EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea
EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea
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DOI：
10.1007/s00122-012-1800-3
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发表时间：
2012-05-01
影响因子：
5.4
通讯作者：
Bhatia, Sabhyata
中科院分区：
文献类型：
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作者：
Choudhary, Shalu;Gaur, Rashmi;Bhatia, Sabhyata
高饱和度的连锁图谱，特别是基于表达序列标签（EST）的基因分子标记（GSTs）构建的连锁图谱是分子育种的前提。这是特别真实的，在重要的豆类，如鹰嘴豆，很少有简单重复序列（SSR），甚至更少的基于GMM的地图已经开发。因此，在这项研究中，2,496个EST从鹰嘴豆种子中产生，并用于开发487个新的EST衍生的功能标记，其中包括125个EST-SSR，151个内含子靶向引物（ITPs），109个表达序列标签多态性（ESTPs），和102个单核苷酸多态性（SNP）。虽然EST-SSRs、ITP和ESTPs是通过对开发的EST序列进行计算机分析来开发的，但SNP是通过等位基因重新测序来鉴定的，并且使用Illumina GoldenGate检测试剂盒对其进行基因分型。对C. arietinum ICC 4958和C. Reticulatum PI 489777，参考鹰嘴豆作图群体的亲本，使用总共872个标记：本研究中开发的487个新的基于基因的标记沿着385个先前公布的标记，其中318个（36.5%）被发现是多态的，并用于基因分型。将基因型数据与先前公布的108个标记的数据整合，生成了一个高级连锁图，其中包含分布在8个连锁群上的406个位点，跨度为1，497.7 cM。平均标记密度为3.68 cM，每个LG的平均标记数为50.8。在绘制的标记中，定义了303个新的基因组位置，其中包括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产生最先进的鹰嘴豆基因丰富的地图。
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 EST-SSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performed using 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.