Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).
Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).
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DOI：
10.1371/journal.pone.0141540
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Zhao X
中科院分区：
文献类型：
--
作者：
Han B;Wang C;Tang Z;Ren Y;Li Y;Zhang D;Dong Y;Zhao X
微卫星或简单重复序列（SSR）分布在原核和真核基因组中，已广泛用于作物遗传研究和分子标记辅助育种。尽管六倍体面包小麦的有序序列草图已经公布，但小麦SSR系统分析的研究至今未见报道。本研究从中国春小麦基因组的10，603，760个序列中鉴定出364，347个SSR，SSR密度为36.68个/Mb。我们总共检测到488种基序，从二核苷酸到六核苷酸，其中二核苷酸重复占主导地位，约占基因组的42.52%。3 ~ 6核苷酸重复序列密度分别为24.97%、4.62%、3.25%和24.65%。AG/CT、AAG/CTT、AGAT/ATCT、AAAAG/CTTTT和AAAATT/AATTTT是二核苷酸至六核苷酸重复序列中出现频率最高的重复序列。在CSW的21条染色体中，2D染色体上的重复频率最高，3A染色体上的重复频率最低。在每条染色体上，甚至在整个基因组上，二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸重复的比例几乎相同。此外，从CSW的21条染色体上成功地开发了295，267个SSR标记，其密度为29.73个/Mb，覆盖了整个基因组。所有的SSR标记进行了验证，通过反向电子聚合酶链反应（re-PCR），70,564（23.9%）被发现是单态和224,703（76.1%）被发现是多态性的。随机选择了45个单态性标记进行验证，其中24个（53.3%）扩增了一个位点，8个（17.8%）扩增了多个相同的位点，13个（28.9%）没有从CSW的基因组DNA中扩增出任何片段。利用这24个单态SSR标记对20个小麦品种及其3个二倍体祖先物种进行聚类分析，结果表明单态SSR标记是一个很有前途的标记来源，可以增加小麦基因组的遗传标记数量。本研究结果将为小麦及其近缘种的遗传多样性和进化研究提供参考。同时，这些结果将促进植物的比较基因组研究和标记辅助育种（MAS）。
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.