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[学术文献 ] Evaluating Water Stress Adaptation in Cotton: Multivariate Analysis in F6-F7 Generations for Yield, Fibre Quality and Variety Selection 进入全文
JOURNAL OF AGRONOMY AND CROP SCIENCE
The impact of drought stress on productivity of cotton (Gossypium hirsutum L.) is a well-known challenge in agricultural production, and concurrently, the question of whether using the same or different selection criteria in well-watered and water-deficit conditions to select drought-tolerant cotton varieties remains unclear. This study aimed to comprehensively assess the single plant progeny lines within the F6 and F7 generations for determine response to DS and select the tolerant lines within the F7 generation. Single plant progeny rows were established, with the deficit water condition comprising 108 and 136 single plants for the F6 and F7 generations, respectively, and the WW condition consisting of 120 and 156 single plants for the F6 and F7 generations, respectively, with four blocks in Augmented experimental design. These progeny rows have length of 12 m, incorporate five control varieties (Karizma, Gloria, Carla, Candia and Claudia) to facilitate a comprehensive comparison. The study findings showed that fibre length, boll number and lint percentage were identified as the most crucial selection criteria under both WW and deficit irrigation conditions through principal component analysis. These indicators are highly beneficial for evaluating cotton's drought tolerance and screening potential drought-tolerant lines under both irrigation scenarios. According to the decision tree analysis, FL and BN have emerged as the most critical decision-making parameter in both irrigation conditions. Furthermore, the analysis revealed that each selection criterion has different impact in the comprehensive selection process. Also, as a result of all statistical analysis results and breeder observations, a total of 10 cotton lines were selected in the F7 generation. These selected genotypes hold promise for future cotton breeding programmes, providing an avenue to enhance drought tolerance and elevate cotton yield and productivity.
[学术文献 ] Grafting based DNA methylation alteration of snoRNAs in upland cotton (Gossypium L.) 进入全文
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
The effects of grafting in response to various biotic and abiotic stressors have been studied, however, the methylation status of small nucleolar RNA (snoRNA) genes in heterograft and homograft cotton needs investigation. This study was undertaken to determine grafting effects on DNA methylation of snoRNA genes in Upland cotton. Rootstocks used were Pima 3-79 (Gossypium barbadense acc. Pima 3-79) and Texas Marker-1 (G. hirsutum acc. TM-1), representing two different species with different fiber properties, adaptations, and morphologies. The methylation ratio and differently methylated cytosines (DMCs) of 10935 snoRNA genes in mature seeds of heterograft and homograft cotton samples were studied using the whole genome bisulfite sequencing method. Seedling vigor and seed weight were studied to investigate phenotype alterations that might be associated with altered methylation levels among grafts. Statistically significant DMC differences among gene elements of snoRNA genes and between homograft and heterograft cotton samples were identified in the absence of DNA sequence alterations. DNA methylation alterations of snoRNA genes associated with seedling vigor and 100 seed weight. The majority of snoRNA genes showed higher numbers of (m)CG + (m)CHG-DMCs with increased methylation levels in heterograft, while there were higher numbers of (m)CG + (m)CHG-DMCs with decreased methylation levels in homograft. Since snoRNAs regulate essential genes for plant growth and development and plant adaptation to different habitats or extreme environments, their altered methylation levels should be related with plant physiology.
[学术文献 ] Genetic parameters and selection index in intraspecific cotton lines in a Brazilian semi-arid region 进入全文
CROP BREEDING AND APPLIED BIOTECHNOLOGY
The climatic and edaphic conditions of the semi-arid Brazilian Northeast region limit the production of several annual crops, including cotton. The aim of this study was to estimate the genetic parameters and select water stress tolerant cotton lines based on yield and fiber quality traits. Twenty cotton lines were evaluated in Alagoinha-PB over two years under rainfed conditions. Individual and joint analysis of variance was performed on the data. Genetic parameters were determined, and lines were selected using the selection index. SA 2019-165 were selected for further tests in the region for recommendation of new cultivars. These lines can form new blocks of crosses, together with the BRS 286 check cultivar, as they have the best mean yield and fiber quality values, with the expectation of significant genetic gains.
[学术文献 ] GhFAD3-4 Promotes Fiber Cell Elongation and Cell Wall Thickness by Increasing PI and IP3 Accumulation in Cotton 进入全文
PLANTS-BASEL
The omega-3 fatty acid desaturase enzyme gene FAD3 is responsible for converting linoleic acid to linolenic acid in plant fatty acid synthesis. Despite limited knowledge of its role in cotton growth, our study focused on GhFAD3-4, a gene within the FAD3 family, which was found to promote fiber elongation and cell wall thickness in cotton. GhFAD3-4 was predominantly expressed in elongating fibers, and its suppression led to shorter fibers with reduced cell wall thickness and phosphoinositide (PI) and inositol triphosphate (IP3) levels. Transcriptome analysis of GhFAD3-4 knock-out mutants revealed significant impacts on genes involved in the phosphoinositol signaling pathway. Experimental evidence demonstrated that GhFAD3-4 positively regulated the expression of the GhBoGH3B and GhPIS genes, influencing cotton fiber development through the inositol signaling pathway. The application of PI and IP6 externally increased fiber length in GhFAD3-4 knock-out plants, while inhibiting PI led to a reduced fiber length in GhFAD3-4 overexpressing plants. These findings suggest that GhFAD3-4 plays a crucial role in enhancing fiber development by promoting PI and IP3 biosynthesis, offering the potential for breeding cotton varieties with superior fiber quality.
[学术文献 ] Genome resources for three modern cotton lines guide future breeding efforts 进入全文
NATURE PLANTS
Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.
[政策法规 ] HudsonAlpha researchers create valuable genomic tools for the cotton industry 进入全文
HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY
We live in an ever-changing and growing world. Changing climates, emerging pests, and other environmental stressors put pressure on the cash crops that feed and fuel the world. As we race to meet the growing demand for sustainable and high-quality food and fiber crops, genomics is emerging as a powerful tool in the fight. By understanding plants’ genetic codes, researchers and breeders can develop crops with increased yields, improved resistance to pests and diseases, and greater adaptability to environmental challenges. Genome-informed breeding primarily benefits crops with existing high-quality genomic resources, like rice and wheat. However, crops with less mature genomic resources must continue to rely on traditional breeding methods, which sometimes suffer due to a lack of genomic diversity within the breeding populations. Cotton, a vital cash crop worldwide, lacks robust genomic resources. The cotton industry is big business, with a global economic impact of $600 billion and providing jobs for more than 250 million people. Successful cotton production relies on cotton varieties with desirable characteristics like high yield, good fiber quality, pest and disease resistance, and drought tolerance. “Cotton breeders have improved fiber yield and quality over the years using traditional breeding methods,” says Jeremy Schmutz, co-director of the HudsonAlpha Genome Sequencing Center, who has been working on cotton genomics for over a decade. “Achieving additional improvements may be difficult for them due to the lack of genetic variation across modern domesticated cotton. Creating new genomic tools for the industry will help take cotton improvements to the next level.” Scientists at the HudsonAlpha Institute for Biotechnology Genome Sequencing Center (GSC) and other collaborators set out to create high-quality genome sequences for three important cotton varieties, providing necessary genome resources for cotton breeders. The results were recently published in Nature Plants. “Cotton research has relied heavily on one reference genome, ‘TM1’, a variety of cotton that is no longer widely used in breeding programs,” says Avinash Sreedasyam, PhD, first author of the manuscript. “In order for molecular breeding to benefit the cotton industry, many, varied genomes must exist to represent the diversity of cotton varieties. This study generated high-quality reference genomes for three modern upland cotton cultivars and updated the ‘TM-1’ cotton genetic standard reference.” Initial analysis of the new reference genomes produced important information about fiber quality. The highly accurate and complete genome assemblies were used to identify genetic material from Pima cotton (known for superior fiber quality) within modern cotton varieties. Small segments of each genome were compared to both Pima and the reference cotton genome. Segments that matched Pima more closely than the reference cotton were classified as potential introgressions, suggesting Pima DNA had been incorporated into the modern cotton's genetic makeup. Knowledge of these Pima introgressions will help breeders to efficiently select progeny with these fiber-quality linked genetic markers in their breeding programs. “Leveraging relatively inexpensive low-pass sequencing alongside these genomes empowers breeders to select progeny rapidly,” says Sreedasyam. “This will not only save time but also reduce costs associated with traditional fiber phenotyping, a laborious process usually requiring hundreds to thousands of samples per breeding cycle.” These findings highlight the significance of using detailed genome assemblies to uncover genetic variations that can improve cotton breeding programs. The more these new, high-quality genomes are used for comparative studies, the more information about economically important cotton traits will emerge. The genomic resources described in this study represent a valuable addition to the cotton breeding toolkit and will reap benefits for years to come. Collaborators on this project include Don C. Jones, Cotton Incorporated, NC; Peng W. Chee, University of Georgia, Tifton, GA; Warwick N. Stiller, CSIRO, Cotton Research Unit, Australia; and Fred Bourland, University of Arkansas, Keiser, AR. This work is supported by Cotton Incorporated (Award 18-753) and the intramural research program of the US Department of Agriculture, National Institute of Food and Agriculture Foundational and Applied Science Program Award 2022-67013-36899. The findings, conclusions, or recommendations expressed here have not been formally disseminated by the US Department of Agriculture and should not be construed to represent any agency determination or policy.
