南方农业学报2024，Vol.55Issue(6)：1583-1593,11.DOI:10.3969/j.issn.2095-1191.2024.06.004
基于SLAF-Seq的阿拉比卡咖啡遗传多样性分析
Genetic diversity of Coffea arabica based on SLAF-Seq technology
摘要
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 co-ffee 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 lc to 11c derived from one of the parents,C.canephora(Robusta coffee).The results of phylogeny,population genetic struc-ture 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.关键词
阿拉比卡咖啡/遗传多样性/SLAF-Seq/SNP/系统发育/群体遗传结构/主成分分析Key words
Coffea arabica/genetic diversity/SLAF-Seq/SNP/phylogeny/population genetic structure/princi-pal component analysis分类
农业科技引用本文复制引用
李学俊,葛宇,王步天,赵猛,施学东,陈治华,谢纯,卢云峰,董相书,马银波..基于SLAF-Seq的阿拉比卡咖啡遗传多样性分析[J].南方农业学报,2024,55(6):1583-1593,11.基金项目
"Yunnan Revitalization Talent Support Project"Young Talents Project(XDYC-QNRC-2022-0711) （XDYC-QNRC-2022-0711）
Yunnan Key Research and Development Project(202303AP140010) （202303AP140010）
Yunnan Expert Basic Scientific Research Station Project(2021RYZJGZZ002) （2021RYZJGZZ002）
Scientific Research Fund Project of Yunnan Education Department(2023Y0915) 云南省"兴滇英才支持计划"青年人才专项(XDYC-QNRC-2022-0711) （2023Y0915）
云南省重点研发计划项目(202303AP140010) （202303AP140010）
云南省专家基层科研工作站项目(2021RYZJGZZ002) （2021RYZJGZZ002）
云南省教育厅科学研究基金项目(2023Y0915) （2023Y0915）
