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.