Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra).
Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra).
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DOI：
10.1186/1471-2164-13-201
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发表时间：
2012-05-23
期刊：
影响因子：
4.4
通讯作者：
Gao ZS
中科院分区：
文献类型：
--
作者：
Jiao Y;Jia HM;Li XW;Chai ML;Jia HJ;Chen Z;Wang GY;Chai CY;van de Weg E;Gao ZS
杨梅（Myrica rubra Sieb.）Zucc）。是一种原产于中国的亚热带万年青乔木。它在中国南方已经种植了几千年，年产量达到110万吨。近年来，在水果中鉴定出的味道和高水平的健康促进特性刺激了其在中国的推广和引入澳大利亚。有限数量的共显性标记已被开发并应用于遗传多样性和身份研究。在这里，我们报告，为第一次，调查的全基因组鸟枪数据，开发了大量的简单重复序列（SSR）标记，以分析常见的栽培杨梅的遗传多样性和与其他三个杨梅物种的关系。杨梅全基因组鸟枪测序获得了9.01Gb的序列数据，约为估计基因组大小323 Mb的26倍覆盖率。基因组序列高度杂合，但几乎没有重复。从覆盖255 Mb序列数据的初始组装支架中，鉴定出28，602个SSR（≥5个重复）。二核苷酸重复序列最多，占84.73%，其次是三核苷酸（13.78%）、四核苷酸（1.34%）、五核苷酸（0.12%）和六核苷酸（0.04%）。从600对引物中筛选出186个多态性位点。其中158个SSR标记用于29份杨梅种质和3种杨梅的筛选，对紫茎杨梅、矮杨梅和角杨梅的特异性分别为91.14%、89.87%和46.84%。UPGMA聚类分析表明，栽培杨梅与原产于我国西南地区的杨梅（Myrica adenophora）和矮杨梅（Myrica nana）亲缘关系较近，与原产于美洲的杨梅（Myrica cerifera）亲缘关系较远。这些标记可用于杨梅属植物遗传多样性研究和连锁图谱的构建。杨梅（Myrica rubra）基因组较小，约323 Mb，具有较高的杂合性。共筛选出158个多态性SSR标记，其中91%的SSR标记可用于杨梅属其他物种的遗传分析。
Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in recent years has stimulated its extension in China and introduction to Australia. A limited number of co-dominant markers have been developed and applied in genetic diversity and identity studies. Here we report, for the first time, a survey of whole genome shotgun data to develop a large number of simple sequence repeat (SSR) markers to analyse the genetic diversity of the common cultivated Chinese bayberry and the relationship with three other Myrica species. The whole genome shotgun survey of Chinese bayberry produced 9.01Gb of sequence data, about 26x coverage of the estimated genome size of 323 Mb. The genome sequences were highly heterozygous, but with little duplication. From the initial assembled scaffold covering 255 Mb sequence data, 28,602 SSRs (≥5 repeats) were identified. Dinucleotide was the most common repeat motif with a frequency of 84.73%, followed by 13.78% trinucleotide, 1.34% tetranucleotide, 0.12% pentanucleotide and 0.04% hexanucleotide. From 600 primer pairs, 186 polymorphic SSRs were developed. Of these, 158 were used to screen 29 Chinese bayberry accessions and three other Myrica species: 91.14%, 89.87% and 46.84% SSRs could be used in Myrica adenophora, Myrica nana and Myrica cerifera, respectively. The UPGMA dendrogram tree showed that cultivated Myrica rubra is closely related to Myrica adenophora and Myrica nana, originating in southwest China, and very distantly related to Myrica cerifera, originating in America. These markers can be used in the construction of a linkage map and for genetic diversity studies in Myrica species. Myrica rubra has a small genome of about 323 Mb with a high level of heterozygosity. A large number of SSRs were identified, and 158 polymorphic SSR markers developed, 91% of which can be transferred to other Myrica species.
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影响因子：
1.5
作者：
Bourguiba, Hedia;Khadari, Bouchaib;Audergon, Jean-Marc
通讯作者：
Audergon, Jean-Marc
DOI：
10.1099/00207713-51-3-731
发表时间：
2001-05-01
影响因子：
2.8
作者：
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通讯作者：
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影响因子：
5.4
作者：
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通讯作者：
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影响因子：
4.4
作者：
Feng C;Chen M;Xu CJ;Bai L;Yin XR;Li X;Allan AC;Ferguson IB;Chen KS
通讯作者：
Chen KS
影响因子：
5.4
作者：
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通讯作者：
De Silva, HN