Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i>
<i>Psathyrostachys juncea</i> is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restorati...
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MDPI AG
2023-10-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/10/1970 |
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| author | Zhen Li Tian Wang Lan Yun Xiaomin Ren Yong Wang Fengling Shi |
| author_facet | Zhen Li Tian Wang Lan Yun Xiaomin Ren Yong Wang Fengling Shi |
| author_sort | Zhen Li |
| collection | DOAJ |
| description | <i>Psathyrostachys juncea</i> is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of <i>P. juncea</i> and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon’s information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (<i>r</i><sup>2</sup>) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker–trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of <i>P. juncea</i> germplasm. |
| first_indexed | 2024-03-11T10:14:37Z |
| format | Article |
| id | doaj.art-4674fe6fc1e64991b1adb20e0d8d11d7 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T10:14:37Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-4674fe6fc1e64991b1adb20e0d8d11d72023-11-16T10:29:57ZengMDPI AGGenes2073-44252023-10-011410197010.3390/genes14101970Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i>Zhen Li0Tian Wang1Lan Yun2Xiaomin Ren3Yong Wang4Fengling Shi5College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, ChinaCollege of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, ChinaCollege of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, ChinaCollege of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, ChinaCollege of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, ChinaCollege of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China<i>Psathyrostachys juncea</i> is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of <i>P. juncea</i> and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon’s information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (<i>r</i><sup>2</sup>) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker–trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of <i>P. juncea</i> germplasm.https://www.mdpi.com/2073-4425/14/10/1970<i>Psathyrostachys juncea</i>plant architecturetillering traitsSSR markersassociation analysis |
| spellingShingle | Zhen Li Tian Wang Lan Yun Xiaomin Ren Yong Wang Fengling Shi Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i> Genes <i>Psathyrostachys juncea</i> plant architecture tillering traits SSR markers association analysis |
| title | Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i> |
| title_full | Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i> |
| title_fullStr | Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i> |
| title_full_unstemmed | Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i> |
| title_short | Association Analysis of Tiller-Related Traits with EST-SSR Markers in <i>Psathyrostachys juncea</i> |
| title_sort | association analysis of tiller related traits with est ssr markers in i psathyrostachys juncea i |
| topic | <i>Psathyrostachys juncea</i> plant architecture tillering traits SSR markers association analysis |
| url | https://www.mdpi.com/2073-4425/14/10/1970 |
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