Table_1_MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.).XLSX

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.

全球范围内，终端干旱是限制鹰嘴豆（Cicer arietinum L.）生产的主要胁迫因素之一。早花基因型可规避终端干旱胁迫，而籽粒增大可弥补终端干旱引发的产量损失。本研究通过将突变体株系ICC4958-M3-2828与野生型ICC 4958杂交，构建了针对早花与大籽粒性状的突变体映射法（MutMap）群体。基于该MutMap群体的表型鉴定结果，针对开花天数与百粒重性状的极端混合池采用Hi-Seq2500平台以10倍测序深度开展测序。将4741万条过滤后测序读段比对至CDC Frontier参考基因组，最终获得3141万条可比对读段，并鉴定得到332395个单核苷酸多态性（single nucleotide polymorphisms，SNPs）。本研究以CDC Frontier基因组为模板，在其特定位点替换上述SNPs，构建了ICC 4958的参考基因组组装序列。各突变体混合池的特异性SNPs数量介于3993至5771之间。本研究在Ca6染色体的9.76 Mb至12.96 Mb区间内鉴定到一个独特的基因组区域，该区域分别包含31、22、17和32个SNPs，对应开花时间低混合池、开花时间高混合池、百粒重高混合池以及百粒重低混合池的SNP指数峰值均为1。其中22个SNPs分布于20个候选基因内，且对这些基因具有中等等位基因效应。本研究基于候选SNPs开发并验证了两个分子标记：分别为针对早花性状的Ca6EF10509893与针对百粒重性状的Ca6HSDW10099486。综上，本研究开发的关联基因、候选SNPs及分子标记可用于培育可缓解干旱胁迫下产量损失的鹰嘴豆新品种。