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

IF 5.7 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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GWAS和eQTL分析揭示了影响陆地棉关键纤维产量性状皮棉率的遗传成分

皮棉率是棉花产量性状的重要组成部分，也是棉花生产的重要经济指标。纤维发育初期是影响衣分性状的关键发育时期，但纤维发育初期的遗传调控还有待解决。本研究利用全基因组关联研究（GWAS）对312份陆地棉材料进行转录组测序，鉴定出与衣分率相关的11个数量性状位点（QTL），共鉴定出13 859个表达QTL （eqtl）。通过全转录组关联研究（TWAS）、共定位分析和差异表达基因分析，确定了改善衣分性状的候选基因。我们通过TWAS定位了9个候选基因，并通过共定位和差异表达分析优先排序了与衣分相关的两个关键候选基因（Ghir_A12G025980和Ghir_A12G025990）。我们发现两个eQTL热点（Hot26和Hot28）协同参与调控纤维起始和发育的生物学途径。此外，我们还解锁了基因组变异通过聚集有利等位基因来提高衣分的潜力。发掘了适合提高衣分的新材料。

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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.