High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).

Rashmi Gaur, Sarwar Azam, Ganga Jeena, Aamir Waseem Khan, Shalu Choudhary, Mukesh Jain, Gitanjali Yadav, Akhilesh K Tyagi, Debasis Chattopadhyay, Sabhyata Bhatia
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引用次数: 129

Abstract

The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.

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鹰嘴豆(Cicer arietinum L.)饱和连锁图谱的高通量SNP发现及基因分型
本研究主要通过对鹰嘴豆种间参考定位群体亲本Cicer arietinum ICC4958及其野生祖先C. reticulatum PI489777两个基因型的下一代测序,大规模发现了鹰嘴豆全基因组单核苷酸多态性(snp)。本文首次介绍了基于Illumina公司GoldenGate基因分型技术的高通量SNP基因分型方法的开发和验证及其在鹰嘴豆高分辨率遗传连锁图谱构建中的应用。本研究共鉴定出1022个snp,选取768个高置信度snp设计定制Oligo Pool All (CpOPA-I)进行基因分型。其中697个snp可成功用于基因分型,成功率高达90.75%。将697个snp的基因分型数据与前期研究中绘制的368个共显性标记的基因分型数据进行汇总,构建鹰嘴豆饱和遗传连锁图谱。共构建了8个连锁群,全长1808.7 cM (cM - morgans),标记间平均距离为1.70 cM,是鹰嘴豆最先进的遗传图谱之一。该图谱用于鹰嘴豆的同源性分析,发现鹰嘴豆与紫花苜蓿的同源性高于与大豆的同源性。本研究开发的第一批经过验证的snp和图谱资源,不仅将为豆科植物的QTL定位、全基因组关联分析和比较定位提供便利,还将为鹰嘴豆全基因组测序奠定基础。
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