Open AccessNext‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea ( C ajanus cajan )
Author(s) -
Singh Vikas K.,
Khan Aamir W.,
Saxena Rachit K.,
Kumar Vinay,
Kale Sandip M.,
Sinha Pallavi,
Chitikineni Annapurna,
Pazhamala Lekha T.,
Garg Vanika,
Sharma Mamta,
Sameer Kumar Chanda Venkata,
Parupalli Swathi,
Vechalapu Suryanarayana,
Patil Suyash,
Muniswamy Sonnappa,
Ghanta Anuradha,
Yamini Kalinati Narasimhan,
Dharmaraj Pallavi Subbanna,
Varshney Rajeev K.
Publication year - 2016
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12470
Subject(s) - biology , candidate gene , bulked segregant analysis , genetics , single nucleotide polymorphism , haplotype , plant disease resistance , gene , fusarium wilt , genotype , fusarium oxysporum , gene mapping , chromosome
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.