Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
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Vikas Singh, Aamir Khan, Rachit Saxena, Vinay Kumar, Sandip Kale, Sinha Pallavi, Annapurna Chitikineni, Pazhamala Lekha, Garg Vanika, Chanda Venkata Sameer Kumar, Swathi Parupalli, Suryanarayana Vechalapu, Suyash Patil, Sonnappa Muniswamy, Anuradha Ghanta, Kalinati Narasimhan Yamini, Pallavi Subanna Dharmaraj, Rajeev Varshney. (31/5/2016). Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). Plant Biotechnology Journal, 14(5), pp. 1183-1194.
Abstract
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 9 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 SNPs 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) SNPs. Of 8362 nsSNPs, 60 were found within the 2-Mb
flanking regions of seven candidate SNPs identified through Seq-BSA. Haplotype analysis
narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by
re-sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis
revealed association of four candidate nsSNPs in four genes with FW resistance and four
candidate nsSNPs 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/
SNPs will be useful for genomics-assisted breeding in pigeonpea.