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Summary  To map resistance genes for  Fusarium  wilt ( FW ) and sterility mosaic disease ( SMD ) in pigeonpea, sequencing‐based bulked segregant analysis (Seq‐ BSA ) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of  ICPL  20096 ×  ICPL  332 were sequenced. Subsequently,  SNP  index was calculated between R‐ and S‐bulks with the help of draft genome sequence and reference‐guided assembly of  ICPL  20096 (resistant parent). Seq‐ BSA  has provided seven candidate  SNP s for  FW  and  SMD  resistance in pigeonpea. In parallel, four additional genotypes were re‐sequenced and their combined analysis with R‐ and S‐bulks has provided a total of 8362 nonsynonymous (ns)  SNP s. Of 8362 ns SNP s, 60 were found within the 2‐Mb flanking regions of seven candidate  SNP s identified through Seq‐ BSA . Haplotype analysis narrowed down to eight ns SNP s in seven genes. These eight ns SNP s were further validated by re‐sequencing 11 genotypes that are resistant and susceptible to  FW  and  SMD . This analysis revealed association of four candidate ns SNP s in four genes with  FW  resistance and four candidate ns SNP s in three genes with  SMD  resistance. Further,  In silico  protein analysis and expression profiling identified two most promising candidate genes namely  C.cajan_01839  for  SMD  resistance and  C.cajan_03203  for  FW  resistance. Identified candidate genomic regions/ SNP s will be useful for genomics‐assisted breeding in pigeonpea.

Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea ( C ajanus cajan )