Location: Coastal Plain Soil, Water and Plant Conservation Research
2024 Annual Report
Objectives
1. Conduct research to broaden the cotton genetic base, improve fiber quality, increase yield stability and adaptation to climate change, and develop cotton germplasm, along with molecular markers for effective selection.
2. Conduct innovative research that producers can use to develop cropping systems that incorporate customized cover crops to improve cotton production and fiber quality, reduce inputs, and determine soil health and/or environmental benefits.
2.A. Develop and implement novel cotton-cover cropping systems that reduce inputs and increase soil health for sustainable cotton production.
2.B. Improve the adaptation and climate resiliency of novel cover crop species that can be incorporated into southeastern US cotton production systems.
3. Develop informed predictive models for cotton breeding using high-throughput phenotyping, environmental, and genomics data.
Approach
Cotton is the world’s primary source of natural, spinnable fiber and accounts for one third of global fiber consumption. There has been slow progress in cotton improvement for yield potential; however, fiber quality, adaptation to climate change, and yield stability improvements are sorely needed. In addition, customized cropping systems are needed that decrease the environmental impacts of cotton production while maximizing ecosystem services. To meet these needs, this research aims to develop improved breeding tools, germplasm, and enhanced management practices for the US cotton. Research in Objective 1 harnesses recent genomic and phenomic advances to develop predictive breeding methods that accelerate cotton’s genetic gain and broaden the genetic base. The research identifies new, beneficial alleles from distant germplasm and deploys a strategy to increase their frequency. Research in Objective 2 develops novel cotton-cover cropping systems that conserve soil moisture, reduce inputs, and increase soil health for sustainable cotton production. The research also improves the adaptation and climate resiliency of novel cover crop species incorporated into southeastern US cotton production systems. The information gained in the research on predictive breeding will better integrate genomic and phenomic research advances into tangible outcomes that drive cotton’s future genetic gains. This research will be of use to public and private plant breeders to provide the industry with future cultivars. Cover crop research will help growers, consultants, and industry maximize cotton production while minimizing environmental impacts in cover crop integrated cotton production systems. Together, the development of new genetic resources and better crop management practices will contribute to enhanced productivity and increased sustainability of the US cotton industry.
Progress Report
Predictive breeding models for cotton improvement. The overall objective is to develop predictive breeding models to improve yield, fiber quality, and climate resiliency in elite and exotic cotton. To accomplish this, training populations must be assembled, genotyped with DNA markers, and evaluated in field trials. In year 1, elite and exotic sets of cotton germplasm were assembled as training populations and grown in a greenhouse. The elite set consists of 400 breeding lines developed from 2005-2020 in the USDA-ARS Pee Dee germplasm enhancement program. The exotic set consists of a collection of 300 naturally occurring day-neutral exotic landrace accessions obtained from the USDA national cotton germplasm collection. For both germplasm sets, leaf tissue was harvested from each breeding line/accession and used to extract genomic DNA for an assay to identify single nucleotide polymorphism markers. In addition, both germplasm sets were seed increased to provide sufficient supplies of seed for multi-location field trials in years 2 and 3. This research supports Objective 1 of the project plan to develop robust predictive breeding models for elite and exotic cotton.
Perennial cover crop integration with cotton production. A pilot-scale (0.5 acre) field study was initiated and the first year completed to assess the efficacy of growing perennial cover crops with cotton in the southeastern U.S. cotton belt. These perennial cover crops can potentially offset chemical, labor, fuel, and time inputs necessary to manage cotton by providing a biological control for weed and insect pest pressure and reducing the number of pesticide applications. First year results from the trial indicated that the presence of cool-season perennial cover crops, particularly red and white clovers, can substantially reduce weeds and insect pests during the growing season compared to using an annual cover crop while applying only a single in-row herbicide application and no insecticide. Data was presented at various scientific and stakeholder meetings during FY24 (American Society of Agronomy/Crop Science Society of America Annual Meeting; Beltwide Cotton Conference). This research supports subobjective 2A of the project plan to develop and implement novel cotton-cover cropping systems that reduce inputs and increase soil health for sustainable cotton production.
Drought tolerant perennial cover crop germplasm development. Initial selection for drought hardy perennial cover crop germplasm began in winter 2023-24 on white clover and Kentucky bluegrass populations that are currently prone to stand losses under drought and heat stress common in the southeastern United States. Each of these species has potential as a perennial groundcover crop that can suppress weed pressure with minimal impacts on cotton production, but drought conditions in the southeastern U.S. cotton belt necessitate genetic improvement in each species for persistence beyond a single growing season. Approximately 100,000 seed of each species were mass screened for germination under 1 -1.5% saline (NaCl) solution in a controlled environment growth chamber. Salt reduces water potential and makes it difficult for a seed to take in water, so if a seed successfully germinated and survived in saline solution, it was advanced to Cycle 1 of selection for drought hardiness. Less than 0.03% of all seed screened germinated and were advanced to Cycle 1. Following several months of mass screening, the 128 most-vigorous plants of each species were selected, and nurseries established for the crops to cross-pollinate. Seed will be harvested in spring 2025 followed by germination testing to compare germination in saline solution of advanced cycles of selection against the initial parental genotypes. This research supports subobjective 2B of the project plan to improve the adaptation and climate resiliency of novel cover crop species that can be incorporated into southeastern US cotton production systems.
Accomplishments
1. Developing cotton genotypes with reduced re-growth. In its native form, cotton is a perennial shrub that is managed as an annual crop in production agriculture. To facilitate annual growth habit management and mechanical harvest, producers apply desiccant and hormonal based chemicals to defoliate the crop and reduce regrowth. As an alternative, native genetic variation for defoliation efficiency and reduced regrowth could be used as a tool to facilitate mechanical harvest but also increase yield by mobilizing important metabolic processes from source tissues (plant body) to sink tissues (bolls). To investigate the feasibility of developing cotton lines with more efficient defoliation and reduced regrowth, ARS researchers at Florence, South Carolina, partnered with scientists at Clemson University to identify and characterize cotton lines with reduced regrowth. The study identified several reduced regrowth cotton lines used to study the heritability of reduced regrowth and the expression of five floral induction and meristem identify genes. Overall, we found that reduced regrowth was heritable and transmissible to offspring. In addition, we found the expression of floral induction and meristem identify genes was associated with reduced regrowth. These results provide critical information that can be used to further develop high yielding cotton varieties with reduced regrowth.
2. Developing a new, innovative, and environmentally sustainable bioeconomy for the southeast USA. New crops and innovative cropping systems are needed to provide new economic opportunities for producers in the southeast USA. Crops that produce a biobased fuel production feedstock, while not displacing food, feed, and fiber crops, are of great interest, especially in the southeast USA. One such crop is Brassica carinata (carinata). As a winter rotational crop, carinata has the potential to provide winter/cover ecosystem services and a bio-feedstock for a high value, renewable aviation fuel without displacing fiber, feed, and food crops. To investigate the feasibility of carinata production in the southeast USA, ARS researchers at Florence, South Carolina, Tifton, Georgia, and Dawson, Georgia, partnered with scientists from private and public institutions through a University of Florida led USDA-NIFA coordinated agricultural project. The study assessed the yield potential and adaptation of carinata varieties grown as a winter crop over three years across the entire southeast USA region. Results demonstrated the feasibility of winter carinata production across the region and separated the region into three, smaller geographical areas to guide placement of commercial seed varieties within the region. Identification of geographical areas of concern due to freeze injury risk, along with areas of best fit for production, provided producers and commercial seed providers critical information to establish a new bioeconomy for the southeast USA that reduces carbon emissions by 68%.
Review Publications
Naveed, S., Jones, M.A., Campbell, B.T., Rustgi, S. 2023. Development of high-yielding upland cotton genotypes with reduced regrowth after defoliation using a combination of molecular and conventional approaches. Genes. 14(11):2081. https://doi.org/10.3390/genes14112081
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Singh, J., Gamble, A.V., Brown, S., Campbell, B.T., Jenkins, J.N., Koebernick, J., Bartley, P.C., Sanz-Saez, A. 2023. Exploring 65 years of progress in cotton nutrient uptake, efficiency and partitioning in the USA. Field Crops Research. 305. Article 109189. https://doi.org/10.1016/j.fcr.2023.109189.
Campbell, B.T., Seepaul, R., Anderson, W.F., Baldwin, B.S., Bennett, R., Crozier, C.R., George, S., Hagan, A.K., Iboyi, J.E., Lee, D., Macoon, B., Malihot, D., Morrison, J.I., Mulvaney, M.J., Post, A., Small, I.M., Wright, D.L. 2023. Agronomic performance and the effect of genotype-by-environment interaction for Brassica carinata in the southeastern US. Industrial Crops and Products. 203. Article 117196. https://doi.org/10.1016/j.indcrop.2023.117196.