Inclusive Market-Oriented Development (IMOD) – our approach to bringing prosperity in the drylands. ICRISAT is a member of the CGIAR Consortium. QTL-Seq: WGS combined with BSA Fast forward genetic mapping combined with whole genome sequencing (WGS) and bulked segregant analysis (BSA) approach was used to identify the candidate genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonepa. To map the targeted genomic regions, F7 RILs developed by crossing ICPL 20096 (R) × ICP 332 (S) and segregating for FW and SMD resistance were phenotyped at two different locations in India. Based on the phenotyping, 16 RILs in each category were selected for development of resistant (R-Bulk) and susceptible bulks (S-Bulk). These two bulks along with resistant parent (ICPL 20096) were re- sequenced and generated ~19GB of 250 bp pair-end data with ~15× genome coverage. WGS data generated from R- and S- Bulks were aligned with resistant parent. As a result a total of 35,877 SNPs with SNP index of ≥3 were identified. Out of 35,877 SNPs only 4,139 (11.54%) SNPs were found homozygous. Based on the SNP index (0 for R-Bulk and 1 for S-Bulk) and SNP substitution effect three significant SNPs including two on CcLG07 and one on CcLG11 affects a total of four candidate genes. Functional annotation of these four genes indicated their role to initiate defence mechanism against fungal and viral diseases. Abstract Phenotyping of mapping population Vikas K. Singh 1 , Aamir W. Khan 1 , Hiroki Takagi 2 , Rachit K. Saxena 1 , Vinay Kumar 1 , Mamta Sharma 1 , C.V. Sameer Kumar 1 , Pallavi Sinha 1 , Annapurna Chitikineni 1 , Suyash Patil 1 , Anuradha Ghanta 3 , K. N. Yamini 3 , Swathi Parupalli 1 , S. Muniswamy 4 , P. S. Dharmaraj 4 , Ryohei Terauchi 2 , Rajeev K. Varshney 1 ,* 1 International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; 3 Agricultural Research Station (ARS)-Tandur, Acharya N G Ranga Agricultural University (ANGRAU), Hyderabad, India; 4 Agricultural Research Station (ARS)- Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India *Address for correspondence: [email protected] Acknowledgements Fast forward genetic mapping provides candidate genes for resistance to fusarium wilt and sterility mosaic disease in pigeonpea Summary SMD Susceptible 0 20 40 60 80 100 120 Disease score Parents and selected susceptible PRILs SMD FW 0 5 10 15 20 25 30 35 40 45 Disease score Parents and selected resistant PRILs SMD FW (b) -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 1.55 1.6 1.65 1.7 1.75 x 10000000 Delta SNP U95 L95 U99 L99 Genotypes Number of reads Number of pair read mapped Coverage at 1× x Coverage Average depth ICPL 20096 19069648 1585188 88.98 15.29 14.44 R-Bulk (RB) 18140041 1779932 88.33 15.85 12.30 S-Bulk (RB) 16958742 1338885 89.15 12.88 14.76 Linkage group Position (bp) R- parent base R- bulk base Read depth SNP Index S- bulk base Read depth SNP Index CcLG02 26551810 T T 7 0 A 7 1 CcLG07 16064896 G G 8 0 C 8 1 CcLG07 18411642 G G 11 0 A 9 1 CcLG08 354473 G G 10 0 C 7 1 CcLG10 7815091 G G 9 0 A 7 1 CcLG11 19958148 A A 9 0 C 10 1 CcLG11 34310320 C C 7 0 A 7 1 SNPs identified between resistant and susceptible bulks Projections of the null distribution of delta SNP index for respective depths Calculating the delta SNP index Simulating the SNP index for the number of individuals in the bulks Excluding the positions if reads aligned are < 7 and SNP index in both the samples < 0.3 Calculating the SNP index with respect to resistant parent Calling of the SNPs through GATK Aligning the RP, RB and SB to the reference Financial support from United States Agency for International Development (USAID) is gratefully acknowledged. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. Sequencing of parents and bulks Delta SNP index plot of CcLG07 Gene function Pigeonpea Genome This is the one of the successful example of application of pigeonpea genome sequence information for identification of targeted genomic regions for FW and SMD resistance combined with whole genome sequencing (WGS) with bulk segregant analysis (BSA). This is fast forward genetic mapping approach for identification of candidate genomic regions for target traits in comparison to the classical method of QTL mapping, which is time consuming and labor intensive process. SNP index between R- and S- Bulk