Genome-wide analysis elucidates the roles of GhHMA genes in different abiotic stresses and fiber development in upland cotton

Wu, Cuicui; Xiao, Shuiping; Zuo, Dongyun; Cheng, Hongyan; Zhang, Youping; Wang, Qiaolian; Lv, Limin; Song, Guoli

doi:10.1016/j.plaphy.2022.11.022

Cited by 7 publications

(4 citation statements)

References 104 publications

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“…Ka/Ks = 1.0 means duplicated gene pairs have undergone neutral selection, Ka/Ks > 1.0 points to a positive selection during rapid evolution and Ka/Ks < 1.0 indicates purifying selection. In G. hirsutum , due to the occurrence of purifying selection, the proliferation of GhCKX family genes was suppressed, which increased fixation, lowered the extent of loss-of-function mutations that were deleterious at duplicated loci, and also preserved the role of newly duplicated genes ( Wu et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

Hamid,

Jacob,

Ghorbanzadeh

et al. 2024

PeerJ

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Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress.

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Section: Discussionmentioning

confidence: 99%

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

Hamid,

Jacob,

Ghorbanzadeh

et al. 2024

PeerJ

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“…The details of the protocol were as follows: (Step 1) initial denaturation step of 30 s at 95 °C; (Step 2) 40 cycles of 5 s at 95 °C, and 34 s at 60 °C; and (Step 3) melting curve analysis. The 2 −ΔΔCT method was used to calculate the relative expression levels of GhTIR1/AFBs [ 32 ]. T -tests were employed for statistical analyses.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Analysis Elucidates the Roles of GhTIR1/AFB Genes Reveals the Function of Gh_D08G0763 (GhTIR1) in Cold Stress in G. hirsutum

Zhang,

Wu,

Guo

et al. 2024

Plants

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This study identified 13 GhTIR1/AFB members in G. hirsutum through bioinformatics methods and divided them into three subgroups by phylogenetic tree analysis. Motif and gene structure analysis showed that the genes in this family were highly conserved. Promoter cis-acting element analysis found that the promoters of GhTIR1/AFBs contained a large number of cis-acting elements in response to growth and development and abiotic stress. Further RT-qPCR results showed that GhTIR1/AFB genes responded to various abiotic stresses such as IAA, ABA, cold, and heat, and the expression levels of each gene changed obviously, especially Gh_D08G0763 (GhTIR1), which responded significantly to cold injury. Using VIGS (virus-induced gene silencing) technology to silence Gh_D08G0763 in the cold-tolerant cotton variety ZM36, it was found that the resistance of ZM36 to cold damage was significantly reduced. The physiological response mechanism of the Gh_D08G0763 in resisting cold damage was further analyzed through trypan blue staining of leaves and determination of enzyme activity levels. This study provided effective genetic resources for cotton cold-tolerance breeding.

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“…A gene expression profile provided essential clues for the function of GhHMA genes in cotton fiber development and response to various abiotic stresses. GhHMA26 was predominantly expressed in 10 DPA fiber cells and the relative expression was higher than any other GhHMAs which indicate that GhHMA26 may positively regulate fiber elongation [11]. Genome-wide analysis of the serine carboxypeptidase-like protein family reveals Ga09G1039 is involved in fiber elongation in cotton with overexpression of Ga09G1039 significantly increasing the length of stem trichomes [12].…”

Section: Introductionmentioning

confidence: 95%

Genetic and Molecular Regulation of Cotton Fiber Initiation and Elongation

Bai,

Scheffler

2024

Preprint

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Cotton fiber, a crucial and sustainable resource for global textile production, undergoes a complex five-stage developmental process, encompassing initiation, elongation, transition, secondary cell wall biosynthesis, and maturation. These elongated single-cell fibers originate from the outer ovule epidermis. The development of cotton fibers involves intricate changes in gene expression and physiological processes, resulting in a nearly pure cellulose product vital for the global cotton industry. Decoding genes associated with fiber development enhances our understanding of cotton fiber mechanisms and facilitates the cultivation of varieties with enhanced quality. In recent decades, advanced omics approaches, including genomics, transcriptomics, and proteomics, have played a pivotal role in identifying genes and gene products linked to cotton fiber development, including the MYB transcription factor family which coordinates cotton fiber development. Molecular studies have revealed transcription factors like MYB, WRKY, Homeodomain Leucine Zipper (HD-ZIP) and basic Helix-Loop-Helix (bHLH) influencing fiber initiation and elongation. The intricate interplay of phytohormones like auxin, gibberellic acid (GA), brassinosteroid (BR), jasmonic acid (JA), ethylene, abscisic acid (ABA), and cytokinin is explored, providing a comprehensive perspective on shaping cotton fibers. Numerous candidate genes and cellular processes affecting various aspects of fiber development hold promise for genetic engineering or marker-assisted breeding to improve fiber quality. This review presents a comprehensive overview of key achievements in cotton molecular biology, with a specific emphasis on recent advancements in understanding transcription factors and phytohormones involved in cotton fiber initiation and elongation.

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Genome-wide analysis elucidates the roles of GhHMA genes in different abiotic stresses and fiber development in upland cotton

Cited by 7 publications

References 104 publications

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

Genome-Wide Analysis Elucidates the Roles of GhTIR1/AFB Genes Reveals the Function of Gh_D08G0763 (GhTIR1) in Cold Stress in G. hirsutum

Genetic and Molecular Regulation of Cotton Fiber Initiation and Elongation

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