Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis

Frontiers in Plant Science

卷:10

Yong Xiao¹  Annaliese S. Mason²  Xiaolong Huang³  Wenqi Tang³  Wei Xia³  Dongyi Huang³  Yajing Dou³  Wei Zhang⁴  Chunyu Zhang⁴  Tingting Luo⁴ 

[1] Coconut Research Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China;

[2] Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany;

[3] Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China;

[4] National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;

关键词: Elaeis guineensis;    SNP;    population structure;    genetic diversity;    linkage disequilibrium;   

DOI  :  10.3389/fpls.2019.00130

来源: DOAJ

【 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 r2 = 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.

【 授权许可】

Unknown