Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing
Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot (<i>P. armeniaca</i>) varieties were analyzed to provide a theoretical basis for revealing the phylogenetic rela...
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2024-12-01
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| author | Qirui Xin Jun Qing Yanhong He |
| author_facet | Qirui Xin Jun Qing Yanhong He |
| author_sort | Qirui Xin |
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| description | Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot (<i>P. armeniaca</i>) varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the “<i>Yinxiangbai</i>” apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software. The average comparison ratio between the sequencing results and the reference genome was 97.66%. After strict screening, 88,332,238 high-quality SNP sites were finally obtained. Based on the statistical SNP variation type, it was found that <i>LNLJX</i> had the largest number of variations (3,951,322) and the lowest base transition/base transversion ratio (ts/tv = 1.77), indicating that its gene exchange events occurred less frequently. Based on the SNP point estimation of the relationship and genetic distance between samples, the relationship between species was 1.41–0.01, among which <i>PLDJX</i> and <i>BK1</i> had the closest relationship of 1.41, and <i>YZH</i> and <i>LGWSX</i> had the farthest relationship of 0.01. The genetic distance between species was 0.00367–0.264344, the genetic distance between <i>HMX</i> and <i>JM</i> was the closest, and the genetic distance between <i>WYX</i> and <i>YX</i> was the farthest, which was the largest. Phylogenetic tree, PCA, and genetic structure analysis results all divided 53 common apricot varieties into four groups, and the classification results were consistent. The SNP markers mined using WGRS technology are useful not only to analyze the variation of common apricots, but also to effectively identify their kinship and genetic structure, which plays a critical role in the classification and utilization of common apricot germplasm resources. |
| format | Article |
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| issn | 1467-3037 1467-3045 |
| language | English |
| publishDate | 2024-12-01 |
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| spelling | doaj-art-8db4f76ce201486ca5a02f3749997fcb2025-08-20T02:00:26ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452024-12-014612141061411810.3390/cimb46120844Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome ResequencingQirui Xin0Jun Qing1Yanhong He2College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, ChinaCollege of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, ChinaCollege of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, ChinaBased on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot (<i>P. armeniaca</i>) varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the “<i>Yinxiangbai</i>” apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software. The average comparison ratio between the sequencing results and the reference genome was 97.66%. After strict screening, 88,332,238 high-quality SNP sites were finally obtained. Based on the statistical SNP variation type, it was found that <i>LNLJX</i> had the largest number of variations (3,951,322) and the lowest base transition/base transversion ratio (ts/tv = 1.77), indicating that its gene exchange events occurred less frequently. Based on the SNP point estimation of the relationship and genetic distance between samples, the relationship between species was 1.41–0.01, among which <i>PLDJX</i> and <i>BK1</i> had the closest relationship of 1.41, and <i>YZH</i> and <i>LGWSX</i> had the farthest relationship of 0.01. The genetic distance between species was 0.00367–0.264344, the genetic distance between <i>HMX</i> and <i>JM</i> was the closest, and the genetic distance between <i>WYX</i> and <i>YX</i> was the farthest, which was the largest. Phylogenetic tree, PCA, and genetic structure analysis results all divided 53 common apricot varieties into four groups, and the classification results were consistent. The SNP markers mined using WGRS technology are useful not only to analyze the variation of common apricots, but also to effectively identify their kinship and genetic structure, which plays a critical role in the classification and utilization of common apricot germplasm resources.https://www.mdpi.com/1467-3045/46/12/844common apricotwhole genome resequencingSNPpopulation genetic structure |
| spellingShingle | Qirui Xin Jun Qing Yanhong He Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing Current Issues in Molecular Biology common apricot whole genome resequencing SNP population genetic structure |
| title | Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing |
| title_full | Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing |
| title_fullStr | Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing |
| title_full_unstemmed | Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing |
| title_short | Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing |
| title_sort | analysis of kinship and population genetic structure of 53 apricot resources based on whole genome resequencing |
| topic | common apricot whole genome resequencing SNP population genetic structure |
| url | https://www.mdpi.com/1467-3045/46/12/844 |
| work_keys_str_mv | AT qiruixin analysisofkinshipandpopulationgeneticstructureof53apricotresourcesbasedonwholegenomeresequencing AT junqing analysisofkinshipandpopulationgeneticstructureof53apricotresourcesbasedonwholegenomeresequencing AT yanhonghe analysisofkinshipandpopulationgeneticstructureof53apricotresourcesbasedonwholegenomeresequencing |