High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).
High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).
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用于构建鹰嘴豆饱和连锁图的高通量SNP发现和基因分型（Cicer Arietinum L.）。
DOI：
10.1093/dnares/dss018
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发表时间：
2012-10
期刊：
影响因子：
--
通讯作者：
Bhatia S
中科院分区：
文献类型：
--
作者：
Gaur R;Azam S;Jeena G;Khan AW;Choudhary S;Jain M;Yadav G;Tyagi AK;Chattopadhyay D;Bhatia S
本研究报告了鹰嘴豆全基因组单核苷酸多态性（SNPs）的大规模发现，主要是通过下一代测序的两种基因型，即鹰嘴豆ICC 4958和其野生祖先C。reticulatum PI 489777，鹰嘴豆种间参考作图群体的亲本。首次描述了基于Illumina GoldenGate基因分型技术的高通量SNP基因分型检测方法的开发和验证及其在构建鹰嘴豆高分辨率遗传连锁图谱中的应用。在这项研究中，鉴定了1022个SNP，其中768个高置信度SNP被选择用于设计用于基因分型的定制寡核苷酸池All（CpOPA-I）。其中，697个SNP可成功用于基因分型，成功率高达90.75%。沿着整理了697个SNPs的基因分型数据和前期研究中绘制的368个共显性标记的基因分型数据，构建了鹰嘴豆的饱和遗传连锁图谱。1063个标记被定位到8个连锁群，跨越1808.7 cM（centiMorgans），平均标记间距离为1.70 cM，从而代表了鹰嘴豆最先进的地图之一。该图谱被用于鹰嘴豆的同线性分析，其揭示了与在遗传学上接近的苜蓿比与大豆的同线性程度更高。本研究开发的第一套有效的SNP和图谱资源不仅有助于豆科植物的QTL定位、全基因组关联分析和比较定位，而且有助于鹰嘴豆全基因组测序产生的锚支架。
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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影响因子：
5.4
作者：
Bindler, Gregor;Plieske, Joerg;Bakaher, Nicolas;Gunduz, Irfan;Ivanov, Nikolai;Van der Hoeven, Rutger;Ganal, Martin;Donini, Paolo
通讯作者：
Donini, Paolo
DOI：
10.1073/pnas.0402251101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Choi, HK;Mun, JH;Cook, DR
通讯作者：
Cook, DR
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
影响因子：
5.4
作者：
Choudhary, Shalu;Gaur, Rashmi;Bhatia, Sabhyata
通讯作者：
Bhatia, Sabhyata
影响因子：
2.7
作者：
Coram, TE;Pang, ECK
通讯作者：
Pang, ECK