Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences
Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences
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DOI：
10.1007/s11105-015-0907-5
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发表时间：
2016-02-01
影响因子：
2.1
通讯作者：
Li, HongYing
中科院分区：
文献类型：
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作者：
Hou, Siyu;Sun, Zhaoxia;Li, HongYing
苦荞是中国重要的食用作物和药用植物。由于苦荞的药用功能，越来越多的研究集中在这种小型粮食作物上，但由于缺乏基因组学，苦荞的分子标记缺乏。本研究对苦荞进行了基因组调查，并开发了SSR标记进行遗传多样性分析。该调查产生了21.9 Gb的原始序列，组装成348.34 Mb的基因组序列，包括204,340个contigs。根据K-mer分析，估计基因组大小约为497mb。从该基因组调查序列中共鉴定出24505个SSR基序。大部分SSR基序为二核苷酸重复序列（67.14%）和三核苷酸重复序列（26.05%）。AT/AT重复基序最为丰富，占二核苷酸重复基序的78.60%。对64份材料进行SSR指纹图谱分析，共获得63个有效等位基因位点49.71个，其中23个引物具有多态性。群体遗传结构分析表明，64份苦荞材料可分为两个不同的亚群。一类主要分布在尼泊尔、不丹和中国云贵高原地区；另一类主要来源于黄土高原地区、中国湖南、湖北和美国。UPMGA聚类分析结果有力地支持了两个亚群的解释。然而，根据不同的分类方法，来自中国青海的材料可以被分为两个亚群中的任何一个。这个地区位于与这两个亚群相关的两个地理区域的交汇处。这些结果和信息可为苦荞种质资源的鉴定和利用提供依据。
Tartary buckwheat is an important edible crop as well as medicinal plant in China. More and more research is being focused on this minor grain crop because of its medicinal functions, but there is a paucity of molecular markers for tartary buckwheat due to the lack of genomics. In this study, a genome survey was carried out in tartary buckwheat, from which SSR markers were developed for analysis of genetic diversity. The survey generated 21.9 Gb raw sequence reads which were assembled into 348.34 Mb genome sequences included 204,340 contigs. The genome size was estimated to be about 497 Mb based on K-mer analysis. In total, 24,505 SSR motifs were identified and characterised from this genomic survey sequence. Most of the SSR motifs were dinucleotide (67.14 %) and tri-nucleotide (26.05 %) repeats. AT/AT repeat motifs were the most abundant, accounting for 78.60 % of di-nucleotide repeat motifs. SSR fingerprinting of 64 accessions yielded 49.71 effective allele loci from a total of 63 with the 23 polymorphic SSR primer combinations. Analyses of the population genetic structure using SSR data strongly suggested that the 64 accessions of tartary buckwheat clustered into two separate subgroups. One group was mainly distributed in Nepal, Bhutan and the Yunnan-Guizhou Plateau regions of China; the other group was mainly derived from the Loess Plateau regions, Hunan and Hubei of China and USA. The cluster analysis of these accession's genetic similarity coefficient by UPMGA methods strongly supported the two subgroup interpretation. However accessions from Qinghai of China could be grouped into either of the two subgroups depending on which classification method was used. This region is at the intersection of the two geographical regions associated with the two subgroups. These results and information could be used to identify and utilize germplasm resources for improving tartary buckwheat breeding.