Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (20): 4447-4460.doi: 10.3864/j.issn.0578-1752.2026.20.002

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

Genetic Identification of the GhAARS Ⅰ Family in Upland Cotton and Functional Analysis of GhAARS Ⅰ-17 in Regulating Plant Height

FENG YuYu1(), ZHOU YaRong1, CHAI YingYing1, YANG JunNing1, WEI JiaZhi1, YU XiaoXue1, ZHAO Yan1, MA XiongFeng2, WANG CaiXiang1(), SU JunJi1()   

  1. 1 College of Life Science and Technology, Gansu Agricultural University/State Key Laboratory of Aridland Crop Science, Lanzhou 730070
    2 Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan
  • Received:2026-02-13 Accepted:2026-04-10 Online:2026-10-16 Published:2026-10-21
  • Contact: WANG CaiXiang, SU JunJi

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Abstract:

【Objective】Plant height is an important agronomic trait of cotton, which directly affects crop yield, fiber quality, and the efficiency of mechanized harvesting. Aminoacyl-tRNA synthetases have been reported to be involved in the developmental regulation process in various plants. This study aimed to identify members of the Class Ⅰ AARS family in upland cotton at the whole-genome level, analyze their evolutionary characteristics and expression patterns, explore the function of GhAARS Ⅰ-17 in regulating plant height, and discover superior allelic variations applicable for marker-assisted breeding, so as to provide genetic resources and a theoretical basis for cultivating cotton varieties suitable for mechanized production.【Method】Based on the cotton multi-omics database and multiple plant genome databases, members of the AARS Ⅰ family in upland cotton and nine other species were identified using the Hidden Markov Model (HMM). A phylogenetic tree was constructed using the maximum likelihood method, and synteny, gene structure, conserved motifs, and promoter cis-acting elements were analyzed to reveal the evolutionary history and structural characteristics of this family. Tissue-specific RNA-seq data and RT-qPCR were used to analyze gene expression patterns and screen candidate genes related to plant height. Functional validation of the candidate gene was performed in upland cotton via Virus-Induced Gene Silencing (VIGS), followed by phenotypic observation of the plants. Based on published genomic data of upland cotton germplasm resources, SNP identification and association analysis were conducted on the coding regions to verify the genetic association with plant height. The distribution frequency of superior allelic variations in different ecological cotton regions was analyzed, and Kompetitive Allele-Specific PCR (KASP) markers were developed.【Result】A total of 18 GhAARS Ⅰ genes were identified in upland cotton. Phylogenetic analysis classified them into three subfamilies, with six members in each. According to the type of catalytic amino acid, they could be further divided into valine-, isoleucine-, leucine-, and methionine-related subclasses, among which valine and isoleucine accounted for more members. Synteny analysis showed that this family was highly conserved among Gossypium species, and its expansion in upland cotton was mainly derived from segmental duplication events. Gene structure and conserved motif analysis indicated that members of the same subfamily shared similar structures. The promoter regions were rich in light-responsive and hormone-responsive cis-acting elements, suggesting their involvement in multiple regulatory pathways during cotton growth and development. RNA-seq data and RT-qPCR analysis showed that GhAARS Ⅰ-17 was highly expressed in roots, stems, and calyxes, with higher expression levels in tall varieties. Functional verification of GhAARS Ⅰ-17 via VIGS showed that compared with the control, GhAARS Ⅰ-17-silenced plants had a 5.45 cm reduction in plant height and a 0.78 mm reduction in stem diameter. Breeding evolution analysis revealed that the C genotype of GhAARS Ⅰ-17 was a superior allelic variant, which was selected during upland cotton breeding. On this basis, KASP molecular markers were developed to distinguish this allelic variation locus.【Conclusion】GhAARS Ⅰ-17 is involved in the regulation of plant height. Its functional deficiency leads to dwarfism of the plant, decreased chlorophyll content and insufficient biomass accumulation; the superior allelic variation of this gene is closely related to the plant height trait.

Key words: Upland cotton, plant height, chlorophyll, GhAARS Ⅰ-17, virus-induced gene silencing (VIGS)

Fig. 1

Phylogenetic tree analysis of AARS Ⅰ proteins A: Combined phylogenetic tree of AARS Ⅰ proteins; B: Phylogenetic tree of IleRS-associated proteins; C: Phylogenetic tree of LeuRS-associated proteins; D: Phylogenetic tree of ValRS-associated proteins; E: Phylogenetic tree of MetRS-associated proteins. At: Arabidopsis thaliana; Gh: Gossypium hirsutum; Gr: Gossypium raimondii; Gb: Gossypium barbadense; Ga: Gossypium arboreum; Zm: Zea mays; Os: Oryza sativa; Tc: Theobroma cacao; Vv: Vitis vinifera"

Fig. 2

Interspecific synteny analysis (A) and intraspecific synteny analysis (B) of the AARS Ⅰ gene family in cotton"

Fig. 3

Analysis of the GhAARS Ⅰ family gene structure (A), conserved Motifs (B), amino acid composition of each Motif (C), and cis-acting elements (D)"

Fig. 4

Analysis of GhAARS Ⅰs expression patterns A: Detection of the relative expression levels of GhAARS Ⅰs by RNA-seq; B: Relative expression levels of 8 genes in different tissues; C: Expression pattern analysis of 8 genes in different tall and short varieties. Different lowercase letters indicate significant differences between treatments (P<0.05). *: P<0.05; **: P<0.01; n.s.: No significant difference. The same as below"

Fig. 5

Phenotypes of GhAARS Ⅰ-17-silenced plants A: Phenotypes of plant height, main stem diameter, the height of the first three internode positions, and corresponding true leaves of TRV:00 and TRV:GhAARS Ⅰ-17 plants. The same as below; B: Quantitative statistics of plant height, main stem diameter and internode positions of the first three internodes in TRV:00 and TRV:GhAARS Ⅰ-17 plants"

Fig. 6

Effects of VIGS-mediated silencing of GhAARS Ⅰ-17 on chlorophyll content and leaf dry matter accumulation"

Fig. 7

Analysis and validation of SNP loci A: Structure of the GhAARS Ⅰ-17 gene; B: Validation of allelic variant loci; C: Association analysis between allelic variants and plant height; D: Frequency distribution of allelic variants in extreme tall- and short-stalk cultivars; E: Allelic discrimination plot; F: Association analysis of genotype with plant height phenotype; G: Geographic distribution frequency of allelic variants. NIR: Northwest Inland Region, YRR: Yellow River Region, YZRR: Yangtze River Region"

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