DNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcriptomes, and genomes obtained from the 20-days-post-anthesis (DPA) cotton fibers of 207 accessions and extended the classical framework of population genetics to epigenetics. Over 287 million single methylation polymorphisms (SMPs) were identified, 100 times more than the number of single nucleotide polymorphisms (SNPs). These SMPs were significantly enriched in intragenic regions while depleted in transposable elements. Association analysis further identified a total of 5,426,782 cis-methylation quantitative trait loci (cis-meQTLs), 5078 cis-expression quantitative trait methylation (cis-eQTMs), and 9157 expression quantitative trait loci (eQTLs). Notably, 36.39% of cis-eQTM genes were not associated with genetic variation, indicating that a large number of SMPs associated with gene expression variation are independent of SNPs. In addition, out of the 1715 epigenetic loci associated with yield and fiber quality traits, only 36 (2.10%) were shared with genome-wide association study (GWAS) loci. The construction of multi-omics regulatory networks revealed 43 cis-eQTM genes potentially involved in fiber development, which cannot be identified by GWAS alone. Among these genes, the role of one encoding CBL-interacting protein kinase 10 in fiber length regulation was successfully validated through gene editing. Taken together, our findings prove that DNA methylation data can serve as an additional resource for breeding purposes and can offer opportunities to enhance and expedite the crop improvement process.

Seed vigor underpins uniform crop establishment, but its dynamic genetics are understudied. Combining high‐resolution temporal phenotyping and genomics in upland cotton, we used the SeedRanger platform to record 17 image‐based traits every 30 min over 120 h, revealing stage‐specific heritability and identifying 541 seed‐vigor loci. These loci show extensive pleiotropy and temporal coordination, forming a genetic network that preserves developmental continuity; 8.9% overlap regions under domestication selection, indicating concurrent optimization with fiber yield. Functional validation of FLA2 , a candidate gene underlying a dynamic QTL, implicates auxin‐mediated control of radicle elongation and cotyledon development. This temporal framework exposes dynamic genetic architecture and breeding targets for high‐vigor crops.

This study examines the reform and development of trade associations in Shanghai, China, one of the main economic hubs of the country and marked by a substantial growth in trade associations since the reform and “opening-up” in 1978. We analyze public policies pertaining to trade associations, survey data collected from 212 local trade associations in Shanghai, and interviews of government officials and trade association leaders. The research results show that trade associations are significantly less dependent on the government and they seem to be more oriented to providing services for and representing corporate members. We trace these changes to public policy reforms and growth in private businesses. The transition reflects the dynamic and changing relationship among the government, trade associations, and business in China. We conclude with a model of these dynamics and a discussion of the implications of this study.