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

Frontiers in Plant Science
Wei XiaYong Xiao

Abstract

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 pa...Continue Reading

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Citations

Jun 21, 2020·Scientific Reports·Javier HerreroEnrique Ritter
Feb 12, 2021·Plant Science : an International Journal of Experimental Plant Biology·Maizura IthninRajinder Singh
Jun 11, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Jian Gao, Xiao-Li Ning
Dec 21, 2019·Journal of Agricultural and Food Chemistry·Tingting LuoYong Xiao
Nov 11, 2021·Omics : a Journal of Integrative Biology·Muliyar Krishna RajeshThottethodi Subrahmanya Keshava Prasad

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Datasets Mentioned

BETA
PRJEB26466

Methods Mentioned

BETA
environmental stress
genotyping
amplified fragment sequencing
PCR
SLAF-seq

Software Mentioned

Dual
TASSEL
MEGA5
Msatfinder
STRUCTURE
GATK
Burrows ( BWA )
RepeatMasker
BWA
SAMtools

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