Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition
The genus <i>Gossypium</i> is one of the most economically important crops in the world. Here, we used RNA-seq to quantify gene expression in a collection of <i>G. arboreum</i> seedlings and performed eGWAS on 28,382 expressed genes. We identified a total of 30,089 eQTLs in 1...
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MDPI AG
2022-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/14/7564 |
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| author | Xiao Han Chenxu Gao Lisen Liu Yihao Zhang Yuying Jin Qingdi Yan Lan Yang Fuguang Li Zhaoen Yang |
| author_facet | Xiao Han Chenxu Gao Lisen Liu Yihao Zhang Yuying Jin Qingdi Yan Lan Yang Fuguang Li Zhaoen Yang |
| author_sort | Xiao Han |
| collection | DOAJ |
| description | The genus <i>Gossypium</i> is one of the most economically important crops in the world. Here, we used RNA-seq to quantify gene expression in a collection of <i>G. arboreum</i> seedlings and performed eGWAS on 28,382 expressed genes. We identified a total of 30,089 eQTLs in 10,485 genes, of which >90% were trans-regulate target genes. Using luciferase assays, we confirmed that different cis-eQTL haplotypes could affect promoter activity. We found ~6600 genes associated with ~1300 eQTL hotspots. Moreover, hotspot 309 regulates the expression of 325 genes with roles in stem length, fresh weight, seed germination rate, and genes related to cell wall biosynthesis and salt stress. Transcriptome-wide association study (TWAS) identified 19 candidate genes associated with the cotton growth and salt stress response. The variation in gene expression across the population played an essential role in population differentiation. Only a small number of the differentially expressed genes between South China, the Yangtze River region, and the Yellow River region sites were located in different chromosomal regions. The eQTLs found across the duplicated gene pairs showed conservative cis- or trans- regulation and that the expression levels of gene pairs were correlated. This study provides new insights into the evolution of gene expression regulation in cotton, and identifies eQTLs in stress-related genes for use in breeding improved cotton varieties. |
| first_indexed | 2024-03-09T13:43:20Z |
| format | Article |
| id | doaj.art-7da17ddc404e4680b95819c29525e9e7 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T13:43:20Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-7da17ddc404e4680b95819c29525e9e72023-11-30T21:03:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-07-012314756410.3390/ijms23147564Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress ConditionXiao Han0Chenxu Gao1Lisen Liu2Yihao Zhang3Yuying Jin4Qingdi Yan5Lan Yang6Fuguang Li7Zhaoen Yang8State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaZhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, ChinaState Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaState Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaState Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaState Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaState Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaState Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaState Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaThe genus <i>Gossypium</i> is one of the most economically important crops in the world. Here, we used RNA-seq to quantify gene expression in a collection of <i>G. arboreum</i> seedlings and performed eGWAS on 28,382 expressed genes. We identified a total of 30,089 eQTLs in 10,485 genes, of which >90% were trans-regulate target genes. Using luciferase assays, we confirmed that different cis-eQTL haplotypes could affect promoter activity. We found ~6600 genes associated with ~1300 eQTL hotspots. Moreover, hotspot 309 regulates the expression of 325 genes with roles in stem length, fresh weight, seed germination rate, and genes related to cell wall biosynthesis and salt stress. Transcriptome-wide association study (TWAS) identified 19 candidate genes associated with the cotton growth and salt stress response. The variation in gene expression across the population played an essential role in population differentiation. Only a small number of the differentially expressed genes between South China, the Yangtze River region, and the Yellow River region sites were located in different chromosomal regions. The eQTLs found across the duplicated gene pairs showed conservative cis- or trans- regulation and that the expression levels of gene pairs were correlated. This study provides new insights into the evolution of gene expression regulation in cotton, and identifies eQTLs in stress-related genes for use in breeding improved cotton varieties.https://www.mdpi.com/1422-0067/23/14/7564<i>Gossypium arbourem</i>eQTLtranscriptomeshotspotTWAS |
| spellingShingle | Xiao Han Chenxu Gao Lisen Liu Yihao Zhang Yuying Jin Qingdi Yan Lan Yang Fuguang Li Zhaoen Yang Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition International Journal of Molecular Sciences <i>Gossypium arbourem</i> eQTL transcriptomes hotspot TWAS |
| title | Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition |
| title_full | Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition |
| title_fullStr | Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition |
| title_full_unstemmed | Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition |
| title_short | Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition |
| title_sort | integration of eqtl analysis and gwas highlights regulation networks in cotton under stress condition |
| topic | <i>Gossypium arbourem</i> eQTL transcriptomes hotspot TWAS |
| url | https://www.mdpi.com/1422-0067/23/14/7564 |
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