Abstract
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.
Highlights
Chickpea (Cicer arietinum L.) is the second most important annual grain legume crop predominantly cultivated on residual soil moisture in the arid and semi-arid areas of the world
The mutant ICC4958-M3-2828 with > 95% similarity to the ICC 4958 wild type and phenotypically distinct for flowering time and seed size was selected for developing a MutMap population
We report the identification of genes and single nucleotide polymorphisms (SNPs) using a MutMap approach, as well as the development of markers for use in chickpea breeding programs toward the development of cultivars with early flowering and large seed size
Summary
Chickpea (Cicer arietinum L.) is the second most important annual grain legume crop predominantly cultivated on residual soil moisture in the arid and semi-arid areas of the world. Global annual cultivation of chickpea is over 14.56 million ha with a total production of 14.77 million tons (FAOSTAT, 2017, accessed on January 26, 2020). In 66% of chickpea-growing areas, the available crop-growing season is about 80–120 days as they are exposed to abiotic stresses such as drought and heat toward the grain-filling stage. A major shift in the chickpea area (about 3 million ha) from Northern India (cooler, longseason environment) to Southern India (warmer, short-season environment) has been observed during the past four decades. No major boost in the total production of chickpea has been substantiated
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