Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea ( C ajanus cajan )
| Autor: | Suryanarayana Vechalapu, Rajeev K. Varshney, Swathi Parupalli, Chanda Venkata Sameer Kumar, Vikas K. Singh, Suyash B. Patil, K. N. Yamini, Annapurna Chitikineni, Lekha T. Pazhamala, Rachit K. Saxena, Aamir W. Khan, Anuradha Ghanta, Vanika Garg, Sonnappa Muniswamy, Sandip M. Kale, Mamta Sharma, Pallavi Subbanna Dharmaraj, Pallavi Sinha, Vinay Kumar |
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| Rok vydání: | 2015 |
| Předmět: |
0106 biological sciences
0301 basic medicine Candidate gene Plant Infertility Genotype Single-nucleotide polymorphism Plant Science Breeding Biology Polymorphism Single Nucleotide whole‐genome re‐sequencing 01 natural sciences Genome DNA sequencing nonsynonymous SNPs 03 medical and health sciences Cajanus Fusarium bulked segregant analysis SNP index sterility mosaic disease Research Articles Fusarium wilt Disease Resistance Plant Diseases Whole genome sequencing Genetics Haplotype Bulked segregant analysis Chromosome Mapping High-Throughput Nucleotide Sequencing Sequence Analysis DNA 030104 developmental biology Agronomy and Crop Science Research Article 010606 plant biology & botany Biotechnology |
| Zdroj: | Plant Biotechnology Journal |
| ISSN: | 1467-7652 1467-7644 |
| DOI: | 10.1111/pbi.12470 |
| Popis: | 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 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. |
| Databáze: | OpenAIRE |
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