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Genetic Studies on Cotton Stress Resistance, Quality Traits, and Drought...
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Genetic Studies on Cotton Stress Resistance, Quality Traits, and Drought Response Mechanisms

A Special Issue of Genes (ISSN 2073-4425) belonging to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 June 2026) | Viewed by 3062

Editors

Dr. Xueyuan Li

E-Mail Website
Guest Editor
Xingjiang Academy of Agricultural Sciences, Urumqi, China
Interests: cotton breeding; drought stress; growth and development; molecular marker-assisted selection
Dr. Juyun Zheng

E-Mail Website
Guest Editor
Xinjiang Academy of Agricultural Sciences, Urumqi, China
Interests: cotton; drought stress; salt stress; molecular breeding; molecular marker-assisted selection
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. Fenglei Sun

E-Mail Website
Co-Guest Editor
Cotton Research Institute of Xinjiang Uyghur Autonomous Region Academy of Agricultural Sciences, Urumqi, China
Interests: cotton; cotton genetics; genomics; drought stress; molecular marker-assisted selection

Special Issue Information

Dear Colleagues,

The growth and development of cotton are significantly affected by extreme climate change and uneven precipitation distribution. Cotton adapts and responds to environmental changes and extreme weather by adjusting its physiological activities and ecological characteristics. Understanding how cotton responds to short- and long-term environmental changes can enhance our in-depth understanding of the mechanisms of plant stress response. The superior characteristics of cotton are enhanced by using techniques such as genome-wide association analysis, multi-omics analysis, molecular marker-assisted selection, genome editing, and transgenic technology. In addition, this field is dedicated to revealing the complex mechanisms that control the growth and development of cotton, as well as identifying genes that are crucial to key traits, such as plant morphology, yield, and cotton quality. Submissions that address these or related topics are welcome.

Dr. Xueyuan Li
Dr. Juyun Zheng
Prof. Dr. Jie Sun
Guest Editors

Dr. Fenglei Sun
Co-Guest Editor

Manuscript Submission Information

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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
  • drought stress
  • growth and development
  • gene editing
  • molecular marker-assisted selection

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Published Papers (4 papers)

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Research

13 pages, 3991 KB  
Article
BSA-Seq-Based QTL Mapping for the Height of the First Fruiting Branch Node of Cotton and the Development of Molecular Markers
by Fuxiang Zhao, Tao Yang, Xuwen Wang, Gang Wang, Jinxin Qiao, Xianhui Kong, Li Liu, Wanli Han and Yu Yu
Genes 2026, 17(9), 1030; https://doi.org/10.3390/genes17091030 - 28 Aug 2026
Viewed by 194
Abstract
The height of the first fruiting branch node (HFFBN) is a core indicator for mechanical harvesting of cotton, and the development of molecular markers for this trait is important for accelerating the breeding process. In this study, using bulked segregant analysis coupled with [...] Read more.
The height of the first fruiting branch node (HFFBN) is a core indicator for mechanical harvesting of cotton, and the development of molecular markers for this trait is important for accelerating the breeding process. In this study, using bulked segregant analysis coupled with whole-genome sequencing (BSA-seq), one quantitative trait locus (QTL) associated with the HFFBN was mapped; a molecular marker, qFBH7, associated with the HFFBN of cotton was developed; and its application value was systematically evaluated. A total of 20 lines with extreme phenotypes were selected from the recombinant inbred lines constructed using upland cotton Z3-146 and Z3-147 as parental lines. The screened lines with extreme phenotypes were used to construct the extreme high-HFFBN pool and the extreme low-HFFBN pool, which were subsequently used for BSA-seq. Using the upland cotton genome as a reference, relevant QTLs were mapped by BSA-seq. One relevant candidate region was identified, with a total length of 2.25 Mb. The validation experiments revealed that the genotyping results of the KASP_FBH7_03 molecular marker in the parental lines Z3-146 and Z3-147 were completely consistent with the BSA-seq data: Z3-146 had the TT genotype, and Z3-147 had the CC genotype. Among the 66 samples from the natural population, there was a significant difference (p < 0.05) in the HFFBN between the CC and TT genotypes, and the mean HFFBN of the TT genotype was greater than that of the CC genotype. In summary, the KASP_FBH7_03 molecular marker can be effectively used for selective breeding for the HFFBN of cotton, and the TT genotype has a positive regulatory effect on the HFFBN. This study not only provides resources for breeding cotton varieties suited to mechanical harvesting but also offers a robust tool for molecular marker-assisted selection. Full article
(This article belongs to the Special Issue Genetic Studies on Cotton Stress Resistance, Quality Traits, and Drought Response Mechanisms)
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13 pages, 49263 KB  
Article
Pan-Genome Analysis of the Tubulin Gene Family Reveals Candidates for Fiber Strength in Gossypium barbadense
by Yajie Duan, Ruihong Zeng, Yongsheng Cai, Xiaoju Liu and Fenglei Sun
Genes 2026, 17(8), 873; https://doi.org/10.3390/genes17080873 - 27 Jul 2026
Viewed by 389
Abstract
Background/Objectives: Tubulins (Tub) are central components of microtubules, but intraspecific variation and developmental expression of the Tub family in Gossypium barbadense remain poorly characterized. This study aimed to characterize the GbTub family using a pan-genome framework and identify candidates associated [...] Read more.
Background/Objectives: Tubulins (Tub) are central components of microtubules, but intraspecific variation and developmental expression of the Tub family in Gossypium barbadense remain poorly characterized. This study aimed to characterize the GbTub family using a pan-genome framework and identify candidates associated with fiber development and strength. Methods: A total of 50 GbTub genes were identified in the G. barbadense 3-79 reference genome, and their orthologous presence–absence patterns were subsequently assessed across 12 additional G. barbadense accessions. Phylogenetic, presence–absence variation (PAV), Ka/Ks, structural variation (SV), RNA-seq, RT-qPCR, co-expression, and GO enrichment analyses were integrated. Results: Among the 50 reference-defined GbTub genes, 43 were classified as core genes, 6 as near-core genes, and 1 as an accessory gene, and the encoded proteins were classified into α-, β-, and γ-tubulin clades. All genes showed Ka/Ks < 1. Twenty-three GbTub genes differed between the fiber-strength-contrasting accessions 5917 and PimaS-7, and representative expression trends were supported by RT-qPCR. Network analysis prioritized 10 GbTub candidates based on degree centrality. GbTub21 was the sole SV-associated GbTub gene displaying significant differential expression between accessions harboring versus lacking the corresponding SV. Non-Tub neighbors of the candidate hub genes were enriched for cytoskeletal, intracellular-transport, and plasma-membrane functions. Conclusions: The pan-genome analysis reveals strong conservation with limited intraspecific variation in the GbTub family. Co-expression profiles nominate candidates associated with fiber secondary-wall development, and their causal contribution to fiber strength awaits functional dissection. Full article
(This article belongs to the Special Issue Genetic Studies on Cotton Stress Resistance, Quality Traits, and Drought Response Mechanisms)
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15 pages, 3888 KB  
Article
Functional Analysis of a Cotton TPX2-like Gene, GbTPX2-35, in Regulating Fiber Cell Development and Strength in Gossypium barbadense
by Yajie Duan, Qianqian Han, Ruihong Zeng, Yongsheng Cai, Xiaowei Niu, Yuhong Wen and Xiaoju Liu
Genes 2026, 17(4), 395; https://doi.org/10.3390/genes17040395 - 30 Mar 2026
Viewed by 596
Abstract
Background/Objectives: Among cotton species, Gossypium barbadense produces the strongest fibers. Examining cytoskeletal dynamics in single epidermal cells of G. barbadense ovules offers a direct approach to investigating fiber quality. Microtubules are major cytoskeletal components whose organization and dynamics are precisely regulated by microtubule-associated [...] Read more.
Background/Objectives: Among cotton species, Gossypium barbadense produces the strongest fibers. Examining cytoskeletal dynamics in single epidermal cells of G. barbadense ovules offers a direct approach to investigating fiber quality. Microtubules are major cytoskeletal components whose organization and dynamics are precisely regulated by microtubule-associated proteins (MAPs). However, information on the TPX2 family remains limited, and characterizing its features in G. barbadense is critical to clarifying the role of TPX2 family members in fiber strength formation. Methods: Using the Arabidopsis thaliana TPX2 sequence as a reference, 40, 49, 26, and 26 TPX2 family members were identified in the genomes of G. barbadense, Gossypium hirsutum, Gossypium arboreum, and Gossypium raimondii, respectively. We further analyzed the expression pattern of GbTPX2-35 and validated its function via virus-induced gene silencing (VIGS). Results: In G. barbadense, GbTPX2-35 (Gbar_D11G59825.1) was significantly upregulated in fiber samples of the parental lines at 25 days post-anthesis, and this expression pattern was further validated in G. barbadense lines with extreme fiber strength phenotypes. Next, VIGS-mediated silencing of GbTPX2-35 downregulated the transcript levels of cellulose synthase and microtubule-related protein genes, a finding further validated by mature fiber strength phenotypic data. Conclusions: This study preliminarily validated a pathway in which GbTPX2-35 regulates fiber strength by coordinating cellulose biosynthesis with microtubule cytoskeleton dynamics, providing valuable candidate genes and theoretical support for molecular breeding of high-strength cotton fibers. Full article
(This article belongs to the Special Issue Genetic Studies on Cotton Stress Resistance, Quality Traits, and Drought Response Mechanisms)
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14 pages, 2135 KB  
Article
Casparian Strip Fortification as a Defense Mechanism to Fusarium oxysporum f. sp. vasinfectum Race 4 Infection in a Highly Resistant Gossypium barbadense Cultivar
by Stephen Parris, Sonika Kumar, Zhigang Li, Jim Olvey, Mike Olvey, Don C. Jones and Christopher A. Saski
Genes 2025, 16(10), 1158; https://doi.org/10.3390/genes16101158 - 29 Sep 2025
Cited by 1 | Viewed by 1159
Abstract
Background/Objectives: Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (FOV), is a destructive vascular disease that severely impacts cotton production. Among its variants, race 4 (FOV4) is especially aggressive, leading to early season stand losses and yield reductions. While resistant [...] Read more.
Background/Objectives: Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (FOV), is a destructive vascular disease that severely impacts cotton production. Among its variants, race 4 (FOV4) is especially aggressive, leading to early season stand losses and yield reductions. While resistant cultivars of Gossypium barbadense (pima cotton) have been developed, the molecular basis of this resistance remains unclear. This study aimed to characterize transcriptomic responses associated with FOV4 resistance in pima cotton. Methods: We conducted an in vitro infection assay using two G. barbadense cultivars with contrasting phenotypes: the highly resistant ‘DP348RF’ and the highly susceptible ‘GB1031’. Root tissues were sampled at multiple stages of infection, and RNA sequencing was performed to identify differentially expressed genes and pathways contributing to resistance. Results: Resistant plants ‘DP348RF’ showed strong induction of genes related to reactive oxygen species (ROS) metabolism, chitinase activity, and lignification compared to the susceptible cultivar. Notably, genes involved in the biosynthesis and reinforcement of the Casparian strip, a critical biochemical barrier limiting pathogen penetration into vascular tissues, were uniquely and significantly upregulated in resistant roots. These transcriptional responses suggest that fortification of cell wall barriers and enhanced antimicrobial defenses contribute to effective restriction of FOV4 colonization. Conclusions: Our findings identify a distinct molecular signature of resistance to FOV4 in pima cotton, with Casparian strip reinforcement emerging as a potential mechanism limiting vascular infection. These insights provide a foundation for breeding strategies aimed at improving Fusarium wilt resistance in cotton. Full article
(This article belongs to the Special Issue Genetic Studies on Cotton Stress Resistance, Quality Traits, and Drought Response Mechanisms)
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