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Advances in Cotton Genomics, Genetics and Breeding
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Advances in Cotton Genomics, Genetics and Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Crop Physiology and Crop Production".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 10640

Special Issue Editors

Dr. Tianlun Zhao

E-Mail Website
Guest Editor
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: cotton genomics; genetics; breeding; single-cell RNA transcriptome analysis
Dr. Zhanfeng Si

E-Mail Website
Guest Editor
The Rural Development Academy, Zhejiang University, Hangzhou 310058, China
Interests: cotton germplasm; genetics and breeding; QTL mapping
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

Special Issue Information

Dear Colleagues,

Cotton is one of the most critical cash crops worldwide, providing not only natural fiber for the textile industry, but also cottonseeds containg superior oil and protein for other industries. The cotton industry is worthing an economic value of about 500 billion USD per annum, and provides work positions and incomes for about 100 million families worldwide. Due to the demand for high-yeild cotton varieties, high-quality cotton fiber and cottonseeds, modern cotton breeding practices need to integrate diverse germplasm with a wide range of genetic tools and to take account of dynamic climate changes, such as global warming and drought. With the rapid development of high-throughput genome sequencing, many cotton genomes have been sequenced, assemblied and annotated, providing a great opportunity for comparative genomics research, genetic analysis and fine mapping of agronomic traits, mining genes underpinning important agronomic traits, gene functional verification, genetic transformation, etc. Molecular technology and biotechnology have achieved tremendous progress, especially gene editing technology, for instance, CRISPR/Cas9, which has enormous potential in cotton breeding through harnessing genetic diversities related to superior agronomic traits. Nowadays, marker-assisted selection, genetic transformation and genomic prediction enabled precision breeding, revolutionizing cotton breeding practices, and they are anticipated to have a profound impact on cotton production in the near future. In this Special Issue, we will report progresses on all aspects of cotton genomics, genetics and breeding.

Dr. Tianlun Zhao
Dr. Zhanfeng Si
Dr. Qian-Hao Zhu
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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
  • genomics
  • genetics
  • breeding
  • fiber
  • seed
  • yield
  • quality
  • agronomic trait

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Published Papers (7 papers)

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Editorial

Jump to: Research, Review

3 pages, 163 KiB  
Editorial
Advances in Cotton Genomics, Genetics and Breeding
by Tianxu Zhang, Shuhui Wang, Jinhong Chen, Shuijin Zhu, Qianhao Zhu and Tianlun Zhao
Plants 2024, 13(18), 2579; https://doi.org/10.3390/plants13182579 - 14 Sep 2024
Viewed by 672
Abstract
The cotton is an industrial crop of global significance, providing its fibers for the predominant textile material and its seed accumulating abundant oil and protein for other utilizations [...] Full article
(This article belongs to the Special Issue Advances in Cotton Genomics, Genetics and Breeding)

Research

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15 pages, 2891 KiB  
Article
Quantitative Trait Locus Mapping for Plant Height and Branch Number in CCRI70 Recombinant Inbred Line Population of Upland Cotton (Gossypium hirsutum)
by Gangling Li, Jincan Che, Juwu Gong, Li Duan, Zhen Zhang, Xiao Jiang, Peng Xu, Senmiao Fan, Wankui Gong, Yuzhen Shi, Aiying Liu, Junwen Li, Pengtao Li, Jingtao Pan, Xiaoying Deng, Youlu Yuan and Haihong Shang
Plants 2024, 13(11), 1509; https://doi.org/10.3390/plants13111509 - 30 May 2024
Cited by 1 | Viewed by 779
Abstract
Upland cotton accounts for a high percentage (95%) of the world’s cotton production. Plant height (PH) and branch number (BN) are two important agronomic traits that have an impact on improving the level of cotton mechanical harvesting and cotton yield. In this research, [...] Read more.
Upland cotton accounts for a high percentage (95%) of the world’s cotton production. Plant height (PH) and branch number (BN) are two important agronomic traits that have an impact on improving the level of cotton mechanical harvesting and cotton yield. In this research, a recombinant inbred line (RIL) population with 250 lines developed from the variety CCRI70 was used for constructing a high-density genetic map and identification of quantitative trait locus (QTL). The results showed that the map harbored 8298 single nucleotide polymorphism (SNP) markers, spanning a total distance of 4876.70 centimorgans (cMs). A total of 69 QTLs for PH (9 stable) and 63 for BN (11 stable) were identified and only one for PH was reported in previous studies. The QTLs for PH and BN harbored 495 and 446 genes, respectively. Combining the annotation information, expression patterns and previous studies of these genes, six genes could be considered as potential candidate genes for PH and BN. The results could be helpful for cotton researchers to better understand the genetic mechanism of PH and BN development, as well as provide valuable genetic resources for cotton breeders to manipulate cotton plant architecture to meet future demands. Full article
(This article belongs to the Special Issue Advances in Cotton Genomics, Genetics and Breeding)
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17 pages, 3149 KiB  
Article
Zinc Oxide Nanoparticles and Zinc Sulfate Alleviate Boron Toxicity in Cotton (Gossypium hirsutum L.)
by Ismail Sanusi Nassarawa, Zhuolin Li, Longshuo Xue, Huazu Li, Uzair Muhammad, Shuijin Zhu, Jinhong Chen and Tianlun Zhao
Plants 2024, 13(9), 1184; https://doi.org/10.3390/plants13091184 - 24 Apr 2024
Cited by 1 | Viewed by 1342
Abstract
Boron toxicity significantly hinders the growth and development of cotton plants, therefore affecting the yield and quality of this important cash crop worldwide. Limited studies have explored the efficacy of ZnSO4 (zinc sulfate) and ZnO nanoparticles (NPs) in alleviating boron toxicity. Nanoparticles [...] Read more.
Boron toxicity significantly hinders the growth and development of cotton plants, therefore affecting the yield and quality of this important cash crop worldwide. Limited studies have explored the efficacy of ZnSO4 (zinc sulfate) and ZnO nanoparticles (NPs) in alleviating boron toxicity. Nanoparticles have emerged as a novel strategy to reduce abiotic stress directly. The precise mechanism underlying the alleviation of boron toxicity by ZnO NPs in cotton remains unclear. In this study, ZnO NPs demonstrated superior potential for alleviating boron toxicity compared to ZnSO4 in hydroponically cultivated cotton seedlings. Under boron stress, plants supplemented with ZnO NPs exhibited significant increases in total fresh weight (75.97%), root fresh weight (39.64%), and leaf fresh weight (69.91%). ZnO NPs positively affected photosynthetic parameters and SPAD values. ZnO NPs substantially reduced H2O2 (hydrogen peroxide) by 27.87% and 32.26%, MDA (malondialdehyde) by 27.01% and 34.26%, and O2− (superoxide anion) by 41.64% and 48.70% after 24 and 72 h, respectively. The application of ZnO NPs increased the antioxidant activities of SOD (superoxide dismutase) by 82.09% and 76.52%, CAT (catalase) by 16.79% and 16.33%, and POD (peroxidase) by 23.77% and 21.66% after 24 and 72 h, respectively. ZnO NP and ZnSO4 application demonstrated remarkable efficiency in improving plant biomass, mineral nutrient content, and reducing boron levels in cotton seedlings under boron toxicity. A transcriptome analysis and corresponding verification revealed a significant up-regulation of genes encoding antioxidant enzymes, photosynthesis pathway, and ABC transporter genes with the application of ZnO NPs. These findings provide valuable insights for the mechanism of boron stress tolerance in cotton and provide a theoretical basis for applying ZnO NPs and ZnSO4 to reduce boron toxicity in cotton production. Full article
(This article belongs to the Special Issue Advances in Cotton Genomics, Genetics and Breeding)
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18 pages, 3795 KiB  
Article
Comparative Transcriptomic Analysis of Gossypium hirsutum Fiber Development in Mutant Materials (xin w 139) Provides New Insights into Cotton Fiber Development
by Chunping Li, Jieyin Zhao, Zhongshan Liu, Yanlong Yang, Chengxia Lai, Jun Ma and Alifu Aierxi
Plants 2024, 13(8), 1127; https://doi.org/10.3390/plants13081127 - 17 Apr 2024
Cited by 3 | Viewed by 1311
Abstract
Cotton is the most widely planted fiber crop in the world, and improving cotton fiber quality has long been a research hotspot. The development of cotton fibers is a complex process that includes four consecutive and overlapping stages, and although many studies on [...] Read more.
Cotton is the most widely planted fiber crop in the world, and improving cotton fiber quality has long been a research hotspot. The development of cotton fibers is a complex process that includes four consecutive and overlapping stages, and although many studies on cotton fiber development have been reported, most of the studies have been based on cultivars that are promoted in production or based on lines that are used in breeding. Here, we report a phenotypic evaluation of Gossypium hirsutum based on immature fiber mutant (xin w 139) and wild-type (Xin W 139) lines and a comparative transcriptomic study at seven time points during fiber development. The results of the two-year study showed that the fiber length, fiber strength, single-boll weight and lint percentage of xin w 139 were significantly lower than those of Xin W 139, and there were no significant differences in the other traits. Principal component analysis (PCA) and cluster analysis of the RNA-sequencing (RNA-seq) data revealed that these seven time points could be clearly divided into three different groups corresponding to the initiation, elongation and secondary cell wall (SCW) synthesis stages of fiber development, and the differences in fiber development between the two lines were mainly due to developmental differences after twenty days post anthesis (DPA). Differential expression analysis revealed a total of 5131 unique differentially expressed genes (DEGs), including 290 transcription factors (TFs), between the 2 lines. These DEGs were divided into five clusters. Each cluster functional category was annotated based on the KEGG database, and different clusters could describe different stages of fiber development. In addition, we constructed a gene regulatory network by weighted correlation network analysis (WGCNA) and identified 15 key genes that determined the differences in fiber development between the 2 lines. We also screened seven candidate genes related to cotton fiber development through comparative sequence analysis and qRT–PCR; these genes included three TFs (GH_A08G1821 (bHLH), GH_D05G3074 (Dof), and GH_D13G0161 (C3H)). These results provide a theoretical basis for obtaining an in-depth understanding of the molecular mechanism of cotton fiber development and provide new genetic resources for cotton fiber research. Full article
(This article belongs to the Special Issue Advances in Cotton Genomics, Genetics and Breeding)
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16 pages, 3718 KiB  
Article
Zinc Finger Protein8 (GhZFP8) Regulates the Initiation of Trichomes in Arabidopsis and the Development of Fiber in Cotton
by Yongchang Liu, Xiaomei Ma, Ying Li, Xiaoyu Yang and Wenhan Cheng
Plants 2024, 13(4), 492; https://doi.org/10.3390/plants13040492 - 8 Feb 2024
Cited by 4 | Viewed by 1250
Abstract
Cotton is one of the most important natural fibers used in the textile industry worldwide. It is important to identify the key factors involved in cotton fiber development. In this study, zinc finger protein8 (GhZFP8) encoding a C2H2 [...] Read more.
Cotton is one of the most important natural fibers used in the textile industry worldwide. It is important to identify the key factors involved in cotton fiber development. In this study, zinc finger protein8 (GhZFP8) encoding a C2H2 transcription factor (TF) was cloned from cotton. qPCR showed that the transcripts of GhZFP8 in cotton were detected in the leaves and fibers at 3, 6, and 30 days post-anthesis (DPA), but not in the roots, stems, or flowers. The overexpression of GhZFP8 increased the trichome number on the siliques, leaves, and inflorescence, but inhibited the growth. The expression of trichome development and cell-elongation-related genes decreased obviously in GhZFP8 overexpressor Arabidopsis. Indole-3-acetic acid (IAA) and 1-Aminocyclopropanecarboxylic acid (ACC) contents were much higher in GhZFP8 overexpressors than that found in the wild type, but the gibberellin (GA) content was lower. The interference of GhZFP8 in cotton caused smaller bolls and shorter fibers than that of the control. The results of DNA affinity purification (DAP)-seq showed that GhZFP8 could bind to the promoter, exon, intron, and intergenic region of the target genes, which are involved in photosynthesis, signal transduction, synthesis of biomass, etc. Our findings implied that GhZFP8 processed multiple biological functions and regulated the development of cotton fiber. Full article
(This article belongs to the Special Issue Advances in Cotton Genomics, Genetics and Breeding)
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Review

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16 pages, 2439 KiB  
Review
Applications of Virus-Induced Gene Silencing in Cotton
by Yue Tian, Yao Fang, Kaixin Zhang, Zeyang Zhai, Yujie Yang, Meiyu He and Xu Cao
Plants 2024, 13(2), 272; https://doi.org/10.3390/plants13020272 - 17 Jan 2024
Cited by 2 | Viewed by 2448
Abstract
Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technique that has become an effective tool to investigate gene function in plants. Cotton is one of the most important economic crops globally. In the past decade, VIGS has been successfully applied in cotton [...] Read more.
Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technique that has become an effective tool to investigate gene function in plants. Cotton is one of the most important economic crops globally. In the past decade, VIGS has been successfully applied in cotton functional genomic studies, including those examining abiotic and biotic stress responses and vegetative and reproductive development. This article summarizes the traditional vectors used in the cotton VIGS system, the visible markers used for endogenous gene silencing, the applications of VIGS in cotton functional genomics, and the limitations of VIGS and how they can be addressed in cotton. Full article
(This article belongs to the Special Issue Advances in Cotton Genomics, Genetics and Breeding)
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18 pages, 1180 KiB  
Review
Systematically and Comprehensively Understanding the Regulation of Cotton Fiber Initiation: A Review
by Zeyang Zhai, Kaixin Zhang, Yao Fang, Yujie Yang, Xu Cao, Li Liu and Yue Tian
Plants 2023, 12(21), 3771; https://doi.org/10.3390/plants12213771 - 4 Nov 2023
Cited by 4 | Viewed by 1978
Abstract
Cotton fibers provide an important source of raw materials for the textile industry worldwide. Cotton fiber is a kind of single cell that differentiates from the epidermis of the ovule and provides a perfect research model for the differentiation and elongation of plant [...] Read more.
Cotton fibers provide an important source of raw materials for the textile industry worldwide. Cotton fiber is a kind of single cell that differentiates from the epidermis of the ovule and provides a perfect research model for the differentiation and elongation of plant cells. Cotton fiber initiation is the first stage throughout the entire developmental process. The number of fiber cell initials on the seed ovule epidermis decides the final fiber yield. Thus, it is of great significance to clarify the mechanism underlying cotton fiber initiation. Fiber cell initiation is controlled by complex and interrelated regulatory networks. Plant phytohormones, transcription factors, sugar signals, small signal molecules, functional genes, non-coding RNAs, and histone modification play important roles during this process. Here, we not only summarize the different kinds of factors involved in fiber cell initiation but also discuss the mechanisms of these factors that act together to regulate cotton fiber initiation. Our aim is to synthesize a systematic and comprehensive review of different factors during fiber initiation that will provide the basics for further illustrating these mechanisms and offer theoretical guidance for improving fiber yield in future molecular breeding work. Full article
(This article belongs to the Special Issue Advances in Cotton Genomics, Genetics and Breeding)
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