Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.
Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.
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DOI：
10.1038/srep23765
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发表时间：
2016-04-01
影响因子：
4.6
通讯作者：
Tyagi AK
中科院分区：
文献类型：
--
作者：
Badoni S;Das S;Sayal YK;Gopalakrishnan S;Singh AK;Rao AR;Agarwal P;Parida SK;Tyagi AK
我们开发了全基因组84634 ISM（内含子跨越标记）和16510 InDel片段长度多态性为基础的ILP（内含子长度多态性）标记的基因物理定位在12条水稻染色体上。这些基因标记揭示了更高的扩增效率（80%）和多态性潜力（66%）之间的水稻加入，即使是成本效益的琼脂糖凝胶为基础的分析。利用3052个全基因组标记对籼稻、粳稻、香稻和野生稻的结构化群体进行了分子多样性分析，结果表明，籼稻、粳稻、香稻和野生稻的功能分子多样性在17%~ 79%之间，遗传结构也较为精确。利用2785个已知或候选基因的ISM和ILP标记构建了一张高密度（标记间距离为0.98 cM）遗传连锁图（IR 64 x Sonasal），将6个主要粒重QTL定位在5条水稻染色体上，可解释11.9-21.6%的表型变异。在单个基因中设计多个ISM和ILP标记（2至4个标记/基因）将拓宽用户偏好，以选择合适的引物组合用于有效测定功能等位基因变异/多样性和真实估计水稻种质之间的差异基因表达谱。在我们的研究中产生的基因组信息是公开的，通过用户友好的网络资源，“水稻ISM-ILP标记”数据库。已知/候选基因衍生的ISM和ILP标记可以通过最佳资源费用被大量部署以识别功能相关的性状相关分子标签，从而导致基因组学辅助的水稻作物改良。
We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17–79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9–21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, “Oryza ISM-ILP marker” database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice.