Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations
Cotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibrium-based association mapping has become a powerful molecular tool to dissect and exploit genetic diversity. In the present study, population structure and marker-trait associations for fibre qu...
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| Format: | Article |
| Language: | English |
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Czech Academy of Agricultural Sciences
2017-12-01
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| Series: | Czech Journal of Genetics and Plant Breeding |
| Subjects: | |
| Online Access: | https://cjgpb.agriculturejournals.cz/artkey/cjg-201704-0005_linkage-disequilibrium-and-association-mapping-of-fibre-quality-traits-in-elite-asiatic-cotton-gossypium-arbor.php |
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| author | Khushboo SETHI Priyanka SIWACH Surender Kumar VERMA |
| author_facet | Khushboo SETHI Priyanka SIWACH Surender Kumar VERMA |
| author_sort | Khushboo SETHI |
| collection | DOAJ |
| description | Cotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibrium-based association mapping has become a powerful molecular tool to dissect and exploit genetic diversity. In the present study, population structure and marker-trait associations for fibre quality traits in genotypes belonging to six races of Gossypium arboreum were assessed. Out of 300 simple sequence repeat (SSR) markers, 100 were found polymorphic, yielding a total of 240 alleles (all polymorphic). Structure analysis revealed allelic admixtures between genotypes. A Q-matrix exhibited mixed ancestry for the majority of genotypes, the race indicum forming a significant percent ancestry for almost all genotypes. At significant threshold values of r2 ≥ 0.05, 7.37% of SSR loci showed significant linkage disequilibrium (LD), while at highly significant threshold of r2 ≥ 0.1, the value was reduced to 5.31%. LD clearly decayed within the genetic distance of 9-10 cM, with r2 ≥ 0.1. Twenty-eight SSR markers were found associated with six fibre quality traits using general linear model and mixed linear model. |
| first_indexed | 2024-04-10T08:30:01Z |
| format | Article |
| id | doaj.art-f14af00f78244df882992b7c310800ce |
| institution | Directory Open Access Journal |
| issn | 1212-1975 1805-9325 |
| language | English |
| last_indexed | 2024-04-10T08:30:01Z |
| publishDate | 2017-12-01 |
| publisher | Czech Academy of Agricultural Sciences |
| record_format | Article |
| series | Czech Journal of Genetics and Plant Breeding |
| spelling | doaj.art-f14af00f78244df882992b7c310800ce2023-02-23T03:30:38ZengCzech Academy of Agricultural SciencesCzech Journal of Genetics and Plant Breeding1212-19751805-93252017-12-0153415916710.17221/142/2016-CJGPBcjg-201704-0005Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populationsKhushboo SETHI0Priyanka SIWACH1Surender Kumar VERMA2Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, IndiaDepartment of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, IndiaCentral Institute of Cotton Research, Regional Station, Sirsa, HaryanaCotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibrium-based association mapping has become a powerful molecular tool to dissect and exploit genetic diversity. In the present study, population structure and marker-trait associations for fibre quality traits in genotypes belonging to six races of Gossypium arboreum were assessed. Out of 300 simple sequence repeat (SSR) markers, 100 were found polymorphic, yielding a total of 240 alleles (all polymorphic). Structure analysis revealed allelic admixtures between genotypes. A Q-matrix exhibited mixed ancestry for the majority of genotypes, the race indicum forming a significant percent ancestry for almost all genotypes. At significant threshold values of r2 ≥ 0.05, 7.37% of SSR loci showed significant linkage disequilibrium (LD), while at highly significant threshold of r2 ≥ 0.1, the value was reduced to 5.31%. LD clearly decayed within the genetic distance of 9-10 cM, with r2 ≥ 0.1. Twenty-eight SSR markers were found associated with six fibre quality traits using general linear model and mixed linear model.https://cjgpb.agriculturejournals.cz/artkey/cjg-201704-0005_linkage-disequilibrium-and-association-mapping-of-fibre-quality-traits-in-elite-asiatic-cotton-gossypium-arbor.phpgeneral linear modelgenetic distancegenetic diversitymixed linear modelsimple sequence repeat |
| spellingShingle | Khushboo SETHI Priyanka SIWACH Surender Kumar VERMA Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations Czech Journal of Genetics and Plant Breeding general linear model genetic distance genetic diversity mixed linear model simple sequence repeat |
| title | Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations |
| title_full | Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations |
| title_fullStr | Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations |
| title_full_unstemmed | Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations |
| title_short | Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations |
| title_sort | linkage disequilibrium and association mapping of fibre quality traits in elite asiatic cotton gossypium arboreum germplasm populations |
| topic | general linear model genetic distance genetic diversity mixed linear model simple sequence repeat |
| url | https://cjgpb.agriculturejournals.cz/artkey/cjg-201704-0005_linkage-disequilibrium-and-association-mapping-of-fibre-quality-traits-in-elite-asiatic-cotton-gossypium-arbor.php |
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