Location: Crop Genetics Research
2023 Annual Report
Objectives
1. Use molecular techniques to evaluate near isogenic cotton lines of phenotypic variants to discover novel fiber and leaf trichome traits, and work with breeders to develop and release germplasm with improved fiber traits.
2. Characterize available sources of the cotton ginning efficiency trait, develop and evaluate improved germplasm, and work with ARS cotton ginners to design best ginning practices for effective use of the new germplasm.
3. Determine efficiency of trait transfer in cotton breeding populations that occurs during inter-mating and backcross introgression of fiber traits; select, evaluate, and release lines with improved fiber and lint yield traits, especially reduced negative linkages between fiber quality and lint yield.
4. Identify and introgress into adapted cotton lines, natural variants that improve host plant resistance, including protective compounds and potentially invasive species that are impending or looming threats, such as cotton leaf curl virus.
4a. Identify and test molecular markers associated with traits that will enhance cotton host plant resistance.
4b. Combine into one elite line multiple traits that will enhance cotton host plant resistance.
5. Conduct a regional and national cotton variety testing program to generate supporting data, maintain a database of the evaluation, and use the information to develop genetic and/or production strategies to improve the cotton crop.
6. Identify cotton germplasm with tolerance or resistance to either the vector or the virus of insect-borne viral pathogens, with an initial focus on the cotton leafroll dwarf virus and develop relevant germplasm for the U.S. cotton belt.
Approach
This project will combine the expertise and plant materials of four scientists to provide a coordinated approach for improving grower profits by decreasing input costs and providing high yielding cotton lines that will meet the fiber quality needs of the modern textile industry. This approach includes using cotton variants as a tool, as well as novel cotton lines developed from intermating diverse germplasm, to reduce the existing negative association between yield and fiber quality. Improve the efficiency and accuracy of the intermating and introgression techniques by using DNA markers to track the intermating and introgression process over generations. Use the rapidly expanding arsenal of molecular techniques to develop and evaluate near isogenic lines with phenotypic variants for fiber and leaf trichomes. Study trichome initiation mechanisms using the isogenic lines. Increase the use of cotton seed for animal and fish feed by introgressing traits that make the seed less toxic. Improve cotton’s host plant resistance (HPR) to pests, by introgressing into adapted lines, existing traits that provide genetic resistance to diseases that attack cotton, improve the levels of protective compounds in the plant and the nectariless trait that decreases the plant’s attractiveness to insects. Evaluate the feasibility of using cotton genotypes with low attachment strengths to improve ginning efficiency and decrease fiber damage during the ginning process. Provide a venue to test elite lines and new varieties through coordinated multi-location tests, and use the data generated to compile a database of performance data across locations and years.
Progress Report
This is the final report for this project which has been replace by project #6066-21000-053-000D, "Developing Strategies and Tools to Mitigate Biotic and Abiotic Stresses in Cotton and Managing the National Cotton Variety Testing Program" please refer to this project for additional information.
This project began in April 2018 and is currently about two years behind schedule with 36 month milestones substantially met, but the 60 month milestones only fully met for Objective 6. The delays were due to the 2.5 years of COVID-19 restrictions and two SY vacancies. The project concentrates on research designed to improve cotton grower profits and make U.S. grown fiber more competitive in the global market. The international market requires higher fiber quality and the surviving domestic textile industry has dramatically raised its standards as it modernizes and requires fiber capable of withstanding faster spinning speeds. United States breeders must now search more widely for unique germplasm and find novel ways to generate new cotton lines to improve cultivar fiber quality. However, yield is always the top priority for growers and a major challenge remains, to reduce the existing negative association between yield and fiber quality. Cotton variants are one tool that can be used to reduce this negative association, as well as developing novel cotton lines by crossing (mating) diverse types of cotton and using new and improved methods to make sure they are intermating as expected. Objectives 1 and 3 address these issues. Grower profits can also be increased through reducing input, harvesting and ginning costs or altering the composition of the seed to make it more marketable as animal feed or edible oil. Objectives 2 and 4 evaluate ways to reduce inputs for the grower and ginner. Growers also benefit from growing cultivars resistant to diseases or insect pests and objectives 4 and 6 concentrate on identifying sources of resistance to emerging cotton pest threats and developing cotton resistant to those threats. A venue is then needed to test elite lines and new varieties. Objective 5 provides for a National Cotton Variety Test program that coordinates multi-location testing for breeders and provides a database of performance data across locations and years. This project combines the expertise and plant materials of four scientists to provide a coordinated approach for improving grower profits by decreasing input costs and providing high yielding cotton lines that will meet the fiber quality needs of the modern textile industry.
The research supports National Program 301 (NP 301) “Plant Genetic Resources, Genomics, and Genetic Improvement”. Specific components of the NP 301 Action Plan addressed by this project are Research Component 1: Crop Genetic Improvement, Problem Statement 1A “Trait discovery, analysis, and superior breeding methods” and 1B “New crops, new varieties, and enhanced germplasm with superior traits”. The project also contributes to Component 3: Crop Biological and Molecular Processes, Problem Statement 3A: “Fundamental knowledge of plant biological and molecular processes” in the Action Plan.
Under Objective 1, special lines with the same genetic background except for one trait of interest (near isogenic lines, NILs) have been developed to study the mechanism that makes cotton fibers elongate to one inch or greater. Using one set of NILs, a special form of a cell wall protein was identified that when mutated produces short (<1/4 inch) fiber, whereas the normal form of the protein produces normal length fiber. This information could help scientists develop cotton lines with even longer fiber. Additional NILs are being developed for other traits of interest in cotton. This project is currently on hold as the scientist in charge of this research retired in FY 2021 and there was no one to continue the project until the position is refilled.
Objective 2 aims to increase net ginning efficiency (NGE) by identifying cotton lines that take less force to detach the cotton fiber from the seed. Lines with high NGE were mated with high yielding cotton lines possessing superior fiber quality. Progeny from thirty of the matings between high NGE cotton and high quality cotton were evaluated and eighteen were ultimately chosen based on NGE and fiber quality. These lines are being grown in the field and screened for the nectariless (ne) trait. This ne trait makes the plants less desirable to damaging cotton insects. The fiber from these lines was harvested, but further evaluation for NGE and fiber quality is on hold. Leaf samples for DNA analyses were collected from 630 progeny and their parents. This part of the project is also on hold as the scientist in charge of this project retired in FY 2022, and due to COVID-19 restrictions, we had limited time in the laboratory to complete the DNA analyses needed for this objective.
Previously breeders could develop cotton with high quality fiber or high yield, but it was not possible to have both in one cotton variety. As part of the Objective 3 goal to break the negative linkage between fiber quality and yield, new lines are being selected and evaluated. In 2021, plants, selected from populations developed in the previous project, were tested in the field at two locations near Stoneville, Mississippi and evaluated for yield and fiber quality. In 2022, these plants were further tested in replicated field trials at Stoneville and Las Cruces, New Mexico.
In 2018, two soft funded projects, previously initiated to identify resistance to U.S. cotton disease threats, were expanded and formed the basis for Objective 4 in the current project. Research on cotton leaf curl virus (CLCuV) has progressed and advanced material has been developed with dual resistance to the two most prevalent strains of CLCuV. However, the project was temporarily delayed and is now two years behind schedule as marker assisted selection was delayed and it was not possible to send seed to Pakistan for field screening for CLCuV in 2021. We resumed genotyping and marker assisted selection for CLCuV in the summer of 2022 and we plan to send seed to Pakistan for screening in 2023 and 2024.
Cotton blue disease (CBD) is caused by the cotton leaf roll dwarf virus (CLRDV) and research was initiated in 2016 at ARS Stoneville, Mississippi to develop U.S. adapted cotton lines resistant to CBD. At that time, CBD had not been reported in the U.S.; however, in 2017, CBD-like symptoms were first observed in several southern Alabama fields. Using laboratory diagnostic tests and DNA sequencing, the virus was identified as an atypical form of CLRDV which is transmitted by cotton aphids (Aphis gossypii). In 2018, the virus was detected across the cottonbelt, and caused yield losses for growers. To combat this emerging disease threat, a Task Force of researchers, including one of the scientists on this project, was assembled. Symptomology for CLRDV was studied and a photo key of symptoms developed for other researchers and growers. In 2019, a collaborative multi-location field screening test of cotton cultivars and germplasm, confirmed that all the U.S. cultivars tested were susceptible to CLRDV, but there were a few germplasm lines that had no symptoms and tested negative for the virus. These lines are now being re-tested for the fourth year and additional new lines screened in 2022 at two locations in collaboration with a Task Force breeder from Auburn, Alabama. Five lines have consistently tested as resistant and a program was initiated to transfer the resistance from the potentially resistant lines to adapted cultivars. The program had to be downsized and only a few matings were made in 2020 and 2021 field seasons. Due to limited access to the lab, during the 2021 field season screening was limited to evaluating potential resistant lines for a third year or advancing to the F2 generation mapping population progeny. During the 2023 field season, new crosses and F2 mapping populations are being evaluated with DNA markers to conduct marker assisted selection and attempt to map the resistance trait.
Objective 5 provides for a coordinated National Cotton Variety Test, a multi-location test for breeders to evaluate new cotton material and provides a database of performance data across locations and years. The 2023 tests are being conducted in seven regions across the cotton growing area of the U.S and includes a Regional High Quality Test specifically to identify new lines with better quality fiber. Results for 2021 have been posted online, but 2022 results are not completed due to delays in fiber analyses in the ARS fiber testing lab. To ensure the availability and quality of the national standards seed, a seed distribution system was established with ARS Stoneville, Mississippi obtaining enough seed of the eight national standards from their source companies for a three-year cycle. Seed for the third year of the cycle were distributed to participants in 2022.
In 2020, new funds were appropriated by Congress to mitigate the effects of CLRDV and develop new resistant cultivars, resulting in an additional objective being added to this project. A new Objective 6 was created and as part of the new objective, cotton germplasm are being identified with tolerance or resistance to the virus or it’s insect vector and resistant/tolerant lines developed for U.S. cotton growers. The initial focus was on CLRDV resistant cotton for the U.S. cottonbelt, but in 2022 a germplasm evaluation for resistance to cotton leaf crumple virus (CLCrV) was initiated with a cooperator in Weslaco, Texas where the virus is endemic. This research was extended and expanded in 2023 to screen for additional cotton viruses. Objective 6 complements ongoing research under Objective 4 to mitigate the effects of CLCuV and CLRDV as well as develop resistant cotton cultivars.
Accomplishments
1. A comparative study between trait selections and marker-assisted selections (MAS) to improve fiber strength in Upland cotton. In traditional crop breeding, selections for genetic improvement of quantitative traits such as fiber quality traits in cotton are based on observable traits. In recent decades, selection with the aid of molecular markers has emerged as a new breeding approach. However, there is a lack of reports on the efficiency of this new approach in crop breeding, especially in cotton. It is unknown whether breeding with the aid of molecular markers is advantageous over breeding based on observable traits in terms of efficiency and breeding values. This study, conducted by ARS researchers in Stoneville, Mississippi, was designed to investigate the efficiency of selection for fiber quality using molecular marker assisted cotton breeding in comparison with breeding based on observable traits using two breeding populations. Results varied in the two breeding populations. In one breeding population, breeding assisted by molecular markers was more efficient than the breeding based on observable traits. In another breeding population, the breeding values were similar using marker-assisted breeding and phenotype-based breeding. Considering the cost and time spent with traditional breeding, marker-assisted breeding could still have an advantage over breeding based on observable traits even with similar breeding values between the two systems. These results suggest selection by MAS for fiber quality is better than selection based on observable traits.
2. Identification and transfer of genetic resistance to cotton leaf roll dwarf virus (CLRDV). CLRDV causes cotton blue disease (CBD), a devastating disease that caused millions of dollars in crop losses each year in Brazil before resistant cultivars were developed. In 2017, CLRDV was first reported in the United States and by 2019 had spread across the southern cotton producing states and was classified as an emerging threat to United States cotton production. As part of a collaboration with Mississippi State University using field screening with PCR based diagnostics, evaluation of CBD resistant cultivars from Brazil determined they were susceptible to the United States strain. ARS reseachers in Stoneville, Mississippi, evaluated lines from the ARS Stoneville germplasm collection as well as accessions from the USDA Cotton Germplasm Collection for new sources of resistance to CLRDV to be field screened for resistance. After four years of evaluation, five putative resistant lines were identified. Crosses were made between the five lines and elite lines with progeny now in the F2 generation. The F2 lines are being used to develop DNA markers and the selected plants advanced in a program to develop resistant cotton lines. These lines are the first with identified resistance to the U.S. strain of CLRDV and offer a source public and private breeders can use to develop resistant cultivars for U.S. growers.
Review Publications
Zeng, L., Fang, D.D., Li, P., Delhom, C.D. 2023. A comparative study between trait selections and marker-assisted selections to improve fiber strength in upland cotton. Crop Science. 63:1092-1101. https://doi.org/10.1002/csc2.20881.
Hron, R.J., Hinchliffe, D.J., Thyssen, G.N., Condon, B.D., Zeng, L., Santiago Cintron, M., Jenkins, J.N., Mccarty Jr, J.C., Sui, R. 2023. Interrelationships between cotton fiber quality traits and fluid handling and moisture management properties of nonwoven textiles. Textile Research Journal. https://doi.org/10.1177/00405175221132011.
Mahmood, M.A., Ali, W.R., Naqvi, R.Z., Amin, I., Scheffler, J.A., Mansoor, S. 2023. Mac7 maintains resistance against cotton leaf curl complex associated with the third epidemic of cotton leaf curl disease in Pakistan. Plant Disease. https://doi.org/10.1111/ppa.13722.
Sabanadzovic, N., Allen, T.W., Scheffler, J.A., Sabanadzovic, S. 2022. First report of pothos latent virus infecting upland cotton (Gossypium hirsutum) in the United States. Plant Disease. https://doi.org/10.1094/PDIS-10-22-2325-PDN.
Hinchliffe, D.J., Thyssen, G.N., Condon, B.D., Zeng, L., Hron, R.J., Madison, C.A., Jenkins, J.N., Mccarty Jr, J.C., Delhom, C.D., Sui, R. 2023. Interrelationships between cotton fiber quality traits and tensile properties of hydroentangled nonwoven fabrics. Journal of Industrial Textiles. https://doi.org/10.1177/15280837231171312.
