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Article

Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition

by
Xiao Han
1,†,
Chenxu Gao
2,†,
Lisen Liu
1,
Yihao Zhang
1,2,
Yuying Jin
1,
Qingdi Yan
1,
Lan Yang
1,
Fuguang Li
1,2,* and
Zhaoen Yang
1,2,*
1
State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang 455000, China
2
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2022, 23(14), 7564; https://doi.org/10.3390/ijms23147564
Submission received: 9 June 2022 / Revised: 2 July 2022 / Accepted: 5 July 2022 / Published: 8 July 2022
(This article belongs to the Section Molecular Plant Sciences)
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Abstract

The genus Gossypium is one of the most economically important crops in the world. Here, we used RNA-seq to quantify gene expression in a collection of G. arboreum 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.
Keywords: Gossypium arbourem; eQTL; transcriptomes; hotspot; TWAS Gossypium arbourem; eQTL; transcriptomes; hotspot; TWAS

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MDPI and ACS Style

Han, X.; Gao, C.; Liu, L.; Zhang, Y.; Jin, Y.; Yan, Q.; Yang, L.; Li, F.; Yang, Z. Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition. Int. J. Mol. Sci. 2022, 23, 7564. https://doi.org/10.3390/ijms23147564

AMA Style

Han X, Gao C, Liu L, Zhang Y, Jin Y, Yan Q, Yang L, Li F, Yang Z. Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition. International Journal of Molecular Sciences. 2022; 23(14):7564. https://doi.org/10.3390/ijms23147564

Chicago/Turabian Style

Han, Xiao, Chenxu Gao, Lisen Liu, Yihao Zhang, Yuying Jin, Qingdi Yan, Lan Yang, Fuguang Li, and Zhaoen Yang. 2022. "Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition" International Journal of Molecular Sciences 23, no. 14: 7564. https://doi.org/10.3390/ijms23147564

APA Style

Han, X., Gao, C., Liu, L., Zhang, Y., Jin, Y., Yan, Q., Yang, L., Li, F., & Yang, Z. (2022). Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition. International Journal of Molecular Sciences, 23(14), 7564. https://doi.org/10.3390/ijms23147564

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