Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm
Orchardgrass (Dactylis glomerata L.), a widely cultivated cool-season perennial, is an important forage crop due to its adaptability, high nutritional value, and substantial biomass. Understanding its genetic diversity and population structure is crucial for developing resilient cultivars that can w...
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Frontiers Media S.A.
2025-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1530585/full |
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| author | Muhammad Tanveer Altaf Pablo Federico Cavagnaro Kağan Kökten Amjad Ali Andres Morales Andres Morales Muhammed Tatar Mehmet Bedir Muhammad Azhar Nadeem Muhammad Aasim Nafiz Çeliktaş Sheikh Mansoor Faheem Shehzad Baloch Faheem Shehzad Baloch |
| author_facet | Muhammad Tanveer Altaf Pablo Federico Cavagnaro Kağan Kökten Amjad Ali Andres Morales Andres Morales Muhammed Tatar Mehmet Bedir Muhammad Azhar Nadeem Muhammad Aasim Nafiz Çeliktaş Sheikh Mansoor Faheem Shehzad Baloch Faheem Shehzad Baloch |
| author_sort | Muhammad Tanveer Altaf |
| collection | DOAJ |
| description | Orchardgrass (Dactylis glomerata L.), a widely cultivated cool-season perennial, is an important forage crop due to its adaptability, high nutritional value, and substantial biomass. Understanding its genetic diversity and population structure is crucial for developing resilient cultivars that can withstand climate change, diseases, and resource limitations. Despite its global significance in fodder production, the genetic potential of many regional accessions remains unexplored, limiting breeding efforts. This study investigates the genetic diversity (GD) and population structure of 91 accessions of D. glomerata from Turkey and Iran using genotyping-by-sequencing based single nucleotide polymorphism (SNP) markers. A total of 2913 high-quality SNP markers revealed substantial genetic variability across provinces. Notably, accessions from Erzurum exhibited the highest GD (mean GD: 0.26; He: 0.5328), while provinces such as Bursa and Muğla demonstrated lower GD (mean GD: 0.15; He < 0.22), suggesting potential genetic bottlenecks. Population structure analysis using Bayesian clustering, PCoA and UPGMA dendrograms divided the accessions into three distinct clusters, with cluster membership largely reflecting geographical origins, and dry biomass content. Cluster II revealed higher GD, associated with enhanced biomass production (128 g/plant), the most important agronomic trait in forage species, supporting the notion of heterosis in breeding programs. The majority of the genetic variation (85.8%) was observed within clusters, with minimal differentiation among clusters (FST = 0.007). Genome-wide association studies (GWAS) identified significant marker-trait associations for dry biomass weight, a critical agronomic trait, with markers DArT-100715788, DArT-101043591, and DArT-101171265 and DArT-101090822 located on Chromosomes 1, 6, and 7 respectively. These findings highlight the importance of regional diversity for maintaining adaptive potential in future breeding programs. |
| format | Article |
| id | doaj-art-67cf8b5b69d54369adac427ac26b9d33 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-67cf8b5b69d54369adac427ac26b9d332025-02-06T13:00:03ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-02-011610.3389/fpls.2025.15305851530585Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasmMuhammad Tanveer Altaf0Pablo Federico Cavagnaro1Kağan Kökten2Amjad Ali3Andres Morales4Andres Morales5Muhammed Tatar6Mehmet Bedir7Muhammad Azhar Nadeem8Muhammad Aasim9Nafiz Çeliktaş10Sheikh Mansoor11Faheem Shehzad Baloch12Faheem Shehzad Baloch13Department of Field Crops, Faculty of Agriculture, Recep Tayyip Erdoğan University, Pazar, Rize, TürkiyeConsejo Nacional de Investigaciones Científicas y Técnicas (CONICET), and Instituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria Mendoza, Mendoza, ArgentinaFaculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, TürkiyeFaculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, TürkiyeUniversidad Nacional de Cuyo (UNCuyo) Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza (IBAM CONICET) Laboratorio de Biología Molecular, Mendoza, ArgentinaInstituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria La Consulta, La Consulta, ArgentinaFaculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, TürkiyeFaculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, TürkiyeFaculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, TürkiyeFaculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, TürkiyeDepartment of Field Crops, Faculty of Agriculture, Hatay Mustafa Kemal University, Hatay, TürkiyeDepartment of Plant Resources and Environment, Jeju National University, Jeju, Republic of KoreaDepartment of Plant Resources and Environment, Jeju National University, Jeju, Republic of KoreaDepartment of Biotechnology, Faculty of Science, Mersin University, Yenişehir, Mersin, TürkiyeOrchardgrass (Dactylis glomerata L.), a widely cultivated cool-season perennial, is an important forage crop due to its adaptability, high nutritional value, and substantial biomass. Understanding its genetic diversity and population structure is crucial for developing resilient cultivars that can withstand climate change, diseases, and resource limitations. Despite its global significance in fodder production, the genetic potential of many regional accessions remains unexplored, limiting breeding efforts. This study investigates the genetic diversity (GD) and population structure of 91 accessions of D. glomerata from Turkey and Iran using genotyping-by-sequencing based single nucleotide polymorphism (SNP) markers. A total of 2913 high-quality SNP markers revealed substantial genetic variability across provinces. Notably, accessions from Erzurum exhibited the highest GD (mean GD: 0.26; He: 0.5328), while provinces such as Bursa and Muğla demonstrated lower GD (mean GD: 0.15; He < 0.22), suggesting potential genetic bottlenecks. Population structure analysis using Bayesian clustering, PCoA and UPGMA dendrograms divided the accessions into three distinct clusters, with cluster membership largely reflecting geographical origins, and dry biomass content. Cluster II revealed higher GD, associated with enhanced biomass production (128 g/plant), the most important agronomic trait in forage species, supporting the notion of heterosis in breeding programs. The majority of the genetic variation (85.8%) was observed within clusters, with minimal differentiation among clusters (FST = 0.007). Genome-wide association studies (GWAS) identified significant marker-trait associations for dry biomass weight, a critical agronomic trait, with markers DArT-100715788, DArT-101043591, and DArT-101171265 and DArT-101090822 located on Chromosomes 1, 6, and 7 respectively. These findings highlight the importance of regional diversity for maintaining adaptive potential in future breeding programs.https://www.frontiersin.org/articles/10.3389/fpls.2025.1530585/fullDactylis glomeratagenetic diversitySNP markersforage breedingpopulation structureGWAS |
| spellingShingle | Muhammad Tanveer Altaf Pablo Federico Cavagnaro Kağan Kökten Amjad Ali Andres Morales Andres Morales Muhammed Tatar Mehmet Bedir Muhammad Azhar Nadeem Muhammad Aasim Nafiz Çeliktaş Sheikh Mansoor Faheem Shehzad Baloch Faheem Shehzad Baloch Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm Frontiers in Plant Science Dactylis glomerata genetic diversity SNP markers forage breeding population structure GWAS |
| title | Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm |
| title_full | Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm |
| title_fullStr | Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm |
| title_full_unstemmed | Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm |
| title_short | Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm |
| title_sort | genotyping by sequencing derived snp markers reveal genetic diversity and population structure of dactylis glomerata germplasm |
| topic | Dactylis glomerata genetic diversity SNP markers forage breeding population structure GWAS |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1530585/full |
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