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Cotton Molecular Genomics and Genetics 2.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (15 January 2024) | Viewed by 13999

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Dr. Qian-Hao Zhu

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Guest Editor

CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
Interests: cotton biology; genomics; molecular breeding; plant noncoding RNAs; biostress tolerance
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Jie Sun

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Guest Editor

Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, China
Interests: cotton genetics; genomics; molecular breeding; genetic improvement
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Cotton (Gossypium spp.) is not only the most important fiber crop for the global textile industry, but it also serves as a model system to study plant cell growth and development, because a cotton fiber cell is the longest currently known cell in the plant kingdom. During the past few decades, cotton researchers have devoted tremendous efforts to developing molecular, genetic and genomic tools which are being used to better understand the biology of cotton plants. High-quality genome assemblies have been published. New technologies such as CRISPR gene editing are being exploited for varietal improvement. With many accomplishments achieved and more exciting developments on the horizon, a Special Issue on “Cotton molecular genetics and genomics” is warranted.

Papers submitted to this Special Issue must report highly novel results in the areas of molecular genetics and genomics of cotton. More specifically, this Special Issue will cover a selection of original research and review articles focusing on gene identification and functionality analysis, genomic prediction and selection, trait QTL analysis, application of omics and gene-editing tools to the enhancement of cotton breeding, and new methods/strategies to conduct genetic and genomic research. In addition, databases related to the subject of interest are also welcome.

Dr. Qian-Hao Zhu
Prof. Dr. Jie Sun
Guest Editors

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

cotton
biotic or abiotic stress
disease resistance
fiber yield and quality
gene editing； gene identification and function validation
genome-wide association study
QTL identification

Published Papers (9 papers)

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Research

24 pages, 5212 KiB

Open AccessArticle

Genetic Channelization Mechanism of Four Chalcone Isomerase Homologous Genes for Synergistic Resistance to Fusarium wilt in Gossypium barbadense L.

by Qianli Zu, Xiaojuan Deng, Yanying Qu, Xunji Chen, Yongsheng Cai, Caoyue Wang, Ying Li, Qin Chen, Kai Zheng, Xiaodong Liu and Quanjia Chen

Int. J. Mol. Sci. 2023, 24(19), 14775; https://doi.org/10.3390/ijms241914775 - 30 Sep 2023

Viewed by 763

Abstract

Duplication events occur very frequently during plant evolution. The genes in the duplicated pathway or network can evolve new functions through neofunctionalization and subfunctionalization. Flavonoids are secondary metabolites involved in plant development and defense. Our previous transcriptomic analysis of F6 recombinant inbred lines (RILs) and the parent lines after Fusarium oxysporum f. sp. vasinfectum (Fov) infection showed that CHI genes have important functions in cotton. However, there are few reports on the possible neofunctionalization differences of CHI family paralogous genes involved in Fusarium wilt resistance in cotton. In this study, the resistance to Fusarium wilt, expression of metabolic pathway-related genes, metabolite content, endogenous hormone content, reactive oxygen species (ROS) content and subcellular localization of four paralogous CHI family genes in cotton were investigated. The results show that the four paralogous CHI family genes may play a synergistic role in Fusarium wilt resistance. These results revealed a genetic channelization mechanism that can regulate the metabolic flux homeostasis of flavonoids under the mediation of endogenous salicylic acid (SA) and methyl jasmonate (MeJA) via the four paralogous CHI genes, thereby achieving disease resistance. Our study provides a theoretical basis for studying the evolutionary patterns of homologous plant genes and using homologous genes for molecular breeding. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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27 pages, 13645 KiB

Open AccessArticle

Comprehensive Evaluation and Transcriptome Analysis Reveal the Salt Tolerance Mechanism in Semi-Wild Cotton (Gossypium purpurascens)

by Zhen Peng, Abdul Rehman, Xiawen Li, Xuran Jiang, Chunyan Tian, Xiaoyang Wang, Hongge Li, Zhenzhen Wang, Shoupu He and Xiongming Du

Int. J. Mol. Sci. 2023, 24(16), 12853; https://doi.org/10.3390/ijms241612853 - 16 Aug 2023

Cited by 4 | Viewed by 1381

Abstract

Elevated salinity significantly threatens cotton growth, particularly during the germination and seedling stages. The utilization of primitive species of Gossypium hirsutum, specifically Gossypium purpurascens, has the potential to facilitate the restoration of genetic diversity that has been depleted due to selective breeding in modern cultivars. This investigation evaluated 45 G. purpurascens varieties and a salt-tolerant cotton variety based on 34 morphological, physiological, and biochemical indicators and comprehensive salt tolerance index values. This study effectively identified a total of 19 salt-tolerant and two salt-resistant varieties. Furthermore, transcriptome sequencing of a salt-tolerant genotype (Nayanmian-2; NY2) and a salt-sensitive genotype (Sanshagaopao-2; GP2) revealed 2776, 6680, 4660, and 4174 differentially expressed genes (DEGs) under 0.5, 3, 12, and 24 h of salt stress. Gene ontology enrichment analysis indicated that the DEGs exhibited significant enrichment in biological processes like metabolic (GO:0008152) and cellular (GO:0009987) processes. MAPK signaling, plant-pathogen interaction, starch and sucrose metabolism, plant hormone signaling, photosynthesis, and fatty acid metabolism were identified as key KEGG pathways involved in salinity stress. Among the DEGs, including NAC, MYB, WRKY, ERF, bHLH, and bZIP, transcription factors, receptor-like kinases, and carbohydrate-active enzymes were crucial in salinity tolerance. Weighted gene co-expression network analysis (WGCNA) unveiled associations of salt-tolerant genotypes with flavonoid metabolism, carbon metabolism, and MAPK signaling pathways. Identifying nine hub genes (MYB4, MYB105, MYB36, bZIP19, bZIP43, FRS2 SMARCAL1, BBX21, F-box) across various intervals offered insights into the transcriptional regulation mechanism of salt tolerance in G. purpurascens. This study lays the groundwork for understanding the important pathways and gene networks in response to salt stress, thereby providing a foundation for enhancing salt tolerance in upland cotton. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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19 pages, 9229 KiB

Open AccessArticle

Identification and Evolutionary Analysis of Cotton (Gossypium hirsutum) WOX Family Genes and Their Potential Function in Somatic Embryogenesis

by Ruibin Sun, Xue Zhang, Dan Ma and Chuanliang Liu

Int. J. Mol. Sci. 2023, 24(13), 11077; https://doi.org/10.3390/ijms241311077 - 04 Jul 2023

Cited by 7 | Viewed by 1376

Abstract

WUSCHEL-related homeobox (WOX) proteins participate profoundly in plant development and stress responses. As the difficulty of somatic embryogenesis severely constrains cotton genetic modification, in this study, we identified and comprehensively analyzed WOX genes in cotton. As a result, 40 WOX genes were identified in the upland cotton genome. All these cotton WOX genes were classified into three clades, ancient, intermediate, and modern clades, based on the phylogenetic analysis of previous studies. The majority (24) of the cotton WOX genes belonged to the modern clade, in which all gene members contain the vital functional domain WUS-box, which is necessary for plant stem cell regulation and maintenance. Collinearity analysis indicated that the WOX gene family in cotton expanded to some degree compared to Arabidopsis, especially in the modern clade. Genome duplication and segmental duplication may greatly contribute to expansion. Hormone-response- and abiotic-stress-response-related cis-acting regulatory elements were widely distributed in the promoter regions of cotton WOX genes, suggesting that the corresponding functions of stress responses and the participation of development processes were involved in hormone responses. By RNA sequencing, we profiled the expression patterns of cotton WOX genes in somatic embryogenesis. Only about half of cotton WOX genes were actively expressed during somatic embryogenesis; different cotton WOX genes may function in different development stages. The most representative, GhWOX4 and GhWOX13, may function in almost all stages of somatic embryogenesis; GhWOX2 and GhWOX9 function in the late stages of embryo patterning and embryo development during cotton somatic embryogenesis. Co-expression analysis showed that the cotton WOXs co-expressed with genes involved in extensive genetic information processing, including DNA replication, DNA repair, homologous recombination, RNA transport, protein processing, and several signaling and metabolism pathways, in which plant hormones signal transduction, MAPK signaling pathways, phosphatidylinositol signaling systems, and ABC transporters, as well as the metabolism of fatty acid; valine, leucine, and isoleucine biosynthesis; and cutin, suberine, and wax biosynthesis, were most significantly enriched. Taken together, the present study provides useful information and new insights into the functions of cotton WOX genes during somatic embryogenesis. The specific regulatory roles of some WOX genes in somatic embryogenesis are worthy of further functional research. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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17 pages, 2986 KiB

Open AccessArticle

Genome-Wide Association Study of Lint Percentage in Gossypium hirsutum L. Races

by Yuanyuan Wang, Xinlei Guo, Xiaoyan Cai, Yanchao Xu, Runrun Sun, Muhammad Jawad Umer, Kunbo Wang, Tengfei Qin, Yuqing Hou, Yuhong Wang, Pan Zhang, Zihan Wang, Fang Liu, Qinglian Wang and Zhongli Zhou

Int. J. Mol. Sci. 2023, 24(12), 10404; https://doi.org/10.3390/ijms241210404 - 20 Jun 2023

Cited by 1 | Viewed by 1203

Abstract

Lint percentage is one of the most essential yield components and an important economic index for cotton planting. Improving lint percentage is an effective way to achieve high-yield in cotton breeding worldwide, especially upland cotton (Gossypium hirsutum L.). However, the genetic basis controlling lint percentage has not yet been systematically understood. Here, we performed a genome-wide association mapping for lint percentage using a natural population consisting of 189 G. hirsutum accessions (188 accessions of G. hirsutum races and one cultivar TM-1). The results showed that 274 single-nucleotide polymorphisms (SNPs) significantly associated with lint percentage were detected, and they were distributed on 24 chromosomes. Forty-five SNPs were detected at least by two models or at least in two environments, and their 5 Mb up- and downstream regions included 584 makers related to lint percentage identified in previous studies. In total, 11 out of 45 SNPs were detected at least in two environments, and their 550 Kb up- and downstream region contained 335 genes. Through RNA sequencing, gene annotation, qRT-PCR, protein–protein interaction analysis, the cis-elements of the promotor region, and related miRNA prediction, Gh_D12G0934 and Gh_A08G0526 were selected as key candidate genes for fiber initiation and elongation, respectively. These excavated SNPs and candidate genes could supplement marker and gene information for deciphering the genetic basis of lint percentage and facilitate high-yield breeding programs of G. hirsutum ultimately. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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19 pages, 8681 KiB

Open AccessArticle

Genome-Wide Analysis and Functional Characterization of LACS Gene Family Associated with Lipid Synthesis in Cotton (Gossypium spp.)

by Yike Zhong, Yongbo Wang, Pengtao Li, Wankui Gong, Xiaoyu Wang, Haoliang Yan, Qun Ge, Aiying Liu, Yuzhen Shi, Haihong Shang, Yuanming Zhang, Juwu Gong and Youlu Yuan

Int. J. Mol. Sci. 2023, 24(10), 8530; https://doi.org/10.3390/ijms24108530 - 10 May 2023

Cited by 3 | Viewed by 1428

Abstract

Cotton (Gossypium spp.) is the fifth largest oil crop in the world, and cottonseed provides abundant vegetable oil resources and industrial bioenergy fuels for people; therefore, it is of practical significance to increase the oil content of cotton seeds for improving the oil yield and economic benefits of planting cotton. Long-chain acyl-coenzyme A (CoA) synthetase (LACS) capable of catalyzing the formation of acyl-CoAs from free fatty acids has been proven to significantly participate in lipid metabolism, of which whole-genome identification and functional characterization of the gene family have not yet been comprehensively analyzed in cotton. In this study, a total of sixty-five LACS genes were confirmed in two diploid and two tetraploid Gossypium species, which were divided into six subgroups based on phylogenetic relationships with twenty-one other plants. An analysis of protein motif and genomic organizations displayed structural and functional conservation within the same group but diverged among the different group. Gene duplication relationship analysis illustrates the LACS gene family in large scale expansion through WGDs/segmental duplications. The overall Ka/Ks ratio indicated the intense purifying selection of LACS genes in four cotton species during evolution. The LACS genes promoter elements contain numerous light response cis-elements associated with fatty acids synthesis and catabolism. In addition, the expression of almost all GhLACS genes in high seed oil were higher compared to those in low seed oil. We proposed LACS gene models and shed light on their functional roles in lipid metabolism, demonstrating their engineering potential for modulating TAG synthesis in cotton, and the genetic engineering of cottonseed oil provides a theoretical basis. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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20 pages, 7875 KiB

Open AccessArticle

Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton

by Zhengwen Liu, Zhengwen Sun, Huifeng Ke, Bin Chen, Qishen Gu, Man Zhang, Nan Wu, Liting Chen, Yanbin Li, Chengsheng Meng, Guoning Wang, Liqiang Wu, Guiyin Zhang, Zhiying Ma, Yan Zhang and Xingfen Wang

Int. J. Mol. Sci. 2023, 24(9), 8293; https://doi.org/10.3390/ijms24098293 - 05 May 2023

Cited by 3 | Viewed by 1331

Abstract

Comparative transcriptome analysis of fiber tissues between Gossypium barbadense and Gossypium hirsutum could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in G. barbadense, which showed four distinct expression patterns (I–IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between G. barbadense and G. hirsutum. Subsequently, we overexpressed GbAAR3 and GbTWS1, two of the 42 candidate genes, in Arabidopsis plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I–V) in G. barbadense. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their G. hirsutum orthologs, and the genotyping and phenotyping of a BC₃F₅ population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between G. barbadense and G. hirsutum and provide novel alternative genes for fiber quality improvement. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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20 pages, 4756 KiB

Open AccessArticle

Genome-Wide Investigation and Co-Expression Network Analysis of SBT Family Gene in Gossypium

by Tianxi Xue, Lisen Liu, Xinyi Zhang, Zhongqiu Li, Minghao Sheng, Xiaoyang Ge, Wenying Xu and Zhen Su

Int. J. Mol. Sci. 2023, 24(6), 5760; https://doi.org/10.3390/ijms24065760 - 17 Mar 2023

Cited by 4 | Viewed by 1638

Abstract

Subtilases (SBTs), which belong to the serine peptidases, control plant development by regulating cell wall properties and the activity of extracellular signaling molecules, and affect all stages of the life cycle, such as seed development and germination, and responses to biotic and abiotic environments. In this study, 146 Gossypium hirsutum, 138 Gossypium barbadense, 89 Gossypium arboreum and 84 Gossypium raimondii SBTs were identified and divided into six subfamilies. Cotton SBTs are unevenly distributed on chromosomes. Synteny analysis showed that the members of SBT1 and SBT4 were expanded in cotton compared to Arabidopsis thaliana. Co-expression network analysis showed that six Gossypium arboreum SBT gene family members were in a network, among which five SBT1 genes and their Gossypium hirsutum and Arabidopsis thaliana direct homologues were down-regulated by salt treatment, indicating that the co-expression network might share conserved functions. Through co-expression network and annotation analysis, these SBTs may be involved in the biological processes of auxin transport, ABA signal transduction, cell wall repair and root tissue development. In summary, this study provides valuable information for the study of SBT genes in cotton and excavates SBT genes in response to salt stress, which provides ideas for cotton breeding for salinity resistance. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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14 pages, 1283 KiB

Open AccessArticle

Impact of Caterpillar Increased Feeding Rates on Reduction of Bt Susceptibility

by Anirudh Dhammi, Jaap B. van Krestchmar, Jiwei Zhu, Loganathan Ponnusamy, Fred Gould, Dominic Reisig, Ryan W. Kurtz and R. Michael Roe

Int. J. Mol. Sci. 2022, 23(23), 14856; https://doi.org/10.3390/ijms232314856 - 28 Nov 2022

Viewed by 1380

Abstract

The use of insect-resistant transgenic crops producing Bacillus thuringiensis protein Cry toxins (Bt) to control caterpillars is wide-spread. Development of a mechanism to prevent Bt from reaching its target site in the digestive system could result in Bt resistance and resistance to other insecticides active per os. Increased feeding rates by increasing temperature in tobacco budworms, Chloridea virescens, and bollworms, Helicoverpa zea, decreased Bt Cry1Ac susceptibility and mortality. The same was found in C. virescens for Bollgard II plant extract containing Bt Cry1Ac and Cry2Ab2 toxins. Furthermore, H. zea from the same inbred laboratory colony that fed faster independent of temperature manipulation were less susceptible to Bt intoxication. A laboratory derived C. virescens Bt resistant strain demonstrated a higher feeding rate on non-Bt artificial diet than the parental, Bt susceptible strain. A laboratory-reared Bt resistant fall armyworm, Spodoptera frugiperda, strain also fed faster on non-Bt diet compared to Bt susceptible caterpillars of the same species, both originally collected from corn. The studies in toto and the literature reviewed support the hypothesis that increased feeding rate is a behavioral mechanism for reducing caterpillar susceptibility to Bt. Its possible role in resistance needs further study. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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18 pages, 4311 KiB

Open AccessArticle

Comparative Metabolome and Transcriptome Analysis of Anthocyanin Biosynthesis in White and Pink Petals of Cotton (Gossypium hirsutum L.)

by Dongnan Shao, Qian Liang, Xuefeng Wang, Qian-Hao Zhu, Feng Liu, Yanjun Li, Xinyu Zhang, Yonglin Yang, Jie Sun and Fei Xue

Int. J. Mol. Sci. 2022, 23(17), 10137; https://doi.org/10.3390/ijms231710137 - 04 Sep 2022

Cited by 8 | Viewed by 2155

Abstract

Upland cotton (Gossypium hirsutum L.) is one of the important fiber crops. Cotton flowers usually appear white (or cream-colored) without colored spots at the petal base, and turn pink on the next day after flowering. In this study, using a mutant showing pink petals with crimson spots at their base, we conducted comparative metabolome and transcriptome analyses to investigate the molecular mechanism of coloration in cotton flowers. Metabolic profiling showed that cyanidin-3-O-glucoside and glycosidic derivatives of pelargonidins and peonidins are the main pigments responsible for the coloration of the pink petals of the mutant. A total of 2443 genes differentially expressed (DEGs) between the white and pink petals were identified by RNA-sequencing. Many DEGs are structural genes and regulatory genes of the anthocyanin biosynthesis pathway. Among them, MYB21, UGT88F3, GSTF12, and VPS32.3 showed significant association with the accumulation of cyanidin-3-O-glucoside in the pink petals. Taken together, our study preliminarily revealed the metabolites responsible for the pink petals and the key genes regulating the biosynthesis and accumulation of anthocyanins in the pink petals. The results provide new insights into the biochemical and molecular mechanism underlying anthocyanin biosynthesis in upland cotton. Full article

(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics 2.0)

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