Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq

被引:42
作者
Feng, Junyan [1 ]
Zhao, Shan [2 ]
Li, Ming [1 ]
Zhang, Cong [1 ]
Qu, Huijuan [1 ]
Li, Qing [1 ]
Li, Jianwei [1 ]
Lin, Yang [1 ]
Pu, Zhigang [1 ]
机构
[1] Sichuan Acad Agr Sci, Biotechnol & Nucl Technol Res Inst, Chengdu 610061, Peoples R China
[2] Sichuan Acad Agr Sci, Ctr Anal & Testing, Chengdu 610066, Peoples R China
基金
中国国家自然科学基金;
关键词
Sweetpotato; RAD-seq; SSR marker; Genetic relationship; SNP; L; LAM; LINKAGE MAP; PLOIDY LEVELS; TOOL SET; IDENTIFICATION; EVOLUTION; ORIGIN; AFLP; MICROSATELLITES; HEXAPLOIDS;
D O I
10.1016/j.ygeno.2019.11.010
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in > 100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded > 128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.
引用
收藏
页码:1978 / 1987
页数:10
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