文献类型：期刊文献

中文题名：基于SLAF-seq技术红豆树基因组的SSR位点特征分析

英文题名：The Distribution Types and Characteristics of SSR Loci Based on SLAF-seq in Ormosia hosiei Genome

作者：李峰卿[1,2,3] 谢耀坚[1] 周志春[3] 陈鸿鹏[1] 楚秀丽[3]

第一作者：李峰卿

机构：[1]国家林业局桉树研究开发中心,湛江524022;[2]中国林业科学研究院亚热带林业实验中心,分宜336600;[3]中国林业科学研究院亚热带林业研究所,浙江省林木育种技术研究重点实验室,富阳311400

年份：2017

卷号：15

期号：5

起止页码：1774-1781

中文期刊名：分子植物育种

外文期刊名：Molecular Plant Breeding

收录：CSTPCD;;北大核心:【北大核心2014】；CSCD:【CSCD2017_2018】；

基金：浙江省农业(林木)新品种选育重大科技专项重点课题(2016C02056-3);中国林科院亚热带林业研究所自主立项课题(RISFZ-2016-01)共同资助

语种：中文

中文关键词：红豆树;SLAF-seq;SSR;分布;位点分析

外文关键词：Ormosia hosiei, SLAF-seq, SSR, Distribution, Locus analysis

分类号：S

摘要：简单重复序列(SSR)广泛存在于基因组中,是亲缘关系分析、DNA指纹图谱构建和遗传多样性研究领域中非常重要的遗传标记之一。红豆树群体已处于濒危状态,且属无参基因组,其近缘种开发的SSR引物亦很少,为满足红豆树遗传多样性研究及制定合理的保护策略,本研究基于SLAF-seq(specific-locus amplified fragment sequencing)技术对天然群体中典型红豆树进行简化测序,利用MISA软件对测序获得所有SLAF片段进行SSR位点搜索,并对SSR位点特征进行统计分析,最后利用Primer Premier 5.0软件进行引物批量设计。与日本晴水稻的测序数据相比,红豆树参考基因组的双端比对效率为90.14%,酶切效率为92.37%,说明SLAF建库正常;测序Q30为92.32%,GC含量为37.17%,说明达到测序要求。本研究共获得6 426 462 reads和592 221个SLAF标签,其中16 653个多态性SLAF标签,含有17 868个SSR位点,平均每6.98 kb就分布有1个SSR位点。不同核苷酸重复类型的基元类型数量及SSR位点数量间差异较大,除单核苷酸外,二、三核苷酸重复类型数量较多,分别占总SSR位点的17.15%和15.02%,其中AT/TA和GAA/TTC基元重复数量最多,分别为1 090个(43.1%)和349个(15.2%)。通过批量引物设计共得到2 817对引物,以二、三核苷酸类型较多,两者所占比例高达94.8%。结果表明:SLAF-seq技术可以很好的应用于红豆树(无参基因组)SSR位点的开发,基于简化基因组测序数据发掘的SSR位点能够为SSR分子标记开发提供信息,并有助于后续群体遗传多样性和交配系统分析等。
Simple sequence repeats （SSR） widely existed in the genome, which was one of the important genetic markers in the field of genetic relationship analysis, DNA fingerprint building and the genetic diversity research. The population of Ormosia hosiei was in endangered state, which belonged to no reference genome and had little SSR markers in their relatives. In order to research the genetic diversity and formulate appropriate protection strategy, we took the SLAF-seq （specific locus amplified fragment sequencing） technology to simplify the se- quencing of typical Ormos ia hosiei among natural ones, and searched by MISA software for SSR loci of all the SLAF segments, at the same time we also carried out the statistical analysis on their distribution of SSR locus, and finally designed the primers by utilizing the Primer Premier 5.0 software. Compared of the sequence between Japan＇s fine rice and the reference genome of Ormosia hosiei, the results showed that the construction of SLAF library fitted well to the standard, with its paired-end mapped reads reaching 90.14%, normal digestion ratio reached 92.37%; the quality of Q30 up to 92.32% and the GC content （37.17%） low enough to process sequencing. In this study 6 426 462 reads and 592 221 SLAF labels was obtained, and there were 16 653 SLAF labels containing SSR loci, with a total of 17 868 SSR locus. A SSR loci would be distributed per 6.98 kb on the average. The number of repeated elements types in different nucleotides and SSR loci had bigger difference. In addition to the single nucleotide, the number of dinucleotide and trinucleotide repeated types were much more, accounting for 17.15% and 15.02% in the total SSR loci respectively, among these the elements of AT/TA and the GAA/TTC repeated the most, reached 1 090 （43.1%） and 349 （15.2%） respectively. According to the batch primer designation, a total of 2 817 pairs of primers were obtained, and the types of dinucleotide and trinucleotide were much more, the proportions of them were reached 94.8%. The results showed that the SLAF-seq technology can be well applied in developing SSR of Ormosia hosiei （no reference genome）, which provided information for the development of molecular markers and can be further used for the analysis of genetic diversity and mating system and so on.