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Plant Genetic Resources and Their Use in Cotton Improvement

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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 2022) | Viewed by 18276

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Special Issue Editors

Dr. B. Todd Campbell

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Guest Editor

Coastal Plains Soil, Water, and Plant Research Center, USDA-ARS, Florence, SC 29501, USA
Interests: germplasm enhancement; cotton; plant genetic resources

Dr. Joshua Udall

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Guest Editor

Crop Germplasm Research Unit, USDA-ARS, College Station, TX 77845, USA
Interests: cotton genomics; polyploidy; introgression; germplasm resources

Dr. Lori Hinze

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Guest Editor

Crop Germplasm Research Unit, USDA-ARS, College Station, TX 77845, USA
Interests: cotton; plant genetic resources; germplasm collection characterization and evaluation

Special Issue Information

Dear Colleagues,

Plant genetic resources are a critical part of crop improvement programs. They provide important sources of biotic and abiotic stress tolerance or resistance, enhanced crop quality, increased genetic diversity, and other traits important to crop production. The plant genetic resources available for cotton (Gossypium spp.) improvement are extensive and consist of greater than 50 species. Globally, the majority of cotton production comes from the cultivation of two primary species, G. hirsutum L. (upland) and G. barbadense L. (pima), which account for nearly 35 million hectares of production area that will produce a farmgate value of $35 billion USD. Although the primary use of cotton is for its spinnable fiber that is used to manufacture textile products, other crop constituents such as the seed and its byproducts are used in a number of food chain applications as sources of oil and protein for human and animal consumption. The available cotton plant genetic resources provide a readily available source of genetic diversity for long term cotton improvement. In this Special Issue, our aim is to highlight the use of plant genetic resources for cotton improvement. We invite you to submit a research paper on any aspect of using plant genetic resources to advance cotton improvement.

Dr. B. Todd Campbell
Dr. Joshua Udall
Dr. Lori Hinze
Guest Editors

Manuscript Submission Information

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Keywords

cotton
plant genetic resources
crop breeding
germplasm enhancement
crop genetics
crop genomics
bioinformatics

Published Papers (3 papers)

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Research

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16 pages, 1986 KiB

Open AccessArticle

Outlook for Implementation of Genomics-Based Selection in Public Cotton Breeding Programs

by Grant T. Billings, Michael A. Jones, Sachin Rustgi, William C. Bridges, Jr., James B. Holland, Amanda M. Hulse-Kemp and B. Todd Campbell

Plants 2022, 11(11), 1446; https://doi.org/10.3390/plants11111446 - 29 May 2022

Cited by 3 | Viewed by 4570

Abstract

Researchers have used quantitative genetics to map cotton fiber quality and agronomic performance loci, but many alleles may be population or environment-specific, limiting their usefulness in a pedigree selection, inbreeding-based system. Here, we utilized genotypic and phenotypic data on a panel of 80 important historical Upland cotton (Gossypium hirsutum L.) lines to investigate the potential for genomics-based selection within a cotton breeding program’s relatively closed gene pool. We performed a genome-wide association study (GWAS) to identify alleles correlated to 20 fiber quality, seed composition, and yield traits and looked for a consistent detection of GWAS hits across 14 individual field trials. We also explored the potential for genomic prediction to capture genotypic variation for these quantitative traits and tested the incorporation of GWAS hits into the prediction model. Overall, we found that genomic selection programs for fiber quality can begin immediately, and the prediction ability for most other traits is lower but commensurate with heritability. Stably detected GWAS hits can improve prediction accuracy, although a significance threshold must be carefully chosen to include a marker as a fixed effect. We place these results in the context of modern public cotton line-breeding and highlight the need for a community-based approach to amass the data and expertise necessary to launch US public-sector cotton breeders into the genomics-based selection era. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Their Use in Cotton Improvement)

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16 pages, 2053 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

by Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, J. Todd Campbell, Josh Udall and Dorrie Main

Plants 2021, 10(12), 2805; https://doi.org/10.3390/plants10122805 - 18 Dec 2021

Cited by 45 | Viewed by 5892

Abstract

Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Their Use in Cotton Improvement)

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Review

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12 pages, 2576 KiB

Open AccessReview

Stories from the Greenhouse—A Brief on Cotton Seed Germination

by Andrea B. Maeda, Leslie W. Wells, Monica A. Sheehan and Jane K. Dever

Plants 2021, 10(12), 2807; https://doi.org/10.3390/plants10122807 - 18 Dec 2021

Cited by 12 | Viewed by 6692

Abstract

Seed germination is the basis for the proliferation of sexual-reproducing plants, efficient crop production, and a successful crop improvement research program. Cotton (Gossypium spp.), the subject of this review, can be often sensitive to germination conditions. The hardness of the cotton seed coat, storage, extreme temperatures, and dormancy are some of the factors that can influence cotton seed germination. Research programs conducting studies on exotic and wild cotton species are especially affected by those hurdles. Here, we briefly review the challenges of cotton seed germination and some of the approaches our cotton breeding program explored throughout the years. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Their Use in Cotton Improvement)

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