Genetic diversity of Coffea arabica based on SLAF-Seq technology
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摘要: 【目的】 采用特异性位点扩增片段测序（SLAF-Seq）技术对阿拉比卡咖啡种质资源进行遗传多样性分析，明确本地咖啡种质遗传背景，为阿拉比卡咖啡新品种选育提供理论依据。【方法】 以国内外40份阿拉比卡咖啡和4份非阿拉比卡咖啡（外类群对照）种质资源为材料，采用SLAF-Seq技术对其进行SNP标记开发及系统发育、群体遗传结构及主成分分析。【结果】 所有供试咖啡属种质资源测序共获得220.54 Mb数据，测序样品平均Reads数量为5012189条，测序平均Q30为95.90%，平均GC含量为39.48%。定位到参考基因组的Clean reads占所有Clean reads总数的百分比平均为95.05%。从44份咖啡属种质资源中共检测到214254个SLAF标签，平均每份样品SLAF标签数量为140742。SLAF标签在每份样本中的分布数量为46234～171026个。共开发出1186433个群体SNP分子标记，每个样品的SNP分子标记数目为381105～903823个，SNP分子标记完整度为32.12%～76.18%，杂合率为6.23%～17.49%。阿拉比卡咖啡SNP分布具有一定的区域集中性，主要集中在1c～11c这套来自其中一个亲本卡尼弗拉咖啡（中粒种）染色体组上。系统发育、群体遗传结构及主成分3种聚类结果显示，阿拉比卡咖啡铁皮卡型、阿拉比卡咖啡波邦型和含有Catimor的类群被明显区分开来独立成群，并明确了18份阿拉比卡咖啡种质的遗传背景。【结论】 40份阿拉比卡咖啡主要分为铁皮卡型类群、波邦型类群和含有Catimor商品种质的类群。采用SLAF-Seq技术所开发的SNP分子标记可准确分析阿拉比卡咖啡资源遗传多样性。Abstract: 【Objective】 The study aimed to analyze the genetic diversity of Coffea arabica germplasm resources using specific-locus amplified fragment sequencing（SLAF-Seq） technology. It identified the genetic backgrounds of local coffee germplasms, providing a theoretical basis for the breeding of new C. arabica varieties. 【Method】 The phylogeny, population genetic structure and principal component analysis were carried out through SNP markers using SLAF-Seq technology based on 40 C. arabica germplasms and 4 non-C. arabica germplasms（served as out-group control）. 【Result】 The sequencing of all tested Coffea sp. germplasm resources yielded a total of 220.54 Mb of data. The average number of reads of sequencing sample was 5012189, with an average Q30 of 95.90%, and an average GC content of 39.48%. The percentage of clean reads localized to the reference genome constituted an average of 95.05% of all clean reads. A total of 214254 SLAF tags were detected from 44 coffee germplasm resources, with an average of 140742 SLAF tags per sample.The number of SLAF tags distributed in each sample ranged from 46234 to 171026. A total of 1186433 population SNP molecular markers were developed, with the number of SNP molecular markers per sample ranging from 381105 to 903823, the integrity of SNP markers ranging from 32.12% to 76.18%, and heterozygosity rate from 6.23% to 17.49%.The distribution of SNP in C. arabica showed some regional concentration, primarily on the chromosome set from 1c to 11c derived from one of the parents, C. canephora（Robusta coffee）. The results of phylogeny, population genetic structure and principal component analysis displayed that the groups of C. arabica Typica type, groups of C. arabica Bourban type, and the groups containing Catimor were clearly distinguished from each other and the genetic backgrounds of 18 C.arabica germplasms were clarified. 【Conclusion】 The 40 C. arabica germplasms in the study are mainly divided into Typica type group, Bourbon type group and the group containing Catimor comercial germplasm. The genetic diversity of C. arabica resources can be accurately analyzed based on SNP molecular markers developed by SLAF-Seq technology.
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Keywords:
- Coffea arabica /
- genetic diversity /
- SLAF-Seq /
- SNP /
- phylogeny /
- population genetic structure /
- principal component analysis
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