Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis
文献类型： 外文期刊
作者： Xia, Wei 1 ; Luo, Tingting 3 ; Zhang, Wei 3 ; Mason, Annaliese S. 5 ; Huang, Dongyi 1 ; Huang, Xiaolong 1 ; Tang, Wenq 1 ;
作者机构： 1.Hainan Univ, Inst Trop Agr & Forestry, Haikou, Hainan, Peoples R China
2.Chinese Acad Trop Agr Sci, Coconut Res Inst, Haikou, Hainan, Peoples R China
3.Huazhong Agr Univ, Natl Res Ctr Rapeseed Engn & Technol, Wuhan, Hubei, Peoples R China
4.Huazhong Agr Univ, Coll Plant Sci & Technol, Wuhan, Hubei, Peoples R China
5.Justus Liebig Univ Giessen, IFZ Res Ctr Biosyst Land Use & Nutr, Dept Plant Breeding, Giessen,
关键词： Elaeis guineensis; SNP; population structure; genetic diversity; linkage disequilibrium
期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）
ISSN： 1664-462X
年卷期： 2019 年 10 卷
页码：
收录情况： SCI
摘要： High-density single nucleotide polymorphisms (SNPs) are used as highly favored makers to analyze genetic diversity and population structure, to construct high-density genetic maps and provide genotypes for genome-wide association analysis. In order to develop genome-wide SNP markers in oil palm (Elaeis guineensis), single locus amplified fragment sequencing (SLAF-seq) technology was performed in a diversity panel of 200 oil palm individuals and 1,261,501 SNPs were identified with minor allele frequency > 0.05 and integrity > 1. Among them, only 17.81% can be mapped within the genic region and the remaining was located into the intergenic region. A positive correlation was detected between the distribution of SNP markers and retrotransposons [transposable elements (TEs)]. Population structure analysis showed that the 200 individuals of oil palm can be divided into five subgroups based on cross-validation errors. However, the subpopulations divided for the 200 oil palm individuals based on the SNP markers were not accurately related to their geographical origins and 80 oil palm individuals from Malaysia showed highest genetic diversity. In addition, the physical distance of linkage disequilibrium (LD) decay in the analyzed oil palm population was 14.516 kb when r(2) = 0.1. The LD decay distances for different chromosomes varied from 3.324 (chromosome 15) to 19.983 kb (chromosome 7). Our research provides genome-wide SNPs for future targeted breeding in palm oil.
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