QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population
Abstract Background Cotton is an important cash crop in China and a key component of the global textile market. Verticillium wilt is a major factor affecting cotton yield. Single nucleotide polymorphism (SNP) markers and phenotypic data can be used to identify genetic markers and loci associated wit...
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BMC
2025-02-01
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| Series: | Journal of Cotton Research |
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| Online Access: | https://doi.org/10.1186/s42397-025-00211-7 |
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| author | Muhammad Ayyaz Zewei Chang Shugen Ding Peng Han Lin Xu Abudurezike Abudukeyoumu Irfan Ali Siddho Zhibo Li Hairong Lin Jianwei Xu Yuanlong Wu Xinhui Nie |
| author_facet | Muhammad Ayyaz Zewei Chang Shugen Ding Peng Han Lin Xu Abudurezike Abudukeyoumu Irfan Ali Siddho Zhibo Li Hairong Lin Jianwei Xu Yuanlong Wu Xinhui Nie |
| author_sort | Muhammad Ayyaz |
| collection | DOAJ |
| description | Abstract Background Cotton is an important cash crop in China and a key component of the global textile market. Verticillium wilt is a major factor affecting cotton yield. Single nucleotide polymorphism (SNP) markers and phenotypic data can be used to identify genetic markers and loci associated with cotton resistance to Verticillium wilt. We used eight upland cotton parent materials in this study to construct a multiparent advanced generation inter-cross (MAGIC) population comprising 320 lines. The Verticillium wilt resistance of the MAGIC population was identified in the greenhouse in 2019, and the average relative disease index (ARDI) was calculated. A genome-wide association study (GWAS) was performed to discover SNP markers/genes associated with Verticillium wilt resistance. Results ARDI of the MAGIC population showed wide variation, ranging from 16.7 to 79.4 across three replicates. This variation reflected a diverse range of resistance to Verticillium wilt within the population. Analysis of distribution patterns across the environments revealed consistent trends, with coefficients of variation between 12.25% and 21.96%. Families with higher ARDI values, indicating stronger resistance, were more common, likely due to genetic diversity and environmental factors. Population structure analysis divided the MAGIC population into three subgroups, with Group I showing higher genetic variation and Groups II and III displaying more uniform resistance performance. Principal component analysis (PCA) confirmed these divisions, highlighting the genetic diversity underlying Verticillium wilt resistance. Through GWAS, we identified 19 SNPs significantly associated with Verticillium wilt resistance, distributed across three chromosomes. The screening of candidate genes was performed on the transcriptome derived from resistant and susceptible cultivars, combined with gene annotation and tissue expression patterns, and two key candidate genes, Ghir_A01G006660 and Ghir_A02G008980, were found to be potentially associated with Verticillium wilt resistance. This suggests that these two candidate genes may play an important role in responding to Verticillium wilt. Conclusion This study aims to dissect the genetic basis of Verticillium wilt resistance in cotton by using a MAGIC population and GWAS. The study seeks to provide valuable genetic resources for marker-assisted breeding and enhance the understanding of resistance mechanisms to improve cotton resilience against Verticillium wilt. |
| format | Article |
| id | doaj-art-9ebd69aec9bf4be8bb7506d35813beab |
| institution | OA Journals |
| issn | 2523-3254 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
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| series | Journal of Cotton Research |
| spelling | doaj-art-9ebd69aec9bf4be8bb7506d35813beab2025-08-20T02:16:54ZengBMCJournal of Cotton Research2523-32542025-02-018111510.1186/s42397-025-00211-7QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC populationMuhammad Ayyaz0Zewei Chang1Shugen Ding2Peng Han3Lin Xu4Abudurezike Abudukeyoumu5Irfan Ali Siddho6Zhibo Li7Hairong Lin8Jianwei Xu9Yuanlong Wu10Xinhui Nie11Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityInstitute of Crop Variety Resources, Xinjiang Academy of Agricultural SciencesInstitute of Crop Variety Resources, Xinjiang Academy of Agricultural SciencesKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi UniversityAbstract Background Cotton is an important cash crop in China and a key component of the global textile market. Verticillium wilt is a major factor affecting cotton yield. Single nucleotide polymorphism (SNP) markers and phenotypic data can be used to identify genetic markers and loci associated with cotton resistance to Verticillium wilt. We used eight upland cotton parent materials in this study to construct a multiparent advanced generation inter-cross (MAGIC) population comprising 320 lines. The Verticillium wilt resistance of the MAGIC population was identified in the greenhouse in 2019, and the average relative disease index (ARDI) was calculated. A genome-wide association study (GWAS) was performed to discover SNP markers/genes associated with Verticillium wilt resistance. Results ARDI of the MAGIC population showed wide variation, ranging from 16.7 to 79.4 across three replicates. This variation reflected a diverse range of resistance to Verticillium wilt within the population. Analysis of distribution patterns across the environments revealed consistent trends, with coefficients of variation between 12.25% and 21.96%. Families with higher ARDI values, indicating stronger resistance, were more common, likely due to genetic diversity and environmental factors. Population structure analysis divided the MAGIC population into three subgroups, with Group I showing higher genetic variation and Groups II and III displaying more uniform resistance performance. Principal component analysis (PCA) confirmed these divisions, highlighting the genetic diversity underlying Verticillium wilt resistance. Through GWAS, we identified 19 SNPs significantly associated with Verticillium wilt resistance, distributed across three chromosomes. The screening of candidate genes was performed on the transcriptome derived from resistant and susceptible cultivars, combined with gene annotation and tissue expression patterns, and two key candidate genes, Ghir_A01G006660 and Ghir_A02G008980, were found to be potentially associated with Verticillium wilt resistance. This suggests that these two candidate genes may play an important role in responding to Verticillium wilt. Conclusion This study aims to dissect the genetic basis of Verticillium wilt resistance in cotton by using a MAGIC population and GWAS. The study seeks to provide valuable genetic resources for marker-assisted breeding and enhance the understanding of resistance mechanisms to improve cotton resilience against Verticillium wilt.https://doi.org/10.1186/s42397-025-00211-7Upland cottonVerticillium wiltMAGIC populationQuantitative trait lociAssociation analysis |
| spellingShingle | Muhammad Ayyaz Zewei Chang Shugen Ding Peng Han Lin Xu Abudurezike Abudukeyoumu Irfan Ali Siddho Zhibo Li Hairong Lin Jianwei Xu Yuanlong Wu Xinhui Nie QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population Journal of Cotton Research Upland cotton Verticillium wilt MAGIC population Quantitative trait loci Association analysis |
| title | QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population |
| title_full | QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population |
| title_fullStr | QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population |
| title_full_unstemmed | QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population |
| title_short | QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population |
| title_sort | qtl mapping associated with verticillium wilt resistance in cotton based on magic population |
| topic | Upland cotton Verticillium wilt MAGIC population Quantitative trait loci Association analysis |
| url | https://doi.org/10.1186/s42397-025-00211-7 |
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