Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium
Abstract Background Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat g...
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| Format: | Article |
| Language: | English |
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BMC
2020-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-06835-0 |
| _version_ | 1818858870793043968 |
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| author | Amira M. I. Mourad Vikas Belamkar P. Stephen Baenziger |
| author_facet | Amira M. I. Mourad Vikas Belamkar P. Stephen Baenziger |
| author_sort | Amira M. I. Mourad |
| collection | DOAJ |
| description | Abstract Background Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat genotypes. Also, understanding the genetic diversity is useful in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. Results To understand the genetic diversity in wheat, a set of 103 spring wheat genotypes which represented five different continents were used. These genotypes were genotyped using 36,720 genotyping-by-sequencing derived SNPs (GBS-SNPs) which were well distributed across wheat chromosomes. The tested 103-wheat genotypes contained three different subpopulations based on population structure, principle coordinate, and kinship analyses. A significant variation was found within and among the subpopulations based on the AMOVA. Subpopulation 1 was found to be the more diverse subpopulation based on the different allelic patterns (Na, Ne, I, h, and uh). No high linkage disequilibrium was found between the 36,720 SNPs. However, based on the genomic level, D genome was found to have the highest LD compared with the two other genomes A and B. The ratio between the number of significant LD/number of non-significant LD suggested that chromosomes 2D, 5A, and 7B are the highest LD chromosomes in their genomes with a value of 0.08, 0.07, and 0.05, respectively. Based on the LD decay, the D genome was found to be the lowest genome with the highest number of haplotype blocks on chromosome 2D. Conclusion The recent study concluded that the 103-spring wheat genotypes and their GBS-SNP markers are very appropriate for GWAS studies and QTL-mapping. The core collection comprises three different subpopulations. Genotypes in subpopulation 1 are the most diverse genotypes and could be used in future breeding programs if they have desired traits. The distribution of LD hotspots across the genome was investigated which provides useful information on the genomic regions that includes interesting genes. |
| first_indexed | 2024-12-19T09:03:10Z |
| format | Article |
| id | doaj.art-597c12196cca4a89996914fa64a89b31 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T09:03:10Z |
| publishDate | 2020-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-597c12196cca4a89996914fa64a89b312022-12-21T20:28:25ZengBMCBMC Genomics1471-21642020-06-0121111210.1186/s12864-020-06835-0Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibriumAmira M. I. Mourad0Vikas Belamkar1P. Stephen Baenziger2Department of Agronomy, Faculty of Agricultural, Assuit UniversityDepartment of Agronomy and Horticulture, Plant Science Hall, UNLDepartment of Agronomy and Horticulture, Plant Science Hall, UNLAbstract Background Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat genotypes. Also, understanding the genetic diversity is useful in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. Results To understand the genetic diversity in wheat, a set of 103 spring wheat genotypes which represented five different continents were used. These genotypes were genotyped using 36,720 genotyping-by-sequencing derived SNPs (GBS-SNPs) which were well distributed across wheat chromosomes. The tested 103-wheat genotypes contained three different subpopulations based on population structure, principle coordinate, and kinship analyses. A significant variation was found within and among the subpopulations based on the AMOVA. Subpopulation 1 was found to be the more diverse subpopulation based on the different allelic patterns (Na, Ne, I, h, and uh). No high linkage disequilibrium was found between the 36,720 SNPs. However, based on the genomic level, D genome was found to have the highest LD compared with the two other genomes A and B. The ratio between the number of significant LD/number of non-significant LD suggested that chromosomes 2D, 5A, and 7B are the highest LD chromosomes in their genomes with a value of 0.08, 0.07, and 0.05, respectively. Based on the LD decay, the D genome was found to be the lowest genome with the highest number of haplotype blocks on chromosome 2D. Conclusion The recent study concluded that the 103-spring wheat genotypes and their GBS-SNP markers are very appropriate for GWAS studies and QTL-mapping. The core collection comprises three different subpopulations. Genotypes in subpopulation 1 are the most diverse genotypes and could be used in future breeding programs if they have desired traits. The distribution of LD hotspots across the genome was investigated which provides useful information on the genomic regions that includes interesting genes.http://link.springer.com/article/10.1186/s12864-020-06835-0Linkage disequilibriumHaplotype blocksGenome-wide association studyAnalysis of molecular varianceGenotype-by-sequencing |
| spellingShingle | Amira M. I. Mourad Vikas Belamkar P. Stephen Baenziger Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium BMC Genomics Linkage disequilibrium Haplotype blocks Genome-wide association study Analysis of molecular variance Genotype-by-sequencing |
| title | Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium |
| title_full | Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium |
| title_fullStr | Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium |
| title_full_unstemmed | Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium |
| title_short | Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium |
| title_sort | molecular genetic analysis of spring wheat core collection using genetic diversity population structure and linkage disequilibrium |
| topic | Linkage disequilibrium Haplotype blocks Genome-wide association study Analysis of molecular variance Genotype-by-sequencing |
| url | http://link.springer.com/article/10.1186/s12864-020-06835-0 |
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