Plant Biotechnology Journal (2016) 14, 1183-1194

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Vikas K. Singh, Aamir W. Khan, Rachit K. Saxena, Vinay Kumar, Sandip M. Kale, Pallavi Sinha, Annapurna Chitikineni, Lekha T. Pazhamala, Vanika Garg, Mamta Sharma, Chanda Venkata Sameer Kumar, Swathi Parupalli, Suryanarayana Vechalapu, Suyash Patil, Sonnappa Muniswamy, Anuradha Ghanta, Kalinati Narasimhan Yamini, Pallavi Subbanna Dharmaraj and Rajeev K. Varshney (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), 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 × 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.
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Link to article at publishers website
Database assignments for author(s): Mamta Sharma

Research topic(s) for pests/diseases/weeds:
resistance/tolerance/defence of host

Pest and/or beneficial records:

Beneficial Pest/Disease/Weed Crop/Product Country Quarant.

Pigeonpea sterility mosaic virus 1 Pigeonpea (Cajanus cajan)
Fusarium udum Pigeonpea (Cajanus cajan)