GWAS and eQTL analyses reveal genetic components influencing the key fiber yield trait lint percentage in upland cotton

IF 6.2 1区生物学 Q1 PLANT SCIENCES The Plant Journal Pub Date : 2025-03-03 DOI:10.1111/tpj.70036

Chunping Guo, Ruizhen Pi, Yuanlong Wu, Jiaqi You, Zhenyang Qi, Zhenping Liu, Xinyi Chang, Shugen Ding, Qi Zhang, Peng Han, Xianlong Zhang, Chunyuan You, Maojun Wang, Xinhui Nie

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Abstract

Lint percentage is an important component of cotton yield traits and an important economic indicator of cotton production. The initial stage of fiber development is a critical developmental period that affects the lint percentage trait, but the genetic regulation of the initial stage of fiber development needs to be resolved. In this study, we used a genomewide association study (GWAS) to identify 11 quantitative trait loci (QTLs) related to lint percentage and identified a total of 13 859 expression QTL (eQTLs) through transcriptome sequencing of 312 upland cotton accessions. Candidate genes for improving the lint percentage trait were identified through transcriptome-wide association study (TWAS), colocalization analysis, and differentially expressed gene analysis. We located nine candidate genes through the TWAS, and prioritized two key candidate genes (Ghir_A12G025980 and Ghir_A12G025990) related to lint percentage through colocalization and differential expression analysis. We showed that two eQTL hotspots (Hot26 and Hot28) synergistically participate in regulating the biological pathways of fiber initiation and development. Additionally, we unlocked the potential of genomic variants in improving the lint percentage by aggregating favorable alleles in accessions. New accessions suitable for improving lint percentage were excavated.

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来源期刊

The Plant Journal 生物-植物科学

CiteScore

13.10

自引率

4.20%

发文量

415

审稿时长

2.3 months

期刊介绍： Publishing the best original research papers in all key areas of modern plant biology from the world"s leading laboratories, The Plant Journal provides a dynamic forum for this ever growing international research community. Plant science research is now at the forefront of research in the biological sciences, with breakthroughs in our understanding of fundamental processes in plants matching those in other organisms. The impact of molecular genetics and the availability of model and crop species can be seen in all aspects of plant biology. For publication in The Plant Journal the research must provide a highly significant new contribution to our understanding of plants and be of general interest to the plant science community.