title: Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes.
abstract: Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F(2) lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species.
authors.affiliation: Center of Excellence in Genomics (CEG), International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru 502324, India.
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.forename: R Varma
authors.initials: RV
authors.lastname: Penmetsa
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.forename: Ashish
authors.initials: A
authors.lastname: Kumar
authors.forename: Noelia
authors.initials: N
authors.lastname: Carrasquilla-Garcia
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Schlueter
authors.forename: Andrew
authors.initials: A
authors.lastname: Farmer
authors.forename: Adam M
authors.initials: AM
authors.lastname: Whaley
authors.forename: Birinchi K
authors.initials: BK
authors.lastname: Sarma
authors.forename: Gregory D
authors.initials: GD
authors.lastname: May
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D000483:Alleles; D001483:Base Sequence; D036561:Cajanus / Q000235:genetics*; D002874:Chromosome Mapping / Q000191:economics / Q000379:methods*; D003362:Cost-Benefit Analysis; D007887:Fabaceae / Q000235:genetics*; D005787:Gene Frequency; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics / Q000379:methods*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
chemical_list: D005819:Genetic Markers