Boll opening rate (BOR) is one of the most important indicators reflecting the early maturing trait of upland cotton (Gossypium hirsutum L.). The genome-wide association study (GWAS) was applied to dissect the QTL (quantitative trait locus) and its genetic effect for providing a theoretical basis for molecular breeding of early maturing traits in upland cotton.

The natural population composed of 315 different upland cotton varieties (lines) were used to identify the BOR under three environments. Simultaneously, a total of 9 244 SNP linkage disequilibrium block (SNPLDB) markers with multiple alleles were constructed. Then, the restricted two-stage multi-locus GWAS (RTM-GWAS) was utilized to detect SNPLDB loci significantly associated with BOR, estimate its phenotypic effect value, establish QTL-Allele matrix for significantly associated loci in the population, and further detected the stable major SNPLDB loci and elite haplotypes. Finally, according to the gene expression levels of the two transcriptome data, candidate genes that may be related to the target trait were mined within the 1 Mb genome range of the flanking sequence of the significant SNPLDB loci.

The variation of BOR was ranged from 37.78% to 100.00% and the broad-sense heritability was 67.03% in the natural population under three environments. The multi-environment variance analysis revealed that the BOR was significantly different among genotype, environment and genotype × environment interaction (P<0.001). A total of 52 SNPLDB loci significantly associated with BOR were detected through the RTM-GWAS procedure, containing 179 alleles or haplotypes, among them, the effect values of 90 increasing alleles or haplotypes ranged from 0.014 to 19.43, and the effect values of 89 decreasing alleles or haplotypes ranged from -21.49 to -0.039. Among the significant SNPLDB loci mentioned above, 6 SNPLDB loci were detected simultaneously in both multi-environment and single environment, which were considered as stable SNPLDB loci significantly associated with BOR. Through the significance analysis of phenotypic traits corresponding to different allelic variations of the above six stable SNPLDB loci, the four favorable alleles were identified as LDB_16_37952328(TT), LDB_5_96395565(AA), LDB_16_49503485(TT), and LDB_4_81118668(TT). Besides, further analysis showed that there were significant differences in the frequency distribution of favorable alleles among varieties (lines) in four different ecological regions. Additionally, a total of 178 genes were annotated and 23 potential candidate genes were predicted in the adjacent regions of 4 stable major SNPLDB loci by transcriptome data analysis.

A total of 52 SNPLDB loci significantly associated with BOR were identified, of which 4 loci were stable major SNPLDB loci. Furthermore, it was predicted that 23 genes might be related to the BOR of upland cotton. These SNPLDBs loci and candidate genes will provide a theoretical basis for marker-assisted breeding of early maturity in upland cotton.

This paper evaluated comprehensively early maturity upland cotton varieties in northwest inland cotton-growing region of China, and uncovered the evolution rules of the main traits from the breeding cultivars in the region. It provides a useful reference for recommendation and breeding of main cotton varieties in northwest inland region.

A total of 110 early-maturing upland cotton varieties which were approved in northwest inland cotton-growing region from 1988 to 2021 were applied, and phenotypic identification of 12 main traits related to early maturity, yield, fiber quality and plant architecture was carried out in Dunhuang, Gansu province and Shihezi, Xinjiang Production and Construction Corps in 2020 and 2021, respectively. Clustering analysis, correlation analysis and principal component analysis were respectively used to evaluate the phenotypic characteristics of the cultivars, and carry out the breeding evolution analysis of their main traits.

The phenotype value of 12 main traits had large distribution range from 110 early-maturing upland cotton varieties in northwest inland cotton-growing region of China. The variation coefficient in descending order is: fruit branch length (FBL), boll number per plant (BN), boll opening rate (BOR), boll weight (BW), fiber micronaire (FM), fiber strength (FS), lint percentage (LP), fiber length (FL), flowering time (FT), fruit branch angle (FBA), fiber elongation (FE), and fiber uniformity (FU). By cluster analysis, these cultivars were divided into four groups: Ⅰ, Ⅱ, Ⅲ and Ⅳ, which were the population of high fiber quality, early maturity, loose plant type and high yield, respectively. Correlation analysis showed that early maturity was negatively correlated with yield and fiber quality related to traits, while the yield related to traits were positively correlated with the fiber quality traits, and most of them reached significant or extremely significant level. The 12 main traits were simplified into four principal components which had cumulative contribution rate of 66.92%. Based on the comprehensive evaluation results of these varieties by principal components, an excellent cultivar Zhongmian 113 ranked the first in the 110 early-maturing upland cotton varieties with a score of 0.67, which was characterized by early maturity, high yield and excellent fiber quality, and relatively loose plant type. Additionally, it was found that the early maturity character of cotton varieties approved in Gansu province was significantly better than that of varieties approved in northwest inland region and Xinjiang province, and the traits related to yield and fiber quality of cotton varieties approved in Gansu province were significantly lower than those of varieties approved in northwest inland region and Xinjiang province. During the breeding evolution of early maturing upland cotton varieties in northwest of China for more than 30 years, most of the traits related to yield and fiber quality showed significant upward trends, and the plant type was becoming more compact. BN was negatively correlated with BW, LP, FL and FS in early cultivars, while BN was positively correlated with BW, LP, FL and FS in recent cultivars.

In the process of breeding and improvement of early maturing upland cotton varieties in northwest of China, the main traits related to yield and fiber quality had wide distribution, and they had significant improvement trends year by year. In the recently developed varieties, BN, FL and FS had been improved cooperatively.