Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton
Understanding the genetic diversity and population structure of germplasms is essential when selecting parents for crop breeding. The genomic changes that occurred during the domestication and improvement of Upland cotton (Gossypium hirsutum) remains poorly understood. Besides, the available genetic...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2020.00929/full |
| _version_ | 1819017327498231808 |
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| author | Shoupu He Shoupu He Pengpeng Wang Yuan-Ming Zhang Panhong Dai Mian Faisal Nazir Yinhua Jia Zhen Peng Zhaoe Pan Junling Sun Liru Wang Gaofei Sun Xiongming Du |
| author_facet | Shoupu He Shoupu He Pengpeng Wang Yuan-Ming Zhang Panhong Dai Mian Faisal Nazir Yinhua Jia Zhen Peng Zhaoe Pan Junling Sun Liru Wang Gaofei Sun Xiongming Du |
| author_sort | Shoupu He |
| collection | DOAJ |
| description | Understanding the genetic diversity and population structure of germplasms is essential when selecting parents for crop breeding. The genomic changes that occurred during the domestication and improvement of Upland cotton (Gossypium hirsutum) remains poorly understood. Besides, the available genetic resources from cotton cultivars are limited. By applying restriction site-associated DNA marker sequencing (RAD-seq) technology to 582 tetraploid cotton accessions, we confirmed distinct genomic regions on chromosomes A06 and A08 in Upland cotton cultivar subgroups. Based on the pedigree, reported QTLs, introgression analyses, and genome-wide association study (GWAS), we suggest that these divergent regions might have resulted from the introgression of exotic lineages of G. hirsutum landraces and their wild relatives. These regions were the typical genomic signatures that might be responsible for maturity and fiber quality on chromosome A06 and chromosome A08, respectively. Moreover, these genomic regions are located in the putative pericentromeric regions, implying that their application will be challenging. In the study, based on high-density SNP markers, we reported two genomic signatures on chromosomes A06 and A08, which might originate from the introgression events in the Upland cotton population. Our study provides new insights for understanding the impact of historic introgressions on population divergence and important agronomic traits of modern Upland cotton cultivars. |
| first_indexed | 2024-12-21T03:01:46Z |
| format | Article |
| id | doaj.art-b1c67e733fa5402d91427027001940cf |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T03:01:46Z |
| publishDate | 2020-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-b1c67e733fa5402d91427027001940cf2022-12-21T19:18:10ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-07-011110.3389/fpls.2020.00929550983Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland CottonShoupu He0Shoupu He1Pengpeng Wang2Yuan-Ming Zhang3Panhong Dai4Mian Faisal Nazir5Yinhua Jia6Zhen Peng7Zhaoe Pan8Junling Sun9Liru Wang10Gaofei Sun11Xiongming Du12State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaDepartment of Computer Science and Information Engineering, Data Mining Institute, Anyang Institute of Technology, Anyang, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, ChinaUnderstanding the genetic diversity and population structure of germplasms is essential when selecting parents for crop breeding. The genomic changes that occurred during the domestication and improvement of Upland cotton (Gossypium hirsutum) remains poorly understood. Besides, the available genetic resources from cotton cultivars are limited. By applying restriction site-associated DNA marker sequencing (RAD-seq) technology to 582 tetraploid cotton accessions, we confirmed distinct genomic regions on chromosomes A06 and A08 in Upland cotton cultivar subgroups. Based on the pedigree, reported QTLs, introgression analyses, and genome-wide association study (GWAS), we suggest that these divergent regions might have resulted from the introgression of exotic lineages of G. hirsutum landraces and their wild relatives. These regions were the typical genomic signatures that might be responsible for maturity and fiber quality on chromosome A06 and chromosome A08, respectively. Moreover, these genomic regions are located in the putative pericentromeric regions, implying that their application will be challenging. In the study, based on high-density SNP markers, we reported two genomic signatures on chromosomes A06 and A08, which might originate from the introgression events in the Upland cotton population. Our study provides new insights for understanding the impact of historic introgressions on population divergence and important agronomic traits of modern Upland cotton cultivars.https://www.frontiersin.org/article/10.3389/fpls.2020.00929/fullUpland cottoninterspecific hybridizationintrogressiongenomic divergencematurityfiber quality |
| spellingShingle | Shoupu He Shoupu He Pengpeng Wang Yuan-Ming Zhang Panhong Dai Mian Faisal Nazir Yinhua Jia Zhen Peng Zhaoe Pan Junling Sun Liru Wang Gaofei Sun Xiongming Du Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton Frontiers in Plant Science Upland cotton interspecific hybridization introgression genomic divergence maturity fiber quality |
| title | Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton |
| title_full | Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton |
| title_fullStr | Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton |
| title_full_unstemmed | Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton |
| title_short | Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton |
| title_sort | introgression leads to genomic divergence and responsible for important traits in upland cotton |
| topic | Upland cotton interspecific hybridization introgression genomic divergence maturity fiber quality |
| url | https://www.frontiersin.org/article/10.3389/fpls.2020.00929/full |
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