Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.)
Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.)
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DOI：
10.1111/pbi.12009
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发表时间：
2013-04-01
影响因子：
13.8
通讯作者：
Edwards, Keith J.
中科院分区：
文献类型：
--
作者：
Allen, Alexandra M.;Barker, Gary L. A.;Edwards, Keith J.
在全球范围内，小麦是种植最广泛的作物，也是人类和牲畜饲料最重要的三种作物之一。然而，直到最近，小麦基因组的复杂性导致缺乏基于单核苷酸多态(SNP)的实际用于小麦育种的分子标记。最近，通过使用下一代测序结合各种基因分型平台，大量基于SNP的小麦标记已经成为可能。然而，这些标记和平台中的许多很难区分杂合子和纯合子个体，因此对进行商业规模育种计划的小麦育种者用处有限。为了鉴定基于外显子的共显性SNP分析，它能够区分杂合子和纯合子，我们使用了小麦外显子的靶向重测序来产生来自八个品种的大量基因组序列。利用生物信息学的方法，这些序列已经被用来识别95266个假定的单核苷酸多态，其中10251个被归类为假定的共显性。对这些假定的共显性标记的一个子集的验证证实，96%是真正的多态，65%是共显性SNP分析。本文描述的新的共显性标记能够对多倍体小麦中的一个分离基因座进行基因分类，并可在各种基因分型平台上使用；因此，它们是小麦育种者的有力工具。这些标记和相关信息已在一个基于网络的互动数据库上公开提供，以便利它们在世界各地的基因分型方案中使用。
Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)-based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP-based wheat markers have been made available via the use of next-generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial-scale breeding programmes. To identify exome-based co-dominant SNP-based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re-sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95266 putative single nucleotide polymorphisms, of which 10251 were classified as being putatively co-dominant. Validation of a subset of these putative co-dominant markers confirmed that 96% were true polymorphisms and 65% were co-dominant SNP assays. The new co-dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web-based database to facilitate their use on genotyping programmes worldwide.