title: Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.).
abstract: We report a likely candidate gene, CcTFL1, for determinacy in pigeonpea through candidate gene sequencing analysis, mapping, QTL analysis together with comparative genomics and expression profiling. Pigeonpea (Cajanus cajan) is the sixth most important legume crop grown on ~5 million hectares globally. Determinacy is an agronomically important trait selected during pigeonpea domestication. In the present study, seven genes related to determinacy/flowering pattern in pigeonpea were isolated through a comparative genomics approach. Single nucleotide polymorphism (SNP) analysis of these candidate genes on 142 pigeonpea lines found a strong association of SNPs with the determinacy trait for three of the genes. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a likely candidate for determinacy in pigeonpea since it explained 45-96 % of phenotypic variation for determinacy, 45 % for flowering time and 77 % for plant height. Comparative genomics analysis of CcTFL1 with the soybean (Glycine max) and common bean (Phaseolus vulgaris) genomes at the micro-syntenic level further enhanced our confidence in CcTFL1 as a likely candidate gene. These findings have been validated by expression analysis that showed down regulation of CcTFL1 in a determinate line in comparison to an indeterminate line. Gene-based markers developed in the present study will allow faster manipulation of the determinacy trait in future breeding programs of pigeonpea and will also help in the development of markers for these traits in other related legume species.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Hyderabad, India.
authors.forename: Reyazul Rouf
authors.initials: RR
authors.lastname: Mir
authors.forename: Himabindu
authors.initials: H
authors.lastname: Kudapa
authors.forename: Sandhya
authors.initials: S
authors.lastname: Srikanth
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Sharma
authors.forename: Sarwar
authors.initials: S
authors.lastname: Azam
authors.forename: Kulbhushan
authors.initials: K
authors.lastname: Saxena
authors.forename: R
authors.initials: R
authors.lastname: Varma Penmetsa
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D001483:Base Sequence; D036561:Cajanus / Q000235:genetics* / Q000254:growth & development*; D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D035264:Flowers / Q000254:growth & development*; D020869:Gene Expression Profiling; D017343:Genes, Plant; D008040:Genetic Linkage; D005838:Genotype; D008969:Molecular Sequence Data; D027805:Phaseolus / Q000235:genetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D013025:Glycine max / Q000235:genetics