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Flowering time is an important trait for adaptation and productivity of chickpea in the arid and the semi-arid environments. This study was conducted for molecular mapping of genes/quantitative trait loci (QTLs) controlling flowering time in chickpea using F2 populations derived from four crosses (ICCV 96029 × CDC Frontier, ICC 5810 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier). Genetic studies revealed monogenic control of flowering time in the crosses ICCV 96029 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier, while digenic control with complementary gene action in ICC 5810 × CDC Frontier. The intraspecific genetic maps developed from these crosses consisted 75, 75, 68 and 67 markers spanning 248.8 cM, 331.4 cM, 311.1 cM and 385.1 cM, respectively. A consensus map spanning 363.8 cM with 109 loci was constructed by integrating four genetic maps. Major QTLs corresponding to flowering time genes efl-1 from ICCV 96029, efl-3 from BGD 132 and efl-4 from ICC 16641 were mapped on CaLG04, CaLG08 and CaLG06, respectively. The QTLs and linked markers identified in this study can be used in marker-assisted breeding for developing early maturing chickpea.
Globally terminal drought is one of the major constraints to chickpea (Cicer arietinum L.) production. Early flowering genotypes escape terminal drought, and the increase in seed size compensates for yield losses arising from terminal drought. A MutMap population for early flowering and large seed size was developed by crossing the mutant line ICC4958-M3-2828 with wild-type ICC 4958. Based on the phenotyping of MutMap population, extreme bulks for days to flowering and 100-seed weight were sequenced using Hi-Seq2500 at 10X coverage. On aligning 47.41 million filtered reads to the CDC Frontier reference genome, 31.41 million reads were mapped and 332,395 single nucleotide polymorphisms (SNPs) were called. A reference genome assembly for ICC 4958 was developed replacing these SNPs in particular positions of the CDC Frontier genome. SNPs specific for each mutant bulk ranged from 3,993 to 5,771. We report a single unique genomic region on Ca6 (between 9.76 and 12.96 Mb) harboring 31, 22, 17, and 32 SNPs with a peak of SNP index = 1 for low bulk for flowering time, high bulk for flowering time, high bulk for 100-seed weight, and low bulk for 100-seed weight, respectively. Among these, 22 SNPs are present in 20 candidate genes and had a moderate allelic impact on the genes. Two markers, Ca6EF10509893 for early flowering and Ca6HSDW10099486 for 100-seed weight, were developed and validated using the candidate SNPs. Thus, the associated genes, candidate SNPs, and markers developed in this study are useful for breeding chickpea varieties that mitigate yield losses under drought stress.
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