Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (9): 1836-1847.doi: 10.3864/j.issn.0578-1752.2026.09.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Functional Identification and Breeding Evolution Analysis of the Key Gene GhPDF1 for Fruit Branch Angle in Upland Cotton

ZHANG WenJiao1(), WEI JiaZhi1, ZHOU YaRong1, YANG HaoRan1, GUO RongXin1, MA JunFeng1, YANG JiaHui1, WANG CaiXiang1(), SU JunJi1,2()   

  1. 1 College of Life Science and Technology, Gansu Agricultural University/State Key Laboratory of Aridland Crop Science, Lanzhou 730070
    2 Western Research Institute, Chinese Academy of Agricultural Sciences, Changji 831100, Xinjiang
  • Received:2025-10-19 Accepted:2025-12-05 Online:2026-05-01 Published:2026-05-06
  • Contact: WANG CaiXiang, SU JunJi

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Abstract:

【Objective】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.【Method】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.【Result】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, GhPDF1GG and GhPDF1CC, indicated a significantly smaller branch angle in GhPDF1GG carriers. Moreover, the frequency of this superior allele (GhPDF1GG) increased from 92% to 98% over successive breeding periods.【Conclusion】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 GhPDF1GG has been progressively enriched during modern cotton breeding in China.

Key words: Upland cotton, fruit branch angle, GhPDF1, virus-induced gene silencing, allelic variation

Table 1

Primer list"

引物名称 Primer name 引物序列 Primer sequence (5′-3′) 产物长度 Product length (bp) 用途 Purpose
GhPDF1-F GTGGCAGTCCACCAACTACT 400 克隆
Cloning
GhPDF1-R GCAAGCTTGAAGAGACGAGC
MQGhPDF1-F gactagtGTGGCAGTCCACCAACTACT 415 沉默
VIGS
MQGhPDF1-R aggcgcgccGCAAGCTTGAAGAGACGAGC
qGhPDF1-F TGTGGGTTTTGGTTGCTGC 122 实时荧光定量PCR
qRT-PCR
qGhPDF1-R TGAAGGGGGAGTTCCAGCAT
SNPGhPDF1-F CCGCCCATGTTCCATGAGT 319 SNP验证
SNP validation
SNPGhPDF1-R GCAGCAACCAAAACCCACAT

Fig. 1

Phylogenetic trees and gene structures of PDF1 in different species A: Phylogenetic trees of PDF1 in different species; B: Genetic structure of PDF1 in different species"

Fig. 2

Conserved domains of PDF1 in different species"

Fig. 3

Cis-acting elements of PDF1 in different species"

Fig. 4

Analysis of the expression level and expression characteristics of GhPDF1 in extreme materials of fruit branch angles in upland cotton A: Prediction of GhPDF1 expression patterns across various tissues via RNA‑seq analysis; B: Expression pattern of GhPDF1 in different tissues; C: The expression level of GhPDF1 in extreme materials of fruit branch angles in upland cotton. ** indicates a very significant difference with P≤0.01. The same as below"

Fig. 5

Phenotypic analysis of GhPDF1-silenced plants A: Phenotype of CLCrV:GhchlI positive plants; B: Detection of GhPDF1 silencing efficiency; C: Phenotype of fruit branches in the GhPDF1 silenced plants; D: Statistical analysis of the phenotypes of the silenced plants, the sample size n is greater than 10"

Fig. 6

Histological analysis of the fruit branch angles in the same parts of the GhPDF1-silenced plants A: Histology of parenchyma cells in the cortex at the fruit branch angle; B: Quantification of parenchyma cell numbers in the cortex of the branch crotch"

Fig. 7

Analysis and verification of excellent alternative alleles within the GhPDF1 gene A: Genetic structure of GhPDF1; B: Phenotypic statistical analysis of excellent allelic variations within the GhPDF1 gene; C: Verification of SNP loci in 5 small-angle materials and 5 large-angle materials"

Fig. 8

Analysis of favorable allelic variants in GhPDF1GG A: The distribution of allele frequency in different breeding eras; B: Statistical analysis of phenotypic traits across different breeding generations. * indicates a significant difference with P≤0.05"

Fig. 9

Genetic differentiation index and nucleotide polymorphism analysis of GhPDF1 A: The genetic differentiation index (FST) of GhPDF1 (2 Mb upstream and downstream respectively); B: The nucleotide diversity ratio of GhPDF1 (2 Mb upstream and downstream respectively)"

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