Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis
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 (Ela...
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| Format: | Article |
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Frontiers Media S.A.
2019-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.00130/full |
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| author | Wei Xia Tingting Luo Wei Zhang Annaliese S. Mason Dongyi Huang Xiaolong Huang Wenqi Tang Yajing Dou Chunyu Zhang Yong Xiao |
| author_facet | Wei Xia Tingting Luo Wei Zhang Annaliese S. Mason Dongyi Huang Xiaolong Huang Wenqi Tang Yajing Dou Chunyu Zhang Yong Xiao |
| author_sort | Wei Xia |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T06:20:25Z |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-14T06:20:25Z |
| publishDate | 2019-02-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-3dd07f73fc304e42aa55300f96b1ef1f2022-12-22T02:08:03ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-02-011010.3389/fpls.2019.00130414759Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensisWei Xia0Tingting Luo1Wei Zhang2Annaliese S. Mason3Dongyi Huang4Xiaolong Huang5Wenqi Tang6Yajing Dou7Chunyu Zhang8Yong Xiao9Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, ChinaNational Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaNational Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaDepartment of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, GermanyInstitute of Tropical Agriculture and Forestry, Hainan University, Haikou, ChinaInstitute of Tropical Agriculture and Forestry, Hainan University, Haikou, ChinaInstitute of Tropical Agriculture and Forestry, Hainan University, Haikou, ChinaInstitute of Tropical Agriculture and Forestry, Hainan University, Haikou, ChinaNational Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaCoconut Research Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, ChinaHigh-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.https://www.frontiersin.org/article/10.3389/fpls.2019.00130/fullElaeis guineensisSNPpopulation structuregenetic diversitylinkage disequilibrium |
| spellingShingle | Wei Xia Tingting Luo Wei Zhang Annaliese S. Mason Dongyi Huang Xiaolong Huang Wenqi Tang Yajing Dou Chunyu Zhang Yong Xiao Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis Frontiers in Plant Science Elaeis guineensis SNP population structure genetic diversity linkage disequilibrium |
| title | Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis |
| title_full | Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis |
| title_fullStr | Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis |
| title_full_unstemmed | Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis |
| title_short | Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis |
| title_sort | development of high density snp markers and their application in evaluating genetic diversity and population structure in elaeis guineensis |
| topic | Elaeis guineensis SNP population structure genetic diversity linkage disequilibrium |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.00130/full |
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