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Cotton Genes, Genetics, and Genomics
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Cotton Genes, Genetics, and Genomics

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

Deadline for manuscript submissions: 10 May 2024 | Viewed by 7487

Special Issue Editor

Dr. Guanjing Hu

E-Mail Website
Guest Editor
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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Published Papers (5 papers)

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Research

15 pages, 2552 KiB  
Article
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 595
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 [...] Read more.
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  
Article
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 1941
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. [...] Read more.
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  
Article
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 1 | Viewed by 1331
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 [...] Read more.
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  
Article
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 - 01 Apr 2023
Cited by 1 | Viewed by 1151
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 [...] Read more.
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  
Article
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 1 | Viewed by 1539
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 [...] Read more.
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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