National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No 10531, New Delhi 110067, India.
Theor Appl Genet. 2012 May;124(8):1449-62. doi: 10.1007/s00122-012-1800-3.
Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs) are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs, 151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms (SNPs). Whereas ESTSSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performedusing the Illumina GoldenGate Assay. Parental polymorphism was analyzed between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of chickpea solely based on co-dominant markers.
充分饱和的连锁图谱，特别是基于表达序列标签（EST）衍生基因分子标记（GMM）的图谱，是分子育种的前提。在重要的豆科作物如鹰嘴豆中尤其如此，因为开发的简单重复序列（SSR）较少，甚至基于 GMM 的图谱也较少。因此，在这项研究中，从鹰嘴豆种子中生成了 2496 个 EST，并利用这些 EST 开发了 487 个新的 EST 衍生功能标记，其中包括 125 个 EST-SSR、151 个内含子靶向引物（ITP）、109 个表达序列标签多态性（ESTP）和 102 个单核苷酸多态性（SNP）。EST-SSR、ITP 和 ESTP 是通过对开发的 EST 序列进行计算机分析而开发的，而 SNP 则是通过等位基因重测序和 Illumina GoldenGate 分析进行鉴定的。使用总共 872 个标记分析了参考鹰嘴豆图谱群体的亲本 C. arietinum ICC4958 和 C. reticulatum PI489777 之间的多态性：487 个新的基于基因的标记是本研究中开发的，以及 385 个先前发表的标记，其中 318 个（36.5%）被发现是多态性的，并用于基因分型。基因型数据与先前发表的 108 个标记的数据进行了整合，并生成了一个高级连锁图谱，该图谱包含 406 个位于 8 个连锁群上的位点，跨度为 1497.7cM。标记的平均密度为 3.68cM，每个连锁群上的标记平均数量为 50.8。在图谱上的标记中，定义了 303 个新的基因组位置，包括 177 个基于基因的和 126 个 gSSR（基因组 SSR），从而仅基于共显性标记生成了最先进的鹰嘴豆基因丰富图谱。
