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Genomics-Assisted Breeding for Cotton Improvement
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Genomics-Assisted Breeding for Cotton Improvement

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 November 2023) | Viewed by 4317

Special Issue Editors

Dr. Linghe Zeng

E-Mail Website
Guest Editor
Crop Genetics Research, USDA, Stoneville, MS, USA
Interests: cotton; QTL
Prof. Dr. Jinfa Zhang

E-Mail Website
Guest Editor
Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
Interests: cotton breeding; genetics and genomics
Prof. Dr. Xianlong Zhang

E-Mail Website
Guest Editor
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
Interests: cotton biotechnology and breeding

Special Issue Information

Special Issue Title: Genomics-Assisted Breeding for Cotton Improvement

Cotton breeders are facing challenges for cotton improvement in yield and fiber quality under a rapidly changing climate. The effectiveness of traditional breeding is often limited because quantitative traits are polygenic and because of their interactions with environmental factors, including biotic and abiotic stresses. In recent years, genomic-assisted breeding has emerged as a useful and effective approach to help breeders in selecting desirable lines to increase breeding efficiency for the development of new cultivars. In this Special Issue, we aim to demonstrate new tools in biotechnology and molecular studies and their applications in cotton breeding for cultivar improvement.

We accept original research articles or comprehensive reviews relating to the proposed title. Articles are preferred as defined in the following:

(1) Development of genomic resources including but not limited to identification of quantitative trait loci (QTLs) using molecular markers and transcriptome assembly and analysis of candidate genes;

(2) Genomic-assisted breeding, including marker-assisted selection of desirable parents and further selection of breeding lines based on marker genotypes for cotton improvement;

(3) Genomic selection for accelerating selection efficiency in molecular breeding;

(4) Development of new databases for molecular breeding.

Dr. Linghe Zeng
Prof. Jinfa Zhang
Prof. Dr. Xianlong Zhang
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.

Published Papers (4 papers)

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Research

11 pages, 2323 KiB  
Article
Assessment of Allelopathic Potential of Cotton Chromosome Substitution Lines
by Worlanyo Segbefia, Varsha Singh, Mary Gracen Fuller, Ziming Yue, Fernanda Reolon de Souza and Te Ming Tseng
Plants 2024, 13(8), 1102; https://doi.org/10.3390/plants13081102 - 15 Apr 2024
Viewed by 530
Abstract
Weed interference consistently poses a significant agronomic challenge in cotton production, leading to unfavorable direct and indirect consequences. Consequently, the predominant strategy employed to manage weeds is the application of synthetic herbicides. However, this extensive reliance has resulted in the development of herbicide-resistant [...] Read more.
Weed interference consistently poses a significant agronomic challenge in cotton production, leading to unfavorable direct and indirect consequences. Consequently, the predominant strategy employed to manage weeds is the application of synthetic herbicides. However, this extensive reliance has resulted in the development of herbicide-resistant weed populations due to the prolonged use of a single herbicide and the lack of rotation. This project focused on identifying weed-suppressive cotton chromosome substitution (CS) lines. These CS lines closely resemble the parent TM-1, an upland cotton derivative (Gossypium hirsutum). Each CS line carries a single chromosome or chromosome arm exchanged from G. barbadense, G. tomentosum, or G. mustelinum within the TM-1 background. In a greenhouse experiment utilizing a stepwise approach, five CS lines, along with two conventional varieties (Enlist and UA48) and the parent line (TM1), were assessed to determine their potential for suppressing Palmer amaranth growth. The plant height was measured 7, 14, and 21 days after establishment, and the chlorophyll content was measured 21 days after establishment. The results revealed varying levels of chlorophyll reduction in Palmer amaranth, with the Enlist variety displaying the lowest reduction (32%) and TM-1 exhibiting the highest (78%). Within 14 days of establishment, the CS lines T26lo, BNTN 1-15, and T11sh demonstrated substantial suppression of Palmer amaranth height, with reductions of 79, 70, and 71%, respectively. Conversely, Enlist displayed the least effective performance among the CS lines. Moreover, CS22, CS49, CS50, CS34, UA48, and CS23 displayed a decreasing trend in reducing Palmer amaranth height from 14 to 21 days after establishment. This research demonstrates the inherent herbicidal attributes within cotton CS lines against Palmer amaranth. In light of the versatile applications of cotton fibers and the unique characteristics of the G. hirsutum genome, this study investigates the potential of specific cotton lines in enhancing weed management practices. By elucidating the implications of our findings, we aim to contribute to promoting sustainability and developing alternatives to synthetic herbicides in agricultural systems. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding for Cotton Improvement)
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17 pages, 292 KiB  
Article
Transcriptome Analysis of Resistant Cotton Germplasm Responding to Reniform Nematodes
by Chunda Feng, Salliana R. Stetina and John E. Erpelding
Plants 2024, 13(7), 958; https://doi.org/10.3390/plants13070958 - 26 Mar 2024
Viewed by 612
Abstract
Reniform nematode (Rotylenchulus reniformis) is an important microparasite for Upland cotton (Gossypium hirsutum L.) production. Growing resistant cultivars is the most economical management method, but only a few G. barbadense genotypes and some diploid Gossypium species confer high levels of [...] Read more.
Reniform nematode (Rotylenchulus reniformis) is an important microparasite for Upland cotton (Gossypium hirsutum L.) production. Growing resistant cultivars is the most economical management method, but only a few G. barbadense genotypes and some diploid Gossypium species confer high levels of resistance. This study conducted a transcriptome analysis of resistant genotypes to identify genes involved in host plant defense. Seedlings of G. arboreum accessions PI 529728 (A2-100) and PI 615699 (A2-190), and G. barbadense genotypes PI 608139 (GB 713) and PI 163608 (TX 110), were inoculated with the reniform nematode population MSRR04 and root samples were collected on the fifth (D5) and ninth (D9) day after inoculation. Differentially expressed genes (DEGs) were identified by comparing root transcriptomes from inoculated plants with those from non-inoculated plants. Accessions A2-100 and A2-190 showed 52 and 29 DEGs on D5, respectively, with 14 DEGs in common, and 18 DEGs for A2-100 and 11 DEGs for A2-190 on chromosome 5. On D9, four DEGs were found in A2-100 and two DEGs in A2-190. For GB 713, 52 and 43 DEGs were found, and for TX 110, 29 and 117 DEGs were observed on D5 and D9, respectively. Six DEGs were common at the two sampling times for these genotypes. Some DEGs were identified as Meloidogyne-induced cotton (MIC) 3 and 4, resistance gene analogs, or receptor-like proteins. Other DEGs have potential roles in plant defense, such as peroxidases, programmed cell death, pathogenesis related proteins, and systemic acquired resistance. Further research on these DEGs will aid in understanding the mechanisms of resistance to explore new applications for the development of resistant cultivars. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding for Cotton Improvement)
13 pages, 4770 KiB  
Article
Activation of Gossypium hirsutum ACS6 Facilitates Fiber Development by Improving Sucrose Metabolism and Transport
by Chen Geng, Leilei Li, Shuan Han, Mingzhu Jia and Jing Jiang
Plants 2023, 12(20), 3530; https://doi.org/10.3390/plants12203530 - 11 Oct 2023
Cited by 1 | Viewed by 910
Abstract
Cotton fiber yield depends on the density of fiber cell initials that form on the ovule epidermis. Fiber initiation is triggered by MYB-MIXTA-like transcription factors (GhMMLs) and requires a sucrose supply. Ethylene or its precursor ACC (1-aminocyclopropane-1-carboxylic acid) is suggested to affect fiber [...] Read more.
Cotton fiber yield depends on the density of fiber cell initials that form on the ovule epidermis. Fiber initiation is triggered by MYB-MIXTA-like transcription factors (GhMMLs) and requires a sucrose supply. Ethylene or its precursor ACC (1-aminocyclopropane-1-carboxylic acid) is suggested to affect fiber yield. The Gossypium hirsutum (L.) genome contains 35 ACS genes (GhACS) encoding ACC synthases. Here, we explored the role of a GhACS family member in the regulation of fiber initiation. Expression analyses showed that the GhACS6.3 gene pair was specifically expressed in the ovules during fiber initiation (3 days before anthesis to 5 days post anthesis, −3 to 5 DPA), especially at −3 DPA, whereas other GhACS genes were expressed at very low or undetectable levels. The expression profile of GhACS6.3 during fiber initial development was confirmed by qRT-PCR analysis. Transgenic lines overexpressing GhACS6.3 (GhACS6.3-OE) showed increased ACC accumulation in ovules, which promoted the formation of fiber initials and fiber yield components. This was accompanied by increased transcript levels of GhMML3 and increased transcript levels of genes encoding sucrose transporters and sucrose synthase. These findings imply that GhACS6.3 activation is required for fiber initial development. Our results lay the foundation for further research on increasing cotton fiber production. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding for Cotton Improvement)
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15 pages, 10672 KiB  
Article
Glyphosate-Induced Abscisic Acid Accumulation Causes Male Sterility in Sea Island Cotton
by Guoli Qin, Nan Zhao, Weiran Wang, Meng Wang, Jiahui Zhu, Jing Yang, Feng Lin, Xinglei Huang, Yanhui Zhang, Ling Min, Guodong Chen and Jie Kong
Plants 2023, 12(5), 1058; https://doi.org/10.3390/plants12051058 - 27 Feb 2023
Cited by 1 | Viewed by 1611
Abstract
Sea Island cotton is the best quality tetraploid cultivated cotton in the world, in terms of fiber quality. Glyphosate is a widely used herbicide in cotton production, and the improper use of herbicides has led to pollen abortion in sea island cotton and, [...] Read more.
Sea Island cotton is the best quality tetraploid cultivated cotton in the world, in terms of fiber quality. Glyphosate is a widely used herbicide in cotton production, and the improper use of herbicides has led to pollen abortion in sea island cotton and, consequently, to a dramatic decrease in yield; however, the mechanism remains unclear. In this study, different concentrations (0, 3.75, 7.5, 15, and 30 g/L) of glyphosate were applied to CP4-EPSPS transgenic sea island cotton Xinchang 5 in 2021 and 2022 at Korla, with 15 g/L glyphosate chosen as the suitable concentration. By comparing the paraffin sections of 2–24 mm anthers in the 15 g/L glyphosate treatment group with those in the water control group, we showed that the key period of anther abortion after glyphosate treatment was the formation and development of tetrads, which corresponded to 8–9 mm buds. Transcriptome sequencing analysis of the treated and control anthers revealed a significant enrichment of differentially expressed genes in phytohormone-related pathways, in particular abscisic acid response and regulation pathways. Additionally, after treatment with 15 g/L of glyphosate, there was a significant increase in the amount of abscisic acid in the anthers in the 8–9 mm buds. Further analysis of the differential expression of abscisic acid response and regulatory genes, an abscisic acid response gene GbTCP14 (Gbar_A11G003090) was identified, which was significantly upregulated in buds with 15 g/L glyphosate treatment than the control, and it could be a key candidate gene for the subsequent research involving male sterility induced by glyphosate in sea island cotton. Full article
(This article belongs to the Special Issue Genomics-Assisted Breeding for Cotton Improvement)
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