Location: Coastal Plain Soil, Water and Plant Conservation Research
2023 Annual Report
Objectives
Objective 1. Determine the ability of cotton germplasm to withstand soil water deficits, identify and characterize drought tolerance genes, and develop innovative management practices for optimizing use of the improved genotypes in production systems.
Sub-objective 1A. Identify genotypes with fiber length stability when subject to water deficit stress during fiber elongation.
Sub-objective 1B. Identify cotton genotypes that withstand soil water deficits.
Sub-objective 1C. Evaluate variable rate irrigation using crop feedback for site-specific irrigation management of cotton in the Southeastern U.S. Coastal Plain.
Objective 2. Develop and evaluate new cotton germplasm with increased genetic diversity, improved fiber quality, and lint yield stability traits.
Objective 3. Develop informed predictive models for cotton breeding using high-throughput phenotyping, environmental, and genomics data (NP301, C1 PS1A and PS1B).
Approach
New technologies and new genetic resources are needed to help the nation’s cotton producers face increasing economic and environmental challenges. The proposed research will contribute to the industry’s ability to meet the nation’s fiber needs and become more competitive in world markets. Since water deficit stress is a serious limitation to cotton production, much of this research will be aimed at finding solutions to lessen the impact of this environmental stress. The research has three objectives: (1) determine the ability of cotton germplasm to withstand soil water deficits, identify and characterize genetic variation for drought tolerance, and develop innovative management practices; (2) develop new cotton genetic resources with increased genetic diversity, improved fiber quality, and lint yield stability; and (3) develop predictive breeding models for cotton breeding. In this research, we will conduct genetic studies on the effect of water deficit stress on fiber length and yield, determine how best to use proximal sensing data collected from high throughput phenotyping platforms, design innovative double crop cotton production systems, and develop new cotton genetic resources. We will also develop informed predictive breeding models that improve yield, fiber quality, and climate resiliency. Research methods include field experiments and statistical analyses using modern analytical equipment and innovative analytics. Research products include new knowledge of genetic variation for fiber length stability under water deficit stress, protocols for using proximal sensing data collected from high throughput phenotyping platforms as a water deficit stress breeding selection tool, new water efficient cotton cropping systems, and high quality cotton germplasm containing exotic introgression. 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. All segments of the cotton industry and southern rural economies will benefit from the findings of this research.
Progress Report
This is the final report for this project. Refer to new project 6082-21000-009-000D, "Advancing Cotton Genetics and Innovative Cropping Systems for Improved Quality and Production" for additional information and will be replaced by pending project currently in research review.
Using exotic landrace germplasm in cotton breeding. New genetic variation is needed to broaden the genetic base while also improving the economic competitiveness of United States cotton. ARS researchers in Florence, South Carolina, and College Station, Texas, evaluated the potential of using a number of exotic upland landrace accessions in cotton breeding. These exotic accessions are day-neutral (do not require a short daylength to flower) and represent an untapped, rich diversity for cotton breeding programs. The research showed that using exotic accessions generated offspring with broadened genetic diversity and good fiber quality. However, offspring also suffer from a negative relationship between yield potential and fiber quality. These results provide guidance that public and private breeding programs can use when considering using exotic landrace accessions as new sources of genetic diversity.
Using extra long staple germplasm in cotton breeding. Efforts to transfer improved fiber quality alleles from extra long staple of Gossypium barbadense accessions into upland cotton offers an attractive way to improve the economic competitiveness of United States upland cotton. In partnership with University of Georgia, ARS researchers in Florence, South Carolina, developed upland cotton populations containing small segments of extra long staple DNA. The populations were evaluated in the field to determine the effect(s) of these transferred segments on fiber quality performance. The research showed that a number of extra long staple segments of DNA contained alleles for improved fiber quality. The effect of the beneficial alleles stably expressed across environments and years. These results provide guidance that public and private breeding programs can use when considering using extra long staple accessions as new sources of fiber quality.
Release of high yield and high fiber quality germplasm lines containing 50% exotic parentage. New genetic diversity is desperately needed to broaden the genetic base while also improving the economic competitiveness of U.S. cotton. Upland cotton’s narrow genetic diversity represents a major source of genetic vulnerability for the U.S. cotton industry. To address this genetic vulnerability, ARS researchers in Florence, South Carolina, College Station, Texas, and Maricopa, Arizona, in partnership with Cotton Incorporated and Clemson University, released five high yield and fiber quality germplasm derived from exotic lines originally from Asia, Africa, and South America accessions. The research showed that each new cotton line possesses 50% exotic parentage, excellent fiber quality, and excellent yield performance—significantly better than several commercial cultivars. These results provide public and private breeding firms a set of new, elite germplasm lines that can be used as breeding parents to develop new commercial cultivars with increased genetic diversity.
Documenting the genetic structure of the Pee Dee cotton breeding program. Understanding the landscape and organization of genetic diversity in a breeding program is critical to best formulate future breeding goals and strategies. In partnership with Clemson University, ARS researchers in Florence, South Carolina, and Raleigh, North Carolina, conducted a detailed genetic survey of the program’s eight historical breeding cycles and found that 99% of the total genetic variation was incorporated within the first four breeding cycles. The research showed that a small core collection of eleven lines captured 95% of the program’s genetic diversity. The research also identified genetic signatures differentiating the Pee Dee breeding program relative to other improved upland cotton germplasm across the world. Collectively, this information will be used to set future Pee Dee breeding program goals and directions. These results provide public and private breeding programs critical knowledge for bringing new, genomic assisted methods to cotton breeding that hold great promise to revolutionize cotton improvement.
Overcoming the negative relationship between yield and cotton fiber quality. Future cotton production systems need cultivars with improved fiber quality to meet global market demands and provide the textile industry with high-quality fiber. However, developing cotton cultivars with high yield potential and premium fiber quality has been a major bottleneck because of the negative relationship between yield and cotton fiber quality. To address this bottleneck, ARS researchers in Florence, South Carolina, evaluated the relationship between yield and fiber quality in several large, breeding populations developed using cotton breeding lines with both high yield and premium fiber quality potential as breeding parents. The research showed that the frequency of high yield/high fiber quality offspring was more significant in populations using parents with high yield and fiber quality. Moreover, the research demonstrated that the frequency of identifying high yield/high quality offspring in these populations remained extremely low--generally less than 3%. These results provide critical information that can be used to design breeding methods that simultaneously improve yield and cotton fiber quality.
Bringing high-value Pima cotton production to the southeast United States. Current southeast U.S. cotton production systems include the production of upland cotton only, while Pima cotton production is restricted to arid regions of the western United States. Due to its increased value relative to upland cotton, Pima cotton offers an attractive alternative crop for southeast United States producers. In partnership with Clemson University, ARS researchers in Florence, South Carolina, evaluated the yield performance and fiber quality of Pima cotton grown in the southeast U.S. The research showed that Pima cotton produced premium fiber quality compared to upland cotton but yielded 50% less. Although the net economic return of the highest-yielding Pima lines was not different from upland cotton, the research demonstrates that new Pima cultivars with adaptation to the southeast United States are needed to offset the current reduction in yield potential. These results provide critical information that can be used to evaluate the feasibility of commercial Pima cotton production in the southeast region of United States.
Cotton-Carinata cropping system research. Research was initiated in 2018 to evaluate Brassica carinata (carinata) as a winter cash cover crop in rotation with cotton. Carinata is a multi-use oilseed crop to produce an aviation biofuel for jet engines. Carinata also provides a source of protein meal for animal feed. In 2023, as part of the USDA-NIFA Coordinated Agricultural Project ‘Southeast partnership for advanced renewables from carinata-SPARC’, the sixth year of carinata breeding line evaluations was conducted in Florence, South Carolina. Although the 2018 field trial sustained significant freeze damage that resulted in 100% plant death, results in 2019, 2020, 2021, 2022, and 2023 demonstrate the potential for carinata production in the northern region of the southeast USA. In addition, a two-year study to evaluate the potential of carinata as a cover crop and/or double crop with cotton was completed in 2023. Data collected demonstrated that cotton following carinata had greater lint yields than cotton following wheat or fallow. This was attributed to greater boll density in carinata-cotton systems than wheat-cotton or fallow-cotton, with more prevalent secondary and tertiary bolls per plant. Collectively, this research supports subobjective 1C of the project plan to develop innovative management practices for optimizing production systems by determining the feasibility of carinata as a new part of the cotton production system in the northern southeast United States.
Accomplishments
1. Evaluation of new cover crop species in cotton production. Cover cropping offers an opportunity to improve soil health, maintain soil moisture, and provide more environmentally sustainable cotton production systems. However, cover crop adoption and use in United States cotton production has historically been limited in scale, with only a handful of annual cereal grass or legume species currently in use. Recent evidence suggests that cereal grass cover crops may remove or immobilize essential nutrients needed for optimal cotton growth and development. A new oilseed crop, carinata (Brassica carinata A. Braun), may lessen the impact of growing cover crops prior to cotton while serving as a potential double crop. To test the viability of carinata in rotation with cotton in the southeastern United States, ARS researchers in Florence, South Carolina, compared cotton yield, boll distribution, and fiber quality when following fallow, winter wheat, and carinata cover crop systems. The research showed that cotton grown following a carinata cover crop had 60% more bolls per plant than cotton grown after wheat or fallow systems, driven by greater retention of secondary bolls on reproductive shoots. Consequently, lint yield of cotton grown after carinata was greater than lint yields of cotton grown after winter wheat. These results suggest that carinata can serve as a more effective cover crop in rotation with cotton than established cereal grasses such as winter wheat.
2. Bringing predictive breeding methods to cotton breeding. Innovative breeding methods are needed to boost cotton agronomic performance and fiber quality. Predictive breeding methods that use molecular fingerprints, historical performance data, and advanced statistical techniques to predict future agronomic and fiber quality offer an attractive method to intensify genetic gain. To investigate the feasibility of predictive breeding in cotton, ARS researchers in Florence, South Carolina, and Stoneville, Mississippi, evaluated the prediction ability of using genomic selection for yield performance and fiber quality. Overall, we found that genomic selection programs for fiber quality displayed high prediction abilities and can begin immediately. However, the prediction ability for most other agronomic performance traits is lower but commensurate with heritability. These results provide critical information that can be used to evaluate the feasibility of predictive breeding methods to increase genetic gain.
Review Publications
Billman, E.D., Campbell, B.T., Reay-Jones, F. 2023. Using perennial groundcover crops to suppress weeds and thrips in the Southeast Cotton Belt. Crop Science. 63(5):3037-3050. https://doi.org/10.1002/csc2.21048.
Stone, K.C., Billman, E.D., Bauer, P.J., Sigua, G.C. 2022. Using NDVI for variable rate cotton irrigation prescriptions. Applied Engineering in Agriculture. 38(5):787-795. https://doi.org/10.13031/aea.15071.
Billman, E.D., Campbell, B.T. 2023. Cover cropping history affects cotton boll distribution, lint yields, and fiber quality. Crop Science. 63(3):1209-1220. https://doi.org/10.1002/csc2.20931.
