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Cotton Molecular Genomics and Genetics
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Cotton Molecular Genomics and Genetics

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 (30 June 2022) | Viewed by 16600

Special Issue Editors

Prof. Dr. Jie Sun

E-Mail Website
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
Dr. Qian-Hao Zhu

E-Mail Website
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
Dr. Shoupu He

E-Mail Website
Guest Editor
1. National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang 455000, China
2. School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
Interests: crop germplasm; crop genomics; gene identification; genetic diversity; population genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

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. Jie Sun
Dr. Qian-Hao Zhu
Dr. Shoupu He
Guest Editors

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

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • 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 (6 papers)

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Research

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18 pages, 2626 KiB  
Article
Comparison of Mitochondrial Genomes between a Cytoplasmic Male-Sterile Line and Its Restorer Line for Identifying Candidate CMS Genes in Gossypium hirsutum
by Lisha Xuan, Guoan Qi, Xiaoran Li, Sunyi Yan, Yiwen Cao, Chujun Huang, Lu He, Tianzhen Zhang, Haihong Shang and Yan Hu
Int. J. Mol. Sci. 2022, 23(16), 9198; https://doi.org/10.3390/ijms23169198 - 16 Aug 2022
Cited by 1 | Viewed by 1634
Abstract
As the core of heterosis utilization, cytoplasmic male sterility (CMS) has been widely used in hybrid seed production. Previous studies have shown that CMS is always closely related to the altered programming of mitochondrial genes. To explore candidate CMS genes in cotton ( [...] Read more.
As the core of heterosis utilization, cytoplasmic male sterility (CMS) has been widely used in hybrid seed production. Previous studies have shown that CMS is always closely related to the altered programming of mitochondrial genes. To explore candidate CMS genes in cotton (Gossypium hirsutum), sequencing and de novo assembly were performed on the mitochondrial genome of the G. hirsutum CMS line SI3A, with G. harknessii CMS-D2 cytoplasm, and the corresponding G. hirsutum restorer line 0-613-2R. Remarkable variations in genome structure and gene transcripts were detected. The mitochondrial genome of SI3A has three circle molecules, including one main circle and two sub-circles, while 0-613-2R only has one. RNA-seq and RT-qPCR analysis proved that orf606a and orf109a, which have a chimeric structure and transmembrane domain, were highly expressed in abortive anthers of SI3A. In addition, comparative analysis of RNA-seq and full-length transcripts revealed the complex I gene nad4 to be expressed at a lower level in SI3A than in its restorer and that it featured an intron retention splicing pattern. These two novel chimeric ORFs and nad4 are potential candidates that confer CMS character in SI3A. This study provides new insight into the molecular basis of the nuclear–cytoplasmic interaction mechanism, and that putative CMS genes might be important sources for future precise design cross-breeding of cotton. Full article
(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics)
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11 pages, 2253 KiB  
Article
A Rapid and Efficient Method for Isolation and Transformation of Cotton Callus Protoplast
by Peilin Wang, Yuanchun Pu, Muhammad Ali Abid, Linglin Kang, Yulu Ye, Man Zhang, Chengzhen Liang, Yunxiao Wei, Rui Zhang and Zhigang Meng
Int. J. Mol. Sci. 2022, 23(15), 8368; https://doi.org/10.3390/ijms23158368 - 28 Jul 2022
Cited by 11 | Viewed by 3688
Abstract
Protoplasts, which lack cell walls, are ideal research materials for genetic engineering. They are commonly employed in fusion (they can be used for more distant somatic cell fusion to obtain somatic hybrids), genetic transformation, plant regeneration, and other applications. Cotton is grown throughout [...] Read more.
Protoplasts, which lack cell walls, are ideal research materials for genetic engineering. They are commonly employed in fusion (they can be used for more distant somatic cell fusion to obtain somatic hybrids), genetic transformation, plant regeneration, and other applications. Cotton is grown throughout the world and is the most economically important crop globally. It is therefore critical to study successful extraction and transformation efficiency of cotton protoplasts. In the present study, a cotton callus protoplast extraction method was tested to optimize the ratio of enzymes (cellulase, pectinase, macerozyme R-10, and hemicellulase) used in the procedure. The optimized ratio significantly increased the quantity and activity of protoplasts extracted. We showed that when enzyme concentrations of 1.5% cellulase and 1.5% pectinase, and either 1.5% or 0.5% macerozyme and 0.5% hemicellulase were used, one can obtain increasingly stable protoplasts. We successfully obtained fluorescent protoplasts by transiently expressing fluorescent proteins in the isolated protoplasts. The protoplasts were determined to be suitable for use in further experimental studies. We also studied the influence of plasmid concentration and transformation time on protoplast transformation efficiency. When the plasmid concentration reaches 16 µg and the transformation time is controlled within 12–16 h, the best transformation efficiency can be obtained. In summary, this study presents efficient extraction and transformation techniques for cotton protoplasts. Full article
(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics)
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20 pages, 5675 KiB  
Article
Transcriptome Profiling Provides New Insights into the Molecular Mechanism Underlying the Sensitivity of Cotton Varieties to Mepiquat Chloride
by Zhijun Wang, Yanjun Li, Qianhao Zhu, Liwen Tian, Feng Liu, Xinyu Zhang and Jie Sun
Int. J. Mol. Sci. 2022, 23(9), 5043; https://doi.org/10.3390/ijms23095043 - 02 May 2022
Cited by 2 | Viewed by 1764
Abstract
Mepiquat chloride (MC) is a plant growth regulator widely used in cotton production to control vegetative overgrowth of cotton plants to achieve ideal plant architecture required for high yielding. Cotton varieties respond differently to MC application, but there is little information about the [...] Read more.
Mepiquat chloride (MC) is a plant growth regulator widely used in cotton production to control vegetative overgrowth of cotton plants to achieve ideal plant architecture required for high yielding. Cotton varieties respond differently to MC application, but there is little information about the molecular mechanisms underlying the varietal difference. In this study, comparative transcriptome analysis was conducted by using two Upland cotton varieties with different sensitivity (XLZ74, insensitive; SD1068, sensitive) to MC treatment, aiming to understand the molecular mechanisms responsible for varietal difference of MC sensitivity. RNA-seq data were generated from the two varieties treated with MC or water at three time points, 1, 3 and 6 days post-spray (dps). Genes differentially expressed between the MC and mock treatments of XLZ74 (6252) and SD1068 (6163) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to compare the enriched GO terms and KEGG pathways between the two varieties. Signal transduction of phytohormones, biosynthesis of gibberellins (GAs) and brassinosteroids (BRs) and profiles of transcription factors (TFs) seemed to be differentially affected by MC in the two varieties. The transcriptomic results were further consolidated with the content changes of phytohormones in young stem. Several GA catabolic genes, GA2ox, were highly induced by MC in both varieties especially in SD1068, consistent with a more significant decrease in GA4 in SD1068. Several AUX/IAA and SAUR genes and CKX genes were induced by MC in both varieties, but with a more profound effect observed in SD1068 that showed a significant reduction in indole-3-acetic acid (IAA) and a significant increase in cytokinin (CTK) at 6 days post-spray (dps). BR biosynthesis-related genes were downregulated in SD1068, but not in XLZ74. Additionally, more downregulated TFs were observed in MC-treated SD1068 than in MC-treated XLZ74, and the two varieties had very different profiles of genes involved in starch and sucrose metabolism, with those of SD1068 and XLZ74 being downregulated and upregulated by MC treatment, respectively. Together, these results indicate that although the same or similar biological pathways are affected by MC treatment in cotton varieties showing different MC sensitivity, the extent of effect is variable, leading to their different phenotypic outcomes. How the quantitative effect of MC on the biological processes associated with growth retardation is regulated is still an open question. Full article
(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics)
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31 pages, 6858 KiB  
Article
Dynamic Expression, Differential Regulation and Functional Diversity of the CNGC Family Genes in Cotton
by Junheng Zhao, Song Peng, Hongtu Cui, Panyu Li, Tianming Li, Luole Liu, Hanfeng Zhang, Zengyuan Tian, Haihong Shang and Ruqiang Xu
Int. J. Mol. Sci. 2022, 23(4), 2041; https://doi.org/10.3390/ijms23042041 - 12 Feb 2022
Cited by 8 | Viewed by 2427
Abstract
Cyclic nucleotide-gated channels (CNGCs) constitute a family of non-selective cation channels that are primarily permeable to Ca2+ and activated by the direct binding of cyclic nucleotides (i.e., cAMP and cGMP) to mediate cellular signaling, both in animals and plants. Until now, our [...] Read more.
Cyclic nucleotide-gated channels (CNGCs) constitute a family of non-selective cation channels that are primarily permeable to Ca2+ and activated by the direct binding of cyclic nucleotides (i.e., cAMP and cGMP) to mediate cellular signaling, both in animals and plants. Until now, our understanding of CNGCs in cotton (Gossypium spp.) remains poorly addressed. In the present study, we have identified 40, 41, 20, 20, and 20 CNGC genes in G. hirsutum, G. barbadense, G. herbaceum, G. arboreum, and G. raimondii, respectively, and demonstrated characteristics of the phylogenetic relationships, gene structures, chromosomal localization, gene duplication, and synteny. Further investigation of CNGC genes in G. hirsutum, named GhCNGC1-40, indicated that they are not only extensively expressed in various tissues and at different developmental stages, but also display diverse expression patterns in response to hormones (abscisic acid, salicylic acid, methyl jasmonate, ethylene), abiotic (salt stress) and biotic (Verticillium dahlia infection) stimuli, which conform with a variety of cis-acting regulatory elements residing in the promoter regions; moreover, a set of GhCNGCs are responsive to cAMP signaling during cotton fiber development. Protein–protein interactions supported the functional aspects of GhCNGCs in plant growth, development, and stress responses. Accordingly, the silencing of the homoeologous gene pair GhCNGC1&18 and GhCNGC12&31 impaired plant growth and development; however, GhCNGC1&18-silenced plants enhanced Verticillium wilt resistance and salt tolerance, whereas GhCNGC12&31-silenced plants had opposite effects. Together, these results unveiled the dynamic expression, differential regulation, and functional diversity of the CNGC family genes in cotton. The present work has laid the foundation for further studies and the utilization of CNGCs in cotton genetic improvement. Full article
(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics)
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Review

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16 pages, 2703 KiB  
Review
Molecular Regulation of Cotton Fiber Development: A Review
by Masood Jan, Zhixin Liu, Chenxi Guo and Xuwu Sun
Int. J. Mol. Sci. 2022, 23(9), 5004; https://doi.org/10.3390/ijms23095004 - 30 Apr 2022
Cited by 20 | Viewed by 3906
Abstract
Cotton (Gossypium spp.) is an economically important natural fiber crop. The quality of cotton fiber has a substantial effect on the quality of cotton textiles. The identification of cotton fiber development-related genes and exploration of their biological functions will not only enhance [...] Read more.
Cotton (Gossypium spp.) is an economically important natural fiber crop. The quality of cotton fiber has a substantial effect on the quality of cotton textiles. The identification of cotton fiber development-related genes and exploration of their biological functions will not only enhance our understanding of the elongation and developmental mechanisms of cotton fibers but also provide insights that could aid the cultivation of new cotton varieties with improved fiber quality. Cotton fibers are single cells that have been differentiated from the ovule epidermis and serve as a model system for research on single-cell differentiation, growth, and fiber production. Genes and fiber formation mechanisms are examined in this review to shed new light on how important phytohormones, transcription factors, proteins, and genes linked to fiber development work together. Plant hormones, which occur in low quantities, play a critically important role in regulating cotton fiber development. Here, we review recent research that has greatly contributed to our understanding of the roles of different phytohormones in fiber development and regulation. We discuss the mechanisms by which phytohormones regulate the initiation and elongation of fiber cells in cotton, as well as the identification of genes involved in hormone biosynthetic and signaling pathways that regulate the initiation, elongation, and development of cotton fibers. Full article
(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics)
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11 pages, 1936 KiB  
Review
An Overview of Cotton Gland Development and Its Transcriptional Regulation
by Masood Jan, Zhixin Liu, Chenxi Guo, Yaping Zhou and Xuwu Sun
Int. J. Mol. Sci. 2022, 23(9), 4892; https://doi.org/10.3390/ijms23094892 - 28 Apr 2022
Cited by 5 | Viewed by 2094
Abstract
Cotton refers to species in the genus Gossypium that bear spinnable seed coat fibers. A total of 50 species in the genus Gossypium have been described to date. Of these, only four species, viz. Gossypium, hirsutum, G. barbadense, G. arboretum, and G. [...] Read more.
Cotton refers to species in the genus Gossypium that bear spinnable seed coat fibers. A total of 50 species in the genus Gossypium have been described to date. Of these, only four species, viz. Gossypium, hirsutum, G. barbadense, G. arboretum, and G. herbaceum are cultivated; the rest are wild. The black dot-like structures on the surfaces of cotton organs or tissues, such as the leaves, stem, calyx, bracts, and boll surface, are called gossypol glands or pigment glands, which store terpenoid aldehydes, including gossypol. The cotton (Gossypium hirsutum) pigment gland is a distinctive structure that stores gossypol and its derivatives. It provides an ideal system for studying cell differentiation and organogenesis. However, only a few genes involved in the process of gland formation have been identified to date, and the molecular mechanisms underlying gland initiation remain unclear. The terpenoid aldehydes in the lysigenous glands of Gossypium species are important secondary phytoalexins (with gossypol being the most important) and one of the main defenses of plants against pests and diseases. Here, we review recent research on the development of gossypol glands in Gossypium species, the regulation of the terpenoid aldehyde biosynthesis pathway, discoveries from genetic engineering studies, and future research directions. Full article
(This article belongs to the Special Issue Cotton Molecular Genomics and Genetics)
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