Genome-Wide Identification and Preliminary Functional Analysis of BAM (β-Amylase) Gene Family in Upland Cotton

Yang, Yanlong; Sun, Fenglei; Wang, Penglong; Yusuyin, Mayila; Kuerban, Wumaierjiang; Lai, Chengxia; Li, Chunping; Ma, Jun; Xiao, Fei

doi:10.3390/genes14112077

Cited by 7 publications

(4 citation statements)

References 36 publications

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“…The completion of the cotton genome sequencing has provided great convenience to researchers, enabling them to deeply study the evolution and functional analysis of various gene families. In recent years, many families have been studied in cotton, such as GhCSP [ 44 ], GhWNK [ 45 ], GhTBL [ 46 ], GhBAM [ 47 ], GhACS [ 48 ], GhRF2 [ 49 ], GhGATL [ 50 ], GhANN [ 51 ], and GhWOX [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum

Zhang,

Jiao,

Zhao

et al. 2024

Genes

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Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum

Zhang,

Jiao,

Zhao

et al. 2024

Genes

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“…These results have also indicated BAM genes were highly conservative in plants and their functions may also be similar across plants. In addition, two BAM genes from Annona atemoya , AaBAM3 , and AaBAM9 also reported localization in chloroplasts [ 48 ], while another BAM gene from upland cotton , GhBAM7 , was explored as having important roles in fiber development; the GhBAM7 protein was located in the nuclear using GFP localization [ 49 ]. PbBAM3 was cloned from a pear, which was also validated as a chloroplast-localized protein, and its function was well documented [ 50 ].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Identification of the β-Amylase (BAM) Gene Family in Response to Cold Stress in White Clover

Li,

Chen,

Huang

et al. 2024

Plants

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White clover (Trifolium repens L.) is an allopolyploid plant and an excellent perennial legume forage. However, white clover is subjected to various stresses during its growth, with cold stress being one of the major limiting factors affecting its growth and development. Beta-amylase (BAM) is an important starch-hydrolyzing enzyme that plays a significant role in starch degradation and responses to environmental stress. In this study, 21 members of the BAM gene family were identified in the white clover genome. A phylogenetic analysis using BAMs from Arabidopsis divided TrBAMs into four groups based on sequence similarity. Through analysis of conserved motifs, gene duplication, synteny analysis, and cis-acting elements, a deeper understanding of the structure and evolution of TrBAMs in white clover was gained. Additionally, a gene regulatory network (GRN) containing TrBAMs was constructed; gene ontology (GO) annotation analysis revealed close interactions between TrBAMs and AMY (α-amylase) and DPE (4-alpha-glucanotransferase). To determine the function of TrBAMs under various tissues and stresses, RNA-seq datasets were analyzed, showing that most TrBAMs were significantly upregulated in response to biotic and abiotic stresses and the highest expression in leaves. These results were validated through qRT-PCR experiments, indicating their involvement in multiple gene regulatory pathways responding to cold stress. This study provides new insights into the structure, evolution, and function of the white clover BAM gene family, laying the foundation for further exploration of the functional mechanisms through which TrBAMs respond to cold stress.

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“…Extensive studies have shown that starch metabolism involves a series of enzymes, among which, amylases play an essential role in starch degradation [ 13 , 14 , 15 ]. The products of starch degradation provide essential support for plant growth and development and confer increased stress tolerance [ 16 , 17 ]. Starch degradation involves α-amylase (AMY) and β-amylase (BAM) [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Profiling of the α-Amylase (AMY) Gene Family in Potato

Duan,

Jin

2024

Genes

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Starch degradation provides energy and signaling molecules for plant growth, development, defense, and stress response. α-amylase (AMY) is one of the most important enzymes in this process. Potato tubers are rich in starch, and the hydrolysis of starch into sugar negatively impacts the frying quality of potato. Despite its importance, the AMY gene family has not been fully explored in potatoes. Here, we performed a detailed analysis of the StAMY gene family to determine its role in potato. Twenty StAMY genes were identified across the potato genome and were divided into three subgroups. The promoters of StAMY genes contained an array of cis-acting elements involved in growth and development, phytohormone signaling, and stress and defense responses. StAMY8, StAMY9, StAMY12, and StAMY20 were specifically expressed in mature tubers. Different StAMY gene family members tended to be upregulated in response to β-aminobutyric acid (BABA), Phytophthora infestans (P. infestans), benzothiadiazole (BTH), heat, salt, and drought stress. In addition, different StAMY gene family members tended to be responsive to abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellic acid (GA3), and 6-benzylaminopurine (BAP) treatment. These results suggest that StAMY gene family members may be involved in starch and sugar metabolism, defense, stress response, and phytohormone signaling. The results of this study may be applicable to other starchy crops and lay a foundation for further research on the functions and regulatory mechanisms of AMY genes.

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Genome-Wide Identification and Preliminary Functional Analysis of BAM (β-Amylase) Gene Family in Upland Cotton

Cited by 7 publications

References 36 publications

Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum

Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum

Comprehensive Identification of the β-Amylase (BAM) Gene Family in Response to Cold Stress in White Clover

Genome-Wide Identification and Expression Profiling of the α-Amylase (AMY) Gene Family in Potato

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