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高密度单核苷酸多态性（SNP）标记的开发及其在评估[具体对象]遗传多样性和群体结构中的应用

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

作者信息

Xia Wei, Luo Tingting, Zhang Wei, Mason Annaliese S, Huang Dongyi, Huang Xiaolong, Tang Wenqi, Dou Yajing, Zhang Chunyu, Xiao Yong

机构信息

Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.

National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.

出版信息

Front Plant Sci. 2019 Feb 12;10:130. doi: 10.3389/fpls.2019.00130. eCollection 2019.

DOI:10.3389/fpls.2019.00130
PMID:30809240
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6380268/
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 (), 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 = 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.

摘要

高密度单核苷酸多态性（SNPs）被用作极具优势的标记，用于分析遗传多样性和群体结构、构建高密度遗传图谱以及为全基因组关联分析提供基因型。为了开发油棕全基因组SNP标记，对200个油棕个体的多样性群体进行了单基因座扩增片段测序（SLAF-seq）技术，共鉴定出1,261,501个次要等位基因频率>0.05且完整性>1的SNP。其中，只有17.81%可定位到基因区域内，其余的位于基因间区域。检测到SNP标记的分布与反转录转座子[转座元件（TEs）]之间存在正相关。群体结构分析表明，基于交叉验证错误，200个油棕个体可分为五个亚群。然而，根据SNP标记划分的200个油棕个体的亚群与它们的地理起源并无准确关联，来自马来西亚的80个油棕个体表现出最高的遗传多样性。此外，当r² = 0.1时，分析的油棕群体中连锁不平衡（LD）衰减的物理距离为14.516 kb。不同染色体的LD衰减距离从3.324 kb（第15号染色体）到19.983 kb（第7号染色体）不等。我们的研究为未来油棕的定向育种提供了全基因组SNP。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/f8f67bd93ca8/fpls-10-00130-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/0b76daa970de/fpls-10-00130-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/fd9599232b0d/fpls-10-00130-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/869267269b69/fpls-10-00130-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/52b6c718efd7/fpls-10-00130-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/d5de2d5f8d34/fpls-10-00130-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/f8f67bd93ca8/fpls-10-00130-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/0b76daa970de/fpls-10-00130-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/fd9599232b0d/fpls-10-00130-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/869267269b69/fpls-10-00130-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/52b6c718efd7/fpls-10-00130-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/d5de2d5f8d34/fpls-10-00130-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4a4e/6380268/f8f67bd93ca8/fpls-10-00130-g006.jpg

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