Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i>
Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivate...
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MDPI AG
2023-09-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/18/3321 |
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| author | Barbara Pipan Lovro Sinkovič Mohamed Neji Dagmar Janovská Meiliang Zhou Vladimir Meglič |
| author_facet | Barbara Pipan Lovro Sinkovič Mohamed Neji Dagmar Janovská Meiliang Zhou Vladimir Meglič |
| author_sort | Barbara Pipan |
| collection | DOAJ |
| description | Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (<i>p</i> = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (<i>p</i> < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for <i>F. esculentum</i> and <i>F. tataricum</i>. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among <i>F. esculentum</i> and <i>F. tataricum</i> accessions and pointed to future directions for genomics-based breeding programs and germplasm management. |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T22:12:11Z |
| publishDate | 2023-09-01 |
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| spelling | doaj.art-3a7effd3ff554cd4bb203daa50c47ae12023-11-19T12:33:14ZengMDPI AGPlants2223-77472023-09-011218332110.3390/plants12183321Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i>Barbara Pipan0Lovro Sinkovič1Mohamed Neji2Dagmar Janovská3Meiliang Zhou4Vladimir Meglič5Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, SloveniaCrop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, SloveniaCrop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, SloveniaGene Bank, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech RepublicInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 420, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, ChinaCrop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, SloveniaCharacterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (<i>p</i> = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (<i>p</i> < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for <i>F. esculentum</i> and <i>F. tataricum</i>. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among <i>F. esculentum</i> and <i>F. tataricum</i> accessions and pointed to future directions for genomics-based breeding programs and germplasm management.https://www.mdpi.com/2223-7747/12/18/3321agro-morphological traitsgenetic diversitymicrosatellite markersbuckwheatmarker-trait associationsbreeding |
| spellingShingle | Barbara Pipan Lovro Sinkovič Mohamed Neji Dagmar Janovská Meiliang Zhou Vladimir Meglič Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> Plants agro-morphological traits genetic diversity microsatellite markers buckwheat marker-trait associations breeding |
| title | Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> |
| title_full | Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> |
| title_fullStr | Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> |
| title_full_unstemmed | Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> |
| title_short | Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> |
| title_sort | agro morphological and molecular characterization reveal deep insights in promising genetic diversity and marker trait associations in i fagopyrum esculentum i and i fagopyrum tataricum i |
| topic | agro-morphological traits genetic diversity microsatellite markers buckwheat marker-trait associations breeding |
| url | https://www.mdpi.com/2223-7747/12/18/3321 |
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