclusion:
 The development of first introgression lines (SPV 1411 and ICSB 29004) using marker assisted backcrossing was
comparatively faster than with conventional breeding along with 90% recurrent parent genome recovery.
 Validation of introgressed lines (QTL G) showed the presence of favourable alleles for corresponding QTL.
Introgression lines with other QTLs (E and A) also showed the presence of few SNPs which could be helpful in
imparting shoot fly resistance.
 This data is in correlates with the phenotypic data collected in shoot fly screening block.
 The resistant and donor parents showed favourable alleles for all 10 identified SNPs. Susceptible check Swarna
did not show the presence of favourable allele for any of the SNPs.
 The parent J 2658 (QTL A) possessing the QTL for ovipositional non preference also confirms the presence of
SNPs from J1 and J2 i.e for leaf glossiness and trichome density
Fig 1: Development of MABC Introgression Lines
Fig 2: Chromosomal region on SBI-10 introgressed in the
present study confirmed by amplifying the SSR markers
within and flanking QTL region.
Fig 3: Graphical representation of
heterozygote for QTL on SBI-10 with two
parental alleles, marker used is Xnhsbm1011.
Fig 4: Background screening of introgression lines. M:
100bp ladder, RP: Recurrent Parent band (~250bp), DP:
Donor Parent band (~300bp). The recurrent parent band
was scored as A, donor parent band was scored as B.
Results
Results Contd…
Fig 6: Mature sorghum panicles (rainy season) of introgressed lines along with recurrent
and donor parent. Panicles in red circles are selected lines for shoot fly resistance
Fig 5: Graphical genotypes of selected lines using SSR markers for the carrier chromosomes for
marker-assisted backcrossing lines for resistance to SF
SPV 1411 RP J-2614 DP
6045-3 6045-16 6045-22 6045-24 6045-29 5125-25
Fig 7: Mature sorghum panicles of introgressed lines (post-rainy season)
Sl. No. SNP ID Chromosome Trait QTL Favorable allele Unfavorable allele
1 snpSB0106 C T
2 snpSB0109 C G
3 snpSB0110 T G
4 snpSB0143 C G
5 snpSB0144 G A
6 snpSB0146 T C
7 snpSB0148 A C
8 snpSB0158 C G
9 snpSB0164 G A
10 snpSB0169 C T
SBI-10
Trichome density
(lower side)
QTL-J2
SNP panel for routine selection of (Shoot fly resistance component trait) leaf glossiness, lower leaf
trichome density
SBI-05 Leaf Glossiness QTL-J1
SBI-10 Leaf Glossiness QTL-G
J1 (Leaf Glossiness) G (Leaf Glossiness) J2 (Trichome
density lower
Total No. of Plants 3 SNPs 4 SNPs 3 SNPs
Introgression Lines (QTL A) 40 6 (3) 31 (3) -
Introgression Lines (QTL E) 24 23 (3) 23 (3) 23 (2)
Introgression Lines (QTL G) 8 8 (3) 8 (4) 8(2)
J 2658 (QTL A) (Donor Parent) 5 5 (3) - 5 (2)
J 2714 (QTL E) (Donor Parent) 5 4 (2) 1 (2) 4 (2)
J 2614 (QTL G) (Donor Parent) 5 5 (3) 5 (3) 5 (3)
Resistant Check 5 5 5 5
Susceptible check 5
Favourable alleles in introgression lines
Table 1: Number of introgression lines validated using identified SNPs along with resistant and
susceptible checks. Numbers in parenthesis is no. of SNPs with favourable alleles
Nov
2019
Validation of shoot fly resistance introgression lines using SNP
markers in Sorghum