Early maturity is an important target trait in cotton genetic improvement in China, and flowering time is a key indicator of earliness. H3K9 histone lysine methyltransferases (SUVs) are involved in plant development and flowering regulation in model plants such as Arabidopsis thaliana and rice. This study aimed to investigate the role of the SUV gene family in flowering regulation in upland cotton and to identify elite allelic variations of key members. The findings provide valuable genetic resources for breeding early-maturing cotton cultivars.

Protein sequences of the SUV family from Arabidopsis were used as reference sequences. HMMER, MEME, and TBtools were employed to identify and analyze SUV family members in upland cotton at the whole-genome level. Candidate genes involved in flowering regulation were screened through integrated RNA-seq and RT-qPCR analyses. Virus-induced gene silencing (VIGS) was used to validate the functions of candidate genes in flowering regulation. Resequencing data from 419 upland cotton accessions were analyzed to identify SNPs within GhSUV1, which were further validated by Sanger sequencing. Allele frequencies and genetic differentiation were examined across different cotton ecological regions.

A total of 200 SUV homologous proteins were identified in nine higher plant species, including rice. Phylogenetic analysis divided them into SUVH and SUVR clades, indicating a relatively conserved evolutionary pattern. In upland cotton, 28 GhSUV genes were identified. Their expansion was mainly driven by polyploidization events. Most collinear gene pairs showed Ka/Ks<1, suggesting strong purifying selection. Gene structure and motif analyses revealed high similarity among members within the same clade. Promoter analysis showed that GhSUV genes are enriched in light-responsive and hormone-responsive cis-elements, indicating their involvement in multiple developmental regulatory pathways. RNA-seq and RT-qPCR analyses showed that GhSUV1 and GhSUV13 were expressed at higher levels in early-maturing materials. They were also highly expressed in leaves and certain floral organs. Functional validation using VIGS demonstrated that silencing GhSUV1 delayed squaring and flowering by 5.6 and 6.0 days, respectively. Silencing GhSUV13 delayed these stages by 5.8 and 6.8 days compared with the control. Moreover, suppression of GhSUV1 and GhSUV13 significantly reduced the expression of flowering-related genes GhSOC1, GhAP1, GhFT, and GhCAL, while significantly increasing GhSVP expression. These results indicate that both genes participate in flowering regulation. Sequence analysis identified a SNP in the exon region of GhSUV1 that was significantly associated with flowering time. The early-flowering GG allele increased in frequency with latitude. Genetic differentiation index and nucleotide diversity analyses revealed significant differences in the GhSUV1 genomic region between early- and late-maturing cultivars, suggesting that this locus has undergone breeding selection.

GhSUV1 and GhSUV13 are involved in flowering regulation in upland cotton. The elite allele of GhSUV1 is closely associated with early flowering and has been subject to breeding selection. These findings provide important genetic resources for the improvement of early-maturing cotton varieties.

The fruit branch angle is a key determinant of cotton plant architecture. Previous studies revealed differential expression of GhPDF1 in materials with extreme fruit branch angles. This study aimed to functionally characterize GhPDF1 and systematically dissect its superior allelic variations, thereby providing genetic resources and a theoretical basis for improving plant architecture and breeding machine-harvestable cotton varieties.

The sequences of PDF1 homologs from 25 species, including upland cotton (Gossypium hirsutum), were obtained through homology alignment for phylogenetic analysis. A virus-induced gene silencing (VIGS) vector targeting GhPDF1 was constructed using double digestion and transformed into upland cotton to investigate its role in regulating the fruit branch angle. Single nucleotide polymorphisms (SNPs) within GhPDF1 were identified using resequencing data from 418 upland cotton accessions, with key SNPs validated by Sanger sequencing. The distribution of superior allelic variations of GhPDF1 was analyzed across Chinese cotton varieties from different breeding eras.

A phylogenetic tree of the PDF1 gene from Gossypium hirsutum and its homologous genes from different species revealed that it is most closely related to Malvaceae, while being distantly related to Poaceae. Expression analysis showed that GhPDF1 was lowly expressed in large‑angle materials but highly expressed in small‑angle materials. Tissue‑specific expression profiling revealed high transcript levels in pistils, petals, and stems. VIGS‑mediated silencing of GhPDF1 significantly reduced the cell number at the fruit branch junction by approximately 170 and increased the fruit branch angle by 8.2° compared with empty‑vector controls, demonstrating its crucial role in regulating fruit branch angle. Phenotypic comparison between two allelic variants, GhPDF1^GG and GhPDF1^CC, indicated a significantly smaller branch angle in GhPDF1GG carriers. Moreover, the frequency of this superior allele (GhPDF1^GG) increased from 92% to 98% over successive breeding periods.

Silencing GhPDF1 in upland cotton reduces cell proliferation at the branch junction, leading to a significant increase in the fruit branch angle. The superior allelic variant GhPDF1^GG has been progressively enriched during modern cotton breeding in China.

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.