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Plants
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Molecular Breeding and Genetic Improvement of Cotton
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Molecular Breeding and Genetic Improvement of Cotton

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 14037

Special Issue Editor

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,

Genetic manipulation is the basis for the improvement of cotton yield and fiber quality, and is the most effective approach for addressing the challenges of various biotic and abiotic stresses. Traditional breeding approaches are time-consuming, heavily relying on the field phenotypic evaluation of progeny derived from the crossing of accessions with mutually complementary desired traits. Molecular breeding methods based on the association and linkage of molecular markers with the traits of interest can significantly improve breeding efficacy through marker-assisted selection and genomic prediction. The release of high-quality reference genomes of both diploid and tetraploid cottons, advancements in sequencing and high-throughput genotyping technologies, and the development and application of novel algorithms for the identification of molecular markers tightly linked with fiber yield and quality traits and in prediction of genetic gains of breeding progeny have enabled marker-assisted breeding.

To document the significant progresses achieved in the space of cotton molecular breeding and to further promote molecular-marker-enabled modern cotton breeding, we propose a Special Issue under the theme “Molecular Breeding and Genetic Improvement of Cotton”. It provides a platform for the cotton community to report their latest results and exchange their ideas and views on how the cotton community as a whole can work together to advance studies of cotton genetics, genomics, and biotechnology to breed next-generation cotton cultivars with high yield, superior fiber quality, and tolerance to all major biotic and abiotic stresses.

This Special Issue will cover, but will not be limited to, the following areas:

  • Characterization of cotton germplasm;
  • Development of molecular markers;
  • QTL mapping and genome-wide association studies;
  • Marker-assisted breeding;
  • Genomic prediction and selection;
  • Characterization of cotton gene families;
  • Omics-based gene network analyses;
  • High-throughput phenotyping.

Dr. Qian-Hao Zhu
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. 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
  • molecular marker
  • breeding
  • genetics
  • genomics
  • functional genomics
  • quantitative trait loci
  • genomic prediction

Published Papers (7 papers)

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Research

23 pages, 9584 KiB  
Article
The Molecular Mechanism of GhbHLH121 in Response to Iron Deficiency in Cotton Seedlings
by Jie Li, Ke Nie, Luyao Wang, Yongyan Zhao, Mingnan Qu, Donglei Yang and Xueying Guan
Plants 2023, 12(10), 1955; https://doi.org/10.3390/plants12101955 - 11 May 2023
Cited by 1 | Viewed by 1335
Abstract
Iron deficiency caused by high pH of saline–alkali soil is a major source of abiotic stress affecting plant growth. However, the molecular mechanism underlying the iron deficiency response in cotton (Gossypium hirsutum) is poorly understood. In this study, we investigated the [...] Read more.
Iron deficiency caused by high pH of saline–alkali soil is a major source of abiotic stress affecting plant growth. However, the molecular mechanism underlying the iron deficiency response in cotton (Gossypium hirsutum) is poorly understood. In this study, we investigated the impacts of iron deficiency at the cotton seedling stage and elucidated the corresponding molecular regulation network, which centered on a hub gene GhbHLH121. Iron deficiency induced the expression of genes with roles in the response to iron deficiency, especially GhbHLH121. The suppression of GhbHLH121 with virus-induced gene silence technology reduced seedlings’ tolerance to iron deficiency, with low photosynthetic efficiency and severe damage to the structure of the chloroplast. Contrarily, ectopic expression of GhbHLH121 in Arabidopsis enhanced tolerance to iron deficiency. Further analysis of protein/protein interactions revealed that GhbHLH121 can interact with GhbHLH IVc and GhPYE. In addition, GhbHLH121 can directly activate the expression of GhbHLH38, GhFIT, and GhPYE independent of GhbHLH IVc. All told, GhbHLH121 is a positive regulator of the response to iron deficiency in cotton, directly regulating iron uptake as the upstream gene of GhFIT. Our results provide insight into the complex network of the iron deficiency response in cotton. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Improvement of Cotton)
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16 pages, 3209 KiB  
Article
Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL a New R/Shiny App to Streamline Genetic Mapping
by Ashley N. Schoonmaker, Amanda M. Hulse-Kemp, Ramey C. Youngblood, Zainab Rahmat, Muhammad Atif Iqbal, Mehboob-ur Rahman, Kelli J. Kochan, Brian E. Scheffler and Jodi A. Scheffler
Plants 2023, 12(5), 1153; https://doi.org/10.3390/plants12051153 - 03 Mar 2023
Cited by 1 | Viewed by 2082
Abstract
Cotton leaf curl virus (CLCuV) causes devastating losses to fiber production in Central Asia. Viral spread across Asia in the last decade is causing concern that the virus will spread further before resistant varieties can be bred. Current development depends on screening each [...] Read more.
Cotton leaf curl virus (CLCuV) causes devastating losses to fiber production in Central Asia. Viral spread across Asia in the last decade is causing concern that the virus will spread further before resistant varieties can be bred. Current development depends on screening each generation under disease pressure in a country where the disease is endemic. We utilized quantitative trait loci (QTL) mapping in four crosses with different sources of resistance to identify single nucleotide polymorphism (SNP) markers associated with the resistance trait to allow development of varieties without the need for field screening every generation. To assist in the analysis of multiple populations, a new publicly available R/Shiny App was developed to streamline genetic mapping using SNP arrays and to also provide an easy method to convert and deposit genetic data into the CottonGen database. Results identified several QTL from each cross, indicating possible multiple modes of resistance. Multiple sources of resistance would provide several genetic routes to combat the virus as it evolves over time. Kompetitive allele specific PCR (KASP) markers were developed and validated for a subset of QTL, which can be used in further development of CLCuV-resistant cotton lines. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Improvement of Cotton)
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13 pages, 2072 KiB  
Article
Overexpression of the Caragana korshinskii com58276 Gene Enhances Tolerance to Drought in Cotton (Gossypium hirsutum L.)
by Yuanchun Pu, Peilin Wang, Jiangling Xu, Yejun Yang, Ting Zhou, Kai Zheng, Xinwu Pei, Quanjia Chen and Guoqing Sun
Plants 2023, 12(5), 1069; https://doi.org/10.3390/plants12051069 - 27 Feb 2023
Viewed by 1120
Abstract
The increasing water scarcity associated with environmental change brings significant negative impacts to the growth of cotton plants, whereby it is urgent to enhance plant tolerance to drought. Here, we overexpressed the com58276 gene isolated from the desert plant Caragana korshinskii in cotton [...] Read more.
The increasing water scarcity associated with environmental change brings significant negative impacts to the growth of cotton plants, whereby it is urgent to enhance plant tolerance to drought. Here, we overexpressed the com58276 gene isolated from the desert plant Caragana korshinskii in cotton plants. We obtained three OE plants and demonstrated that com58276 confers drought tolerance in cotton after subjecting transgenic seeds and plants to drought. RNA-seq revealed the mechanisms of the possible anti-stress response, and that the overexpression of com58276 does not affect growth and fiber content in OE cotton plants. The function of com58276 is conserved across species, improving the tolerance of cotton to salt and low temperature, and demonstrating its applicability to improve plant resistance to environmental change. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Improvement of Cotton)
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16 pages, 3871 KiB  
Article
Genetic Analysis of Mutagenesis That Induces the Photoperiod Insensitivity of Wild Cotton Gossypium hirsutum Subsp. purpurascens
by Fakhriddin N. Kushanov, Doniyor J. Komilov, Ozod S. Turaev, Dilrabo K. Ernazarova, Roza S. Amanboyeva, Bunyod M. Gapparov and John Z. Yu
Plants 2022, 11(22), 3012; https://doi.org/10.3390/plants11223012 - 08 Nov 2022
Cited by 4 | Viewed by 1646
Abstract
Cotton genus Gossypium L., especially its wild species, is rich in genetic diversity. However, this valuable genetic resource is barely used in cotton breeding programs. In part, due to photoperiod sensitivities, the genetic diversity of Gossypium remains largely untapped. Herein, we present a [...] Read more.
Cotton genus Gossypium L., especially its wild species, is rich in genetic diversity. However, this valuable genetic resource is barely used in cotton breeding programs. In part, due to photoperiod sensitivities, the genetic diversity of Gossypium remains largely untapped. Herein, we present a genetic analysis of morphological, cytological, and genomic changes from radiation-mediated mutagenesis that induced plant photoperiod insensitivity in the wild cotton of Gossypium hirsutum. Several morphological and agronomical traits were found to be highly inheritable using the progeny between the wild-type G. hirsutum subsp. purpurascens (El-Salvador) and its mutant line (Kupaysin). An analysis of pollen mother cells (PMCs) revealed quadrivalents that had an open ring shape and an adjoining type of divergence of chromosomes from translocation complexes. Using 336 SSR markers and 157 F2 progenies that were grown with parental genotypes and F1 hybrids in long day and short night conditions, five quantitative trait loci (QTLs) associated with cotton flowering were located on chromosomes At-05, At-11, and Dt-07. Nineteen candidate genes related to the flowering traits were suggested through molecular and in silico analysis. The DNA markers associated with the candidate genes, upon future functional analysis, would provide useful tools in marker-assisted selection (MAS) in cotton breeding programs for early flowering and maturity. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Improvement of Cotton)
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12 pages, 2352 KiB  
Article
Root Illumination Promotes Seedling Growth and Inhibits Gossypol Biosynthesis in Upland Cotton
by Jiayi Zhang, Tianlun Zhao, Kuang Sheng, Yue Sun, Yifei Han, Yiran Chen, Zhiying E, Shuijin Zhu and Jinhong Chen
Plants 2022, 11(6), 728; https://doi.org/10.3390/plants11060728 - 09 Mar 2022
Cited by 4 | Viewed by 2017
Abstract
Gossypol, a terpenoid compound mainly synthesized in the cotton roots, acts as a phytoalexin in protecting the plants from biotic stress. Roots are critical for both the secondary metabolism and the growth of the plant. Light plays an important role in plant growth [...] Read more.
Gossypol, a terpenoid compound mainly synthesized in the cotton roots, acts as a phytoalexin in protecting the plants from biotic stress. Roots are critical for both the secondary metabolism and the growth of the plant. Light plays an important role in plant growth and material metabolism, however, the effect of root illumination (RI) on the cotton seedling growth and gossypol metabolism remains unclear. In the present study, the cotton genetic standard line TM-1 and four pairs of near-isogenic lines (NILs) were used as materials to study the impact of RI on cotton seedlings. Results showed that, compared with the cotton seedlings cultivated without RI, the photosynthetic rate, leaf area, and dry weight of roots and leaves were significantly increased, while the gossypol content in leaves and roots was significantly reduced in seedlings cultivated with RI. GO and KEGG enrichment analysis of the differentially expressed genes (DEGs) with and without RI both indicated that photosynthesis and terpenoid biosynthesis-related GO terms and pathways were significantly enriched, the expression profile confirmed that RI positively regulated the photosynthesis system and negatively affected the gossypol biosynthesis pathway in roots. This study revealed the effects of RI on seedlings’ growth and gossypol biosynthesis in upland cotton, and provided important insights for the engineering of cotton with low gossypol accumulation. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Improvement of Cotton)
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19 pages, 12239 KiB  
Article
Genome-Wide Identification of Cotton (Gossypium spp.) Glycerol-3-Phosphate Dehydrogenase (GPDH) Family Members and the Role of GhGPDH5 in Response to Drought Stress
by Jialiang Sun, Hua Cui, Bingjie Wu, Weipeng Wang, Qiuyue Yang, Yaxin Zhang, Song Yang, Yuping Zhao, Dongbei Xu, Guoxiang Liu and Tengfei Qin
Plants 2022, 11(5), 592; https://doi.org/10.3390/plants11050592 - 22 Feb 2022
Cited by 3 | Viewed by 2172
Abstract
Glycerol-3-phosphate dehydrogenase (GPDH) is a key enzyme in plant glycerol synthesis and metabolism, and plays an important role in plant resistance to abiotic stress. Here, we identified 6, 7, 14 and 14 GPDH genes derived from Gossypium arboreum, Gossypium raimondii, Gossypium [...] Read more.
Glycerol-3-phosphate dehydrogenase (GPDH) is a key enzyme in plant glycerol synthesis and metabolism, and plays an important role in plant resistance to abiotic stress. Here, we identified 6, 7, 14 and 14 GPDH genes derived from Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively. Phylogenetic analysis assigned these genes into three classes, and most of the genes within the family were expanded by whole-genome duplication (WGD) and segmental duplications. Moreover, determination of the nonsynonymous substitution rate/synonymous substitution rate (Ka/Ks) ratio showed that the GPDH had an evolutionary preference for purifying selection. Transcriptome data revealed that GPDH genes were more active in the early stages of fiber development. Additionally, numerous stress-related cis-elements were identified in the potential promoter region. Then, a protein–protein-interaction (PPI) network of GPDH5 in G. hirsutum was constructed. In addition, we predicted 30 underlying miRNAs in G. hirsutum. Functional validation results indicated that silencing GhGPDH5 diminished drought tolerance in the upland cotton TM-1 line. In summary, this study provides a fundamental understanding of the GPDH gene family in cotton, GhGPDH5 exerts a positive effect during drought stress and is potentially involved in stomatal closure movements. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Improvement of Cotton)
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19 pages, 3007 KiB  
Article
Genome-Wide Identification of the Thaumatin-like Protein Family Genes in Gossypium barbadense and Analysis of Their Responses to Verticillium dahliae Infection
by Yilin Zhang, Wei Chen, Xiaohui Sang, Ting Wang, Haiyan Gong, Yunlei Zhao, Pei Zhao and Hongmei Wang
Plants 2021, 10(12), 2647; https://doi.org/10.3390/plants10122647 - 02 Dec 2021
Cited by 11 | Viewed by 2344
Abstract
(1) Background: Plants respond to pathogen challenge by activating a defense system involving pathogenesis-related (PR) proteins. The PR-5 family includes thaumatin, thaumatin-like proteins (TLPs), and other related proteins. TLPs play an important role in response to biotic and abiotic stresses. Many TLP-encoding genes [...] Read more.
(1) Background: Plants respond to pathogen challenge by activating a defense system involving pathogenesis-related (PR) proteins. The PR-5 family includes thaumatin, thaumatin-like proteins (TLPs), and other related proteins. TLPs play an important role in response to biotic and abiotic stresses. Many TLP-encoding genes have been identified and functionally characterized in the model plant species. (2) Results: We identified a total of 90 TLP genes in the G. barbadense genome. They were phylogenetically classified into 10 subfamilies and distributed across 19 chromosomes and nine scaffolds. The genes were characterized by examining their exon–intron structures, promoter cis-elements, conserved domains, synteny and collinearity, gene family evolution, and gene duplications. Several TLP genes were predicted to be targets of miRNAs. Investigation of expression changes of 21 GbTLPs in a G. barbadense cultivar (Hai7124) resistance to Verticillium dahliae revealed 13 GbTLPs being upregulated in response to V. dahliae infection, suggesting a potential role of these GbTLP genes in disease response. (3) Conclusions: The results of this study allow insight into the GbTLP gene family, identify GbTLP genes responsive to V. dahliae infection, and provide candidate genes for future studies of their roles in disease resistance. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Improvement of Cotton)
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