In the present study, genetic linkage analysis was carried out to map the fiber color loci Lc ₁ and Lc ₂ on two brown cotton cultivars with SSR and EST-SSR markers in the reference map by F₂ segregation populations. The Lc ₁ locus carried by Xincaimian6 (Gossypium hirsutum L.) was flanked by the marker NAU2862 and NAU1043 on the long arm of Chromosome 07, with genetic distance 7.8 cM and 3.8 cM, respectively. The Lc ₂ carried by Xincaimian 5 (Gossypium hirsutum L.) was flanked by the marker NAU5433 and NAU2968 on the short arm of Chromosome 06, with genetic distance 4.4 cM and 7.4 cM respectively. Moreover, the marker NAU3735 and marker NAU5434 co-segregated with the Lc ₁ and the Lc ₂ locus, respectively. The results of marker association studies with these two loci provides the basic information for the final isolation of these important genes in colored cotton, and these linkage markers also could facilitate application of marker assisted selection in the future.

Cotton is an important cash crop with a certain salt tolerance, but its germination stage is very susceptible to the damage of salt stress, causing significant yield loss. However, few studies have evaluated the cotton salt tolerance and selected salt tolerance traits at germination stage. Therefore, in this study, 16 cotton samples with geographical representation were randomly selected from 308 cotton germplasms to determine the optimal 200 mmol·L^-1 NaCl in cotton germination experiments. On this basis, the salt tolerance of 308 upland cotton varieties and the growth, ion distribution and transport of highly salt-tolerant and non salt-tolerant cotton germplasms were analyzed. The results showed that the 308 germplasms were classified into five classes through cluster analysis, i.e, (1) highly salt-tolerant germplasms (HST, 49), (2) salt-tolerant germplasms (ST, 169), (3) moderately salt-tolerant class (MST,43), (4) lowly salt-tolerant germplasms (LST, 16), and (5) non-salt-tolerant germplasms (NST, 31). By calculating the salt tolerance index (STI) of various cotton germination and growth parameters and principal component analysis, combined with the correlation analysis and linear regression between mean membership function value (MFV) and STI, the key indexes of cotton germination and growth under salt stress, including total fresh weight, shoot fresh weight, and shoot length, were determined. In addition, three salt tolerance evaluation models constructed with different variables (6 variables in Model 1; 3 variables in Model 2; 1 variable in Model 3) found that the total fresh weight was the most reliable trait for the salt tolerance evaluation. In practical application, the variable selection for modelling could be adjusted based on the experimental workload. The comparison of the K⁺, Na⁺, and Ca²⁺ contents between HST and NST found that the higher the salt tolerance of cotton germplasms, the lower the Na⁺ content in the root system. Besides, the ion ratios and ion selective transport coefficients (ST) was found to be significantly positively correlated with the salt tolerance of cotton. This study will provide a basis for evaluating and breeding salt-tolerant cotton germplasms.

This study aims to reveal the genetic variation of fruit branch angle (FBA) in upland cotton, thereby providing a scientific basis and practical guidance for cotton architecture breeding. We explored the genetic variation pattern of FBA in 300 upland cottons from different regions and different periods, respectively. Cluster analysis and principal component analysis were used to comprehensively evaluate the plant architecture traits and yield traits in 300 upland cottons. The results demonstrated that the range of variation of FBA in cotton was 43.59–69.32°, the coefficient of variation ranged from 6.06% to 7.42%, and the broad-sense heritability was 75.50%. The order of FBA in different regions was as follows: Foreign Germplasm (FG; 56.77°) > Yellow River Region (YRR; 56.24°) > Yangtze River Region (YZRR; 56.16°) > Liaoning Special Maturing Region (LSMR; 55.35°) > Northwest Inland Region (NIR; 55.25), which is rich in genetic diversity. FBA in cotton in different periods had obvious differences. FBA was the largest before 1960, and as the period progressed, FBA showed an overall fluctuating decrease, whose coefficient of variation and genetic diversity index tended to increase. In this study, it was found that when the range of FBA was 50.46–55.31°, cotton had the best overall performance, with compact architecture, fewer empty fruit branches, more bells, and higher yield, which can be further developed and utilized as an excellent cotton germplasm resource.

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.