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Cotton Genes, Genetics, and Genomics

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (10 May 2024) | Viewed by 19992

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Dr. Guanjing Hu

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1. State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455 000, China
2. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518 120, China
Interests: cotton; polyploidy; domestication; multi-omics; gene regulatory network; duplicated gene expression; abiotic stress

Special Issue Information

Dear Colleagues,

Cotton is the most important fiber crop worldwide. Cotton fibers (unicellular seed trichomes) provide an excellent model system for studying cell differentiation, polarity, and expansion. The evolutionary history of the cotton genus (Gossypium) also presents an ideal model for investigating the genome evolution of speciation, allopolyploidization, and domestication. However, the allopolyploid nature of tetraploid cotton species still hinders genetic dissection and a mechanistic understanding of phenotypic traits of interest, especially in cultivated upland cotton (G. hirsutum) and sea-island cotton (G. barbadense). In recent years, high-quality genomic resources and the development of emerging technologies (i.e., genome editing, multi-omics technology and bioinformatics) have facilitated insight into the complicated gene regulatory networks underlying cotton biology and evolution.

In light of these advances, the goal of this Special Issue is to showcase how cotton researchers have leveraged up-to-date resources and new technologies to gain new knowledge of the molecular and functional genomics of cotton. We welcome both original research and review manuscripts on diverse topics and scales across cotton genetics and genomics. Submissions on (but not limited to) the following topics are invited: (1) cotton germplasm and genomic resources in terms of evolutionary characterization and genetic dissection, (2) the molecular basis and biological networks of key cotton traits under static and stressed conditions, and (3) biotechnology, bioinformatics, and databases.

Dr. Guanjing Hu
Guest Editor

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Keywords

cotton
gene identification and functional validation
functional genomics
multi-omics
gene networks
stress tolerance

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Published Papers (10 papers)

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Research

15 pages, 6435 KiB

Open AccessArticle

Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton

by Guiling Fu, Haotian Luo, Juqing Jia, Mingming Hou and Guanjing Hu

Genes 2024, 15(9), 1130; https://doi.org/10.3390/genes15091130 - 27 Aug 2024

Viewed by 1201

Abstract

Polyploidy, a prevalent event in plant evolution, drives phenotypic diversification and speciation. While transcriptional changes and regulation in polyploids have been extensively studied, the translational level impact remains largely unexplored. To address this gap, we conducted a comparative transcriptomic and translatomic analysis of cotton leaves from allopolyploid species G. hirsutum (AD₁) and G. barbadense (AD₂) relative to their model A-genome and D-genome diploid progenitors. Our data revealed that while allopolyploidization significantly affects the transcriptional landscape, its impact on translation was relatively modest, evidenced by a narrower expression range and fewer expression changes in ribosome-protected fragments than in mRNA levels. Allopolyploid-specific changes commonly identified in both AD₁ and AD₂ were observed in 7393 genes at either transcriptional or translational levels. Interestingly, the majority of translational changes exhibited concordant down-regulation in both ribosome-protected fragments and mRNA, particularly associated with terpenoid synthesis and metabolism (352 genes). Regarding translational efficiency (TE), at least one-fifth of cotton genes exhibit translational level regulation, with a general trend of more down-regulation (13.9–15.1%) than up-regulation (7.3–11.2%) of TE. The magnitude of translational regulation was slightly reduced in allopolyploids compared with diploids, and allopolyploidy tends to have a more profound impact on genes and functional associations with ultra-low TE. Moreover, we demonstrated a reduced extent of homeolog expression biases during translation compared with transcription. Our study provides insights into the regulatory consequences of allopolyploidy post-transcription, contributing to a comprehensive understanding of regulatory mechanisms of duplicated gene expression evolution. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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14 pages, 10653 KiB

Open AccessCommunication

Proteomic and Phosphoproteomic Analyses during Plant Regeneration Initiation in Cotton (Gossypium hirsutum L.)

by Haixia Guo, Jin Wang, Xuehui Huo, Xiwang Cui, Li Zhang, Xiushan Qi, Xiaoying Wu, Junchen Liu, Aijuan Wang, Jialin Liu, Xiangyu Chen, Fanchang Zeng and Huihui Guo

Genes 2024, 15(8), 1079; https://doi.org/10.3390/genes15081079 - 15 Aug 2024

Cited by 1 | Viewed by 1209

Abstract

Somatic embryogenesis (SE) is a biotechnological tool used to generate new individuals and is the preferred method for rapid plant regeneration. However, the molecular basis underlying somatic cell regeneration through SE is not yet fully understood, particularly regarding interactions between the proteome and post-translational modifications. Here, we performed association analysis of high-throughput proteomics and phosphoproteomics in three representative samples (non-embryogenic calli, NEC; primary embryogenic calli, PEC; globular embryos, GE) during the initiation of plant regeneration in cotton, a pioneer crop for genetic biotechnology applications. Our results showed that protein accumulation is positively regulated by phosphorylation during SE, as revealed by correlation analyses. Of the 1418 proteins that were differentially accumulated in the proteome and the 1106 phosphoproteins that were differentially regulated in the phosphoproteome, 115 proteins with 229 phosphorylation sites overlapped (co-differential). Furthermore, seven dynamic trajectory patterns of differentially accumulated proteins (DAPs) and the correlated differentially regulated phosphoproteins (DRPPs) pairs with enrichment features were observed. During the initiation of plant regeneration, functional enrichment analysis revealed that the overlapping proteins (DAPs-DRPPs) were considerably enriched in cellular nitrogen metabolism, spliceosome formation, and reproductive structure development. Moreover, 198 DRPPs (387 phosphorylation sites) were specifically regulated at the phosphorylation level and showed four patterns of stage-enriched phosphorylation susceptibility. Furthermore, enrichment annotation analysis revealed that these phosphoproteins were significantly enriched in endosomal transport and nucleus organization processes. During embryogenic differentiation, we identified five DAPs-DRPPs with significantly enriched characteristic patterns. These proteins may play essential roles in transcriptional regulation and signaling events that initiate plant regeneration through protein accumulation and/or phosphorylation modification. This study enriched the understanding of key proteins and their correlated phosphorylation patterns during plant regeneration, and also provided a reference for improving plant regeneration efficiency. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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11 pages, 7875 KiB

Open AccessArticle

Overexpression of GhGSTF9 Enhances Salt Stress Tolerance in Transgenic Arabidopsis

by Huimin Li, Yihui Liu, Jie Wu, Kexin Chang, Guangqiang Zhang, Hang Zhao, Nianwei Qiu and Ying Bao

Genes 2024, 15(6), 695; https://doi.org/10.3390/genes15060695 - 27 May 2024

Viewed by 1725

Abstract

Soil salinization is a major abiotic stress factor that negatively impacts plant growth, development, and crop yield, severely limiting agricultural production and economic development. Cotton, a key cash crop, is commonly cultivated as a pioneer crop in regions with saline-alkali soil due to its relatively strong tolerance to salt. This characteristic renders it a valuable subject for investigating the molecular mechanisms underlying plant salt tolerance and for identifying genes that confer salt tolerance. In this study, focus was placed on examining a salt-tolerant variety, E991, and a salt-sensitive variety, ZM24. A combined analysis of transcriptomic data from these cotton varieties led to the identification of potential salt stress-responsive genes within the glutathione S-transferase (GST) family. These versatile enzyme proteins, prevalent in animals, plants, and microorganisms, were demonstrated to be involved in various abiotic stress responses. Our findings indicate that suppressing GhGSTF9 in cotton led to a notably salt-sensitive phenotype, whereas heterologous overexpression in Arabidopsis plants decreases the accumulation of reactive oxygen species under salt stress, thereby enhancing salt stress tolerance. This suggests that GhGSTF9 serves as a positive regulator in cotton’s response to salt stress. These results offer new target genes for developing salt-tolerant cotton varieties. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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15 pages, 41162 KiB

Open AccessArticle

GhCLCc-1, a Chloride Channel Gene from Upland Cotton, Positively Regulates Salt Tolerance by Modulating the Accumulation of Chloride Ions

by Wenhao Li, Siqi Gao, Yinghao Zhao, Yuchen Wu, Xiaona Li, Jianing Li, Wei Zhu, Zongbin Ma and Wei Liu

Genes 2024, 15(5), 555; https://doi.org/10.3390/genes15050555 - 26 Apr 2024

Cited by 4 | Viewed by 1355

Abstract

The ionic toxicity induced by salinization has adverse effects on the growth and development of crops. However, researches on ionic toxicity and salt tolerance in plants have focused primarily on cations such as sodium ions (Na⁺), with very limited studies on chloride ions (Cl⁻). Here, we cloned the homologous genes of Arabidopsis thaliana AtCLCc, GhCLCc-1A/D, from upland cotton (Gossypium hirsutum), which were significantly induced by NaCl or KCl treatments. Subcellular localization showed that GhCLCc-1A/D were both localized to the tonoplast. Complementation of Arabidopsis atclcc mutant with GhCLCc-1 rescued its salt-sensitive phenotype. In addition, the silencing of the GhCLCc-1 gene led to an increased accumulation of Cl⁻ in the roots, stems, and leaves of cotton seedlings under salt treatments, resulting in compromised salt tolerance. And ectopic expression of the GhCLCc-1 gene in Arabidopsis reduced the accumulation of Cl⁻ in transgenic lines under salt treatments, thereby enhancing salt tolerance. These findings elucidate that GhCLCc-1 positively regulates salt tolerance by modulating Cl⁻ accumulation and could be a potential target gene for improving salt tolerance in plants. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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10 pages, 2078 KiB

Open AccessArticle

Identification of Crucial Modules and Genes Associated with Bt Gene Expression in Cotton

by Guiyuan Zhao, Zhao Geng, Jianguang Liu, Haiyan Tian, Xu Liu, Zetong An, Ning Zhao, Hanshuang Zhang, Liqiang Wu, Xingfen Wang, Yongqiang Wang and Guiyin Zhang

Genes 2024, 15(4), 515; https://doi.org/10.3390/genes15040515 - 19 Apr 2024

Cited by 1 | Viewed by 1639

Abstract

The expression of Bacillus thuringiensis (Bt) toxins in transgenic cotton confers resistance to insect pests. However, it has been demonstrated that its effectiveness varies among cotton cultivars and different tissues. In this study, we evaluated the expression of Bt protein in 28 cotton cultivars and selected 7 cultivars that differed in Bt protein expression for transcriptome analysis. Based on their Bt protein expression levels, the selected cultivars were categorized into three groups: H (high Bt protein expression), M (moderate expression), and L (low expression). In total, 342, 318, and 965 differentially expressed genes were detected in the H vs. L, M vs. L, and H vs. M comparison groups, respectively. And three modules significantly associated with Bt protein expression were identified by weighted gene co-expression network analysis. Three hub genes were selected to verify their relationships with Bt protein expression using virus-induced gene silencing (VIGS). Silencing GhM_D11G1176, encoding an MYC transcription factor, was confirmed to significantly decrease the expression of Bt protein. The present findings contribute to an improved understanding of the mechanisms that influence Bt protein expression in transgenic cotton. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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15 pages, 2552 KiB

Open AccessEditor’s ChoiceArticle

Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement

by Shang Liu, Hailiang Cheng, Youping Zhang, Man He, Dongyun Zuo, Qiaolian Wang, Limin Lv, Zhongxv Lin and Guoli Song

Genes 2024, 15(3), 378; https://doi.org/10.3390/genes15030378 - 19 Mar 2024

Viewed by 1636

Abstract

Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort’s fingerprint genomic sites. The FPFinder was developed based on the term frequency–inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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19 pages, 4891 KiB

Open AccessArticle

Development of High-Yielding Upland Cotton Genotypes with Reduced Regrowth after Defoliation Using a Combination of Molecular and Conventional Approaches

by Salman Naveed, Johnson Toyinbo, Hrishikesh Ingole, Prasanna Valavanur Shekar, Michael Jones, B. Todd Campbell and Sachin Rustgi

Genes 2023, 14(11), 2081; https://doi.org/10.3390/genes14112081 - 15 Nov 2023

Viewed by 3008

Abstract

Cotton is an economically important crop. However, the yield gain in cotton has stagnated over the years, probably due to its narrow genetic base. The introgression of beneficial variations through conventional and molecular approaches has helped broaden its genetic base to some extent. The growth habit of cotton is one of the crucial factors that determine crop maturation time, yield, and management. This study used 44 diverse upland cotton genotypes to develop high-yielding cotton germplasm with reduced regrowth after defoliation and early maturity by altering its growth habit from perennial to somewhat annual. We selected eight top-scoring genotypes based on the gene expression analysis of five floral induction and meristem identity genes (FT, SOC1, LFY, FUL, and AP1) and used them to make a total of 587 genetic crosses in 30 different combinations of these genotypes. High-performance progeny lines were selected based on the phenotypic data on plant height, flower and boll numbers per plant, boll opening date, floral clustering, and regrowth after defoliation as surrogates of annual growth habit, collected over four years (2019 to 2022). Of the selected lines, 8×5-B3, 8×5-B4, 9×5-C1, 8×9-E2, 8×9-E3, and 39×5-H1 showed early maturity, and 20×37-K1, 20×37-K2, and 20×37-D1 showed clustered flowering, reduced regrowth, high quality of fiber, and high lint yield. In 2022, 15 advanced lines (F₈/F₇) from seven cross combinations were selected and sent for an increase to a Costa Rica winter nursery to be used in advanced testing and for release as germplasm lines. In addition to these breeding lines, we developed molecular resources to breed for reduced regrowth after defoliation and improved yield by converting eight expression-trait-associated SNP markers we identified earlier into a user-friendly allele-specific PCR-based assay and tested them on eight parental genotypes and an F₂ population. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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24 pages, 3777 KiB

Open AccessArticle

Domestication over Speciation in Allopolyploid Cotton Species: A Stronger Transcriptomic Pull

by Josef J. Jareczek, Corrinne E. Grover, Guanjing Hu, Xianpeng Xiong, Mark A. Arick II, Daniel G. Peterson and Jonathan F. Wendel

Genes 2023, 14(6), 1301; https://doi.org/10.3390/genes14061301 - 20 Jun 2023

Cited by 5 | Viewed by 2386

Abstract

Cotton has been domesticated independently four times for its fiber, but the genomic targets of selection during each domestication event are mostly unknown. Comparative analysis of the transcriptome during cotton fiber development in wild and cultivated materials holds promise for revealing how independent domestications led to the superficially similar modern cotton fiber phenotype in upland (G. hirsutum) and Pima (G. barbadense) cotton cultivars. Here we examined the fiber transcriptomes of both wild and domesticated G. hirsutum and G. barbadense to compare the effects of speciation versus domestication, performing differential gene expression analysis and coexpression network analysis at four developmental timepoints (5, 10, 15, or 20 days after flowering) spanning primary and secondary wall synthesis. These analyses revealed extensive differential expression between species, timepoints, domestication states, and particularly the intersection of domestication and species. Differential expression was higher when comparing domesticated accessions of the two species than between the wild, indicating that domestication had a greater impact on the transcriptome than speciation. Network analysis showed significant interspecific differences in coexpression network topology, module membership, and connectivity. Despite these differences, some modules or module functions were subject to parallel domestication in both species. Taken together, these results indicate that independent domestication led G. hirsutum and G. barbadense down unique pathways but that it also leveraged similar modules of coexpression to arrive at similar domesticated phenotypes. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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13 pages, 4343 KiB

Open AccessEditor’s ChoiceArticle

Molecular Characterization of the Acyl-CoA-Binding Protein Genes Reveals Their Significant Roles in Oil Accumulation and Abiotic Stress Response in Cotton

by Yizhen Chen, Mingchuan Fu, Hao Li, Liguo Wang, Renzhong Liu and Zhanji Liu

Genes 2023, 14(4), 859; https://doi.org/10.3390/genes14040859 - 1 Apr 2023

Cited by 3 | Viewed by 1817

Abstract

Members of the acyl-CoA-binding protein (ACBP) gene family play vital roles in diverse processes related to lipid metabolism, growth and development, and environmental response. Plant ACBP genes have been well-studied in a variety of species including Arabidopsis, soybean, rice and maize. However, the identification and functions of ACBP genes in cotton remain to be elucidated. In this study, a total of 11 GaACBP, 12 GrACBP, 20 GbACBP, and 19 GhACBP genes were identified in the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium babardense, and Gossypium hirsutum, respectively, and grouped into four clades. Forty-nine duplicated gene pairs were identified in Gossypium ACBP genes, and almost all of which have undergone purifying selection during the long evolutionary process. In addition, expression analyses showed that most of the GhACBP genes were highly expressed in the developing embryos. Furthermore, GhACBP1 and GhACBP2 were induced by salt and drought stress based on a real-time quantitative PCR (RT-qPCR) assay, indicating that these genes may play an important role in salt- and drought-stress tolerance. This study will provide a basic resource for further functional analysis of the ACBP gene family in cotton. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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19 pages, 9132 KiB

Open AccessArticle

Identification, Classification and Characterization Analysis of FBXL Gene in Cotton

by Jingwen Pan, Muhammad Zulfiqar Ahmad, Shouhong Zhu, Wei Chen, Jinbo Yao, Yan Li, Shengtao Fang, Tengyu Li, Akwasi Yeboah, Liangrong He and Yongshan Zhang

Genes 2022, 13(12), 2194; https://doi.org/10.3390/genes13122194 - 23 Nov 2022

Cited by 2 | Viewed by 2555

Abstract

F-box/LR (FBXL), Leucine-rich repeats in F-box proteins, belongs to the Skp1-Cullin1-F-box protein (SCF) E3 ligase family. FBXL genes play important roles in plant growth, such as plant hormones, responses to environmental stress, and floral organ development. Here, a total of 518 FBXL genes were identified and analyzed in six plant species. Phylogenetic analysis showed that AtFBXLs, VvFBXLs, and GrFBXLs were clustered into three subfamilies (Ⅰ-Ⅲ). Based on the composition of the F-box domain and carboxyl-terminal amino acid sequence, FBXL proteins were classified into three types (Type-A/-B/-C). Whole-genome duplication (WGD) along with tandem duplications and segmental contributed to the expansion of this gene family. The result indicates that four cotton species are also divided into three subfamilies. FBXLs in cotton were classified into three clades by phylogenetic and structural analyses. Furthermore, expression analyses indicated that the expression patterns of GhFBXLs in different cotton tissues were different. The highly expressed of GH_A07G2363 in 5–8 mm anthers, indicates that this gene might play a role in the reproductive process, providing candidate genes for future studies on cotton fertility materials. This study provides an original functional opinion and a useful interpretation of the FBXL protein family in cotton. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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