Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data
The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six dif...
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MDPI AG
2021-09-01
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| author | Shyryn Almerekova Yuliya Genievskaya Saule Abugalieva Kazuhiro Sato Yerlan Turuspekov |
| author_facet | Shyryn Almerekova Yuliya Genievskaya Saule Abugalieva Kazuhiro Sato Yerlan Turuspekov |
| author_sort | Shyryn Almerekova |
| collection | DOAJ |
| description | The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars. |
| first_indexed | 2024-03-10T06:15:09Z |
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| language | English |
| last_indexed | 2024-03-10T06:15:09Z |
| publishDate | 2021-09-01 |
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| series | Plants |
| spelling | doaj.art-466f57d3445e4e8e948e70849e0acd1a2023-11-22T19:42:33ZengMDPI AGPlants2223-77472021-09-011010202510.3390/plants10102025Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping DataShyryn Almerekova0Yuliya Genievskaya1Saule Abugalieva2Kazuhiro Sato3Yerlan Turuspekov4Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, KazakhstanLaboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, KazakhstanLaboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, KazakhstanInstitute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, JapanLaboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, KazakhstanThe genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.https://www.mdpi.com/2223-7747/10/10/2025barleygenetic diversitypopulation structuregenetic geographysingle-nucleotide polymorphismIllumina Infinium assay |
| spellingShingle | Shyryn Almerekova Yuliya Genievskaya Saule Abugalieva Kazuhiro Sato Yerlan Turuspekov Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data Plants barley genetic diversity population structure genetic geography single-nucleotide polymorphism Illumina Infinium assay |
| title | Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data |
| title_full | Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data |
| title_fullStr | Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data |
| title_full_unstemmed | Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data |
| title_short | Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data |
| title_sort | population structure and genetic diversity of two rowed barley accessions from kazakhstan based on snp genotyping data |
| topic | barley genetic diversity population structure genetic geography single-nucleotide polymorphism Illumina Infinium assay |
| url | https://www.mdpi.com/2223-7747/10/10/2025 |
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