Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L.
Abstract Enhancing cotton yield and fiber quality is challenging due to the limited genetic variation, highlighting the need for efficient use of germplasm resources. Therefore, 10 morpho-physiological characters and 10 simple sequence repeat (SSR) markers were used to investigate the genetic variab...
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2025-03-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06363-7 |
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| author | Syeda Yashfeen Fatima Tahira Luqman Shabbir Hussain Sahar Nadeem Muhammad Kashif Riaz Khan Allah Ditta Muhammad Asif |
| author_facet | Syeda Yashfeen Fatima Tahira Luqman Shabbir Hussain Sahar Nadeem Muhammad Kashif Riaz Khan Allah Ditta Muhammad Asif |
| author_sort | Syeda Yashfeen Fatima |
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| description | Abstract Enhancing cotton yield and fiber quality is challenging due to the limited genetic variation, highlighting the need for efficient use of germplasm resources. Therefore, 10 morpho-physiological characters and 10 simple sequence repeat (SSR) markers were used to investigate the genetic variability of 50 cotton genotypes. Principal component analysis and Mahalanobis’ generalized distance (D2) were applied to morpho-physiological data. Two principal components presented 53.83% of the cumulative variability in the raw data on biomass-related variables. Four different clusters were exposed by cluster analysis (D2): Cluster I included 20 genotypes, whereas clusters II, III, and IV had 6, 18, and 6 genotypes, respectively. Intra-cluster distances were highest in Cluster IV (222.79) and Cluster I (213.65), while Cluster III had the lowest (124.89), indicating greater genetic similarity. The largest inter-cluster distance was among Clusters II and IV (109.28), whereas the smallest was among Clusters II and III (20.67). A greater inter-cluster than intra-cluster distance suggests substantial genetic diversity among genotypes. Molecular-based explorations of genetic variability generated a matrix of similarity coefficients and grouped the accessions into two main clusters. Ten markers revealed polymorphism and produced a total of 35 clearly identifiable bands, with an average of 3.5 alleles per marker. In this study, the highest number of alleles (6) were amplified by DPL0009. Polymorphism Information Content values ranged from 0.076 to 0.731. Clustering based on molecular data classified the germplasm into three groups and measuring genetic distance through Euclidean distance while structure analysis revealed three gene-exchanging populations, representing a limited genetic basis in breeding programs. DNA clustering of upland cotton germplasm revealed genetic relationships independent of geographical origin, indicating its diversity and potential for use in hybridization schemes to develop superior F1 transgressive segregates or hybrids in subsequent generations. |
| format | Article |
| id | doaj-art-b3cb0905d095411fa00d5424e45f6037 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-b3cb0905d095411fa00d5424e45f60372025-08-20T03:41:49ZengBMCBMC Plant Biology1471-22292025-03-0125111410.1186/s12870-025-06363-7Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L.Syeda Yashfeen Fatima0Tahira Luqman1Shabbir Hussain2Sahar Nadeem3Muhammad Kashif Riaz Khan4Allah Ditta5Muhammad Asif6Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS)Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS)Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS)Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS)Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS)Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS)Ayub Agriculture Research InstituteAbstract Enhancing cotton yield and fiber quality is challenging due to the limited genetic variation, highlighting the need for efficient use of germplasm resources. Therefore, 10 morpho-physiological characters and 10 simple sequence repeat (SSR) markers were used to investigate the genetic variability of 50 cotton genotypes. Principal component analysis and Mahalanobis’ generalized distance (D2) were applied to morpho-physiological data. Two principal components presented 53.83% of the cumulative variability in the raw data on biomass-related variables. Four different clusters were exposed by cluster analysis (D2): Cluster I included 20 genotypes, whereas clusters II, III, and IV had 6, 18, and 6 genotypes, respectively. Intra-cluster distances were highest in Cluster IV (222.79) and Cluster I (213.65), while Cluster III had the lowest (124.89), indicating greater genetic similarity. The largest inter-cluster distance was among Clusters II and IV (109.28), whereas the smallest was among Clusters II and III (20.67). A greater inter-cluster than intra-cluster distance suggests substantial genetic diversity among genotypes. Molecular-based explorations of genetic variability generated a matrix of similarity coefficients and grouped the accessions into two main clusters. Ten markers revealed polymorphism and produced a total of 35 clearly identifiable bands, with an average of 3.5 alleles per marker. In this study, the highest number of alleles (6) were amplified by DPL0009. Polymorphism Information Content values ranged from 0.076 to 0.731. Clustering based on molecular data classified the germplasm into three groups and measuring genetic distance through Euclidean distance while structure analysis revealed three gene-exchanging populations, representing a limited genetic basis in breeding programs. DNA clustering of upland cotton germplasm revealed genetic relationships independent of geographical origin, indicating its diversity and potential for use in hybridization schemes to develop superior F1 transgressive segregates or hybrids in subsequent generations.https://doi.org/10.1186/s12870-025-06363-7MicrosatellitesGenetic diversityPhylogenetic analysisGossypium hirsutumMolecular markers |
| spellingShingle | Syeda Yashfeen Fatima Tahira Luqman Shabbir Hussain Sahar Nadeem Muhammad Kashif Riaz Khan Allah Ditta Muhammad Asif Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L. BMC Plant Biology Microsatellites Genetic diversity Phylogenetic analysis Gossypium hirsutum Molecular markers |
| title | Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L. |
| title_full | Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L. |
| title_fullStr | Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L. |
| title_full_unstemmed | Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L. |
| title_short | Genetic diversity and phylogenetic relationship through the use of microsatellites in Gossypium hirsutum L. |
| title_sort | genetic diversity and phylogenetic relationship through the use of microsatellites in gossypium hirsutum l |
| topic | Microsatellites Genetic diversity Phylogenetic analysis Gossypium hirsutum Molecular markers |
| url | https://doi.org/10.1186/s12870-025-06363-7 |
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