Genome-wide association analysis and transcriptomics were used to investigate salt tolerance traits during germination in 300 Gossypium hirsutum L. germplasm accessions, with the objective of identifying genes and molecular markers associated with salt tolerance. Under 200 mmol L⁻¹ NaCl stress, six traits were evaluated, germination rate, root length, shoot length, root fresh weight, shoot fresh weight, and total fresh weight, as well as their respective salt tolerance indices. A total of 1277 significantly associated single-nucleotide polymorphism (SNP) markers were identified and mapped to 94 quantitative trait loci (QTLs). Of these, 49 QTLs were detected by three or more analytical models, and three QTLs were prioritized for further investigation. Subsequent analysis of these QTLs identified 73 candidate genes potentially involved in cotton salt tolerance. Integration of transcriptomic data revealed that three candidate genes were among the differentially expressed genes (DEGs). Examination of their RNA-seq expression profiles demonstrated significant differences in fragments per kilobase of transcript per million mapped reads (FPKM) values across sampling time points. These three candidate genes are therefore predicted to be associated with salt tolerance during cotton germination. The results provide new insights into the molecular regulatory mechanisms of salt stress tolerance in cotton and offer valuable genetic resources and molecular markers for the genetic improvement of salt tolerance.

To identify upland cotton varieties with consistently high yields and stable performance across variable growing seasons in Xinjiang, we evaluated yield data for 11 varieties over 4 consecutive years (2022–2025). Among the tested varieties, 02 achieved the highest average yield (10.85 kg per plot). Variety ZMBH1939 showed the most stable yield across years (coefficient of variation = 0.1557). Analysis of variance showed that variety, year, and their interaction significantly affected yield (p < 0.01 for all). Further evaluation using two complementary multi-environment trial models (AMMI and GGE) revealed consistent findings: 02 and FC190 were high-yielding but moderately stable; W21 and TH02 showed moderate yield with good stability; and XLM108 combined high yield potential with excellent stability. The control variety Z49 (CK) exhibited good stability but only moderate yield. Among the four trial years, 2023 was the most representative and discriminatory environment, making it ideal for screening superior varieties. Exploratory analysis of climatic covariates suggested that accumulated temperature (≥10 °C) may be associated with interannual yield variation (R² = 0.464), and low precipitation was linked to stronger environmental discrimination. However, given the limited number of environments (n = 4), these findings are preliminary and hypothesis-generating rather than confirmatory. This study provides a framework for understanding climate-driven yield variation in regional cotton trials and identifies promising germplasm (notably XLM108 and 02) for further breeding and promotion. Validation in multi-location or longer-term trials is required before drawing definitive conclusions.