title: Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan).
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.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Vikas K
authors.initials: VK
authors.lastname: Singh
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Aamir W
authors.initials: AW
authors.lastname: Khan
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Vinay
authors.initials: V
authors.lastname: Kumar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Sandip M
authors.initials: SM
authors.lastname: Kale
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Pallavi
authors.initials: P
authors.lastname: Sinha
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Annapurna
authors.initials: A
authors.lastname: Chitikineni
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Lekha T
authors.initials: LT
authors.lastname: Pazhamala
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Vanika
authors.initials: V
authors.lastname: Garg
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Mamta
authors.initials: M
authors.lastname: Sharma
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Chanda Venkata
authors.initials: CV
authors.lastname: Sameer Kumar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Swathi
authors.initials: S
authors.lastname: Parupalli
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Suryanarayana
authors.initials: S
authors.lastname: Vechalapu
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Suyash
authors.initials: S
authors.lastname: Patil
authors.affiliation: Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India.
authors.forename: Sonnappa
authors.initials: S
authors.lastname: Muniswamy
authors.affiliation: Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India.
authors.forename: Anuradha
authors.initials: A
authors.lastname: Ghanta
authors.affiliation: Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India.
authors.forename: Kalinati Narasimhan
authors.initials: KN
authors.lastname: Yamini
authors.affiliation: Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India.
authors.forename: Pallavi Subbanna
authors.initials: PS
authors.lastname: Dharmaraj
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.|School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D001947:Breeding; D036561:Cajanus / Q000235:genetics* / Q000276:immunology; D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics; D005670:Fusarium / Q000502:physiology*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010935:Plant Diseases / Q000276:immunology*; D051479:Plant Infertility / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: Fusarium wilt; SNP index; bulked segregant analysis; nonsynonymous SNPs; sterility mosaic disease; whole-genome re-sequencing