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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Research Project #434500

Research Project: Utilizing Conventional and Molecular Approaches to Enhance Seed and Fiber Quality Traits, and Conducting a National Cotton Variety Testing Program

Location: Crop Genetics Research

2021 Annual Report

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.

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 project began in April 2018 and is currently on track with most of the thirty-six month milestones substantially met. 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. U.S. 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 also can 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. 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 lines were not planted in the field due to the recent retirement of the SY conducting the research. 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 will be harvested and further evaluated for NGE and fiber quality. Leaf samples for DNA analyses were collected in 2019 from 630 of the progeny and their parents. This part of the project is pending. 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 2019, eighty-four plants were selected from populations developed in the previous project. In 2021, these selected lines are being tested in the field at two locations near Stoneville, Mississippi and being evaluated for yield and fiber quality. 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 is temporarily on hold. 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 cotton leafroll dwarf virus (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. During 2019-2020, 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 are being re-tested for the third year and additional new lines screened at multiple locations in collaboration with Task Force members. A program was also initiated to transfer the resistance from the potentially resistant lines to adapted cultivars. However, for 2020 the program had to be downsized and only a few matings made. The 2021 field season has also been restricted to testing the potential resistant lines for another year. As a priority, CLRDV crosses will be attempted during the limited time available. Objective 5 provides for a coordinated National Cotton Variety Test (NCVT), a multi-location test for breeders to evaluate new cotton material and provides a database of performance data across locations and years. The 2021 tests are being conducted in seven regions across the cotton growing area of the U.S and includes a Regional High Quality Test (RHQ) specifically to identify new lines with better quality fiber. Results for 2018 have been posted online, but 2019 and 2020 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 second year of the cycle were distributed to participants and seeds for the third year are stored in a coldroom at Stoneville for distribution next year. 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. As part of the new Objective 6, cotton germplasm will be 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 will be on CLRDV resistant cotton for the U.S. cottonbelt. Objective 6 complements ongoing research under Objective 4 to mitigate the effects of CLCuV and CLRDV as well as develop resistant cotton cultivars.

1. Identifying simple sequence repeat (SSR) markers associated with the nectariless trait. ARS researchers in Stoneville, Mississippi, identified DNA markers associated with the nectariless trait that can be used by breeders to develop cotton with decreased attractiveness to damaging insects and reduce the need for insecticides. Cotton has nectaries containing concentrated nectar. The nectar attracts some beneficial insects such as bees that feed on the nectar, but also insects that damage the plant. There is a naturally occurring mutation that eliminates the nectaries and makes the cotton plants less attractive to insects. Transferring this “no nectary” (nectariless) trait to cotton cultivars is difficult because it is hard to score the trait visually. Checking for presence of the nectariless trait can be done faster and more efficiently with DNA markers to help the plant breeder accurately select for this trait in early generations of the breeding process.

2. Transgenic traits could affect genetic variation in field crops. It was not clear how or if transgenic traits affect genetic variation in field crops. In this study, led by ARS researchers in Stoneville, Mississippi, fiber yield, fiber quality, and genetic variation were compared between transgenic and non-transgenic cotton in 18 years of Regional High Quality (RHQ) tests across the U.S. Cotton Belt. Results showed that yield of transgenic cotton was higher than non-transgenic cotton. However, fiber quality of non-transgenic cotton was higher than transgenic cotton. Genetic variation of fiber yield and fiber quality in transgenic cotton were lower than non-transgenic cotton. The discrepancy between the two types of cotton in the 18 years of RHQ tests reflects the influence of differential breeding schemes in private and public breeding programs on yield and fiber quality and their genetic variances. In the private sector, backcrossing is the primary breeding scheme in development of transgenic cotton to incorporate transgenic traits into elite lines used as the recurrent parent. Therefore, the genetic variation within transgenic lines in the 18 years of RHQ tests was limited to the extant cultivars within each commercial program. These results highlight the importance of diverse breeding schemes to maintain genetic variation in cotton cultivars. Cotton breeders in both the public and private sectors can use this information to improve fiber yield and quality in their breeding programs.

Review Publications
Bellaloui, N., Saha, S., Tonos, J.L., Scheffler, J.A., Jenkins, J.N., McCarty Jr, J.C., Stelly, D.M. 2020. Effects of interspecific chromosome substitution in upland cotton on cottonseed micronutrients. Plants. 9(9):1-17.
Zeng, L., Wu, J., Bourland, F.M., Campbell, B.T., Dever, J.K., Hague, S.S., Myers, G.O., Raper, T.B., Smith, C.W., Zhang, J. 2021. Comparative study of transgenic and nontransgenic cotton. Crop Science. 61:2467-2477.
Bellaloui, N., Saha, S., Tonos, J.L., Scheffler, J.A., Jenkins, J.N., McCarty Jr, J.C., Stelly, D.M. 2021. Effects of interspecific chromosome substitution in upland cotton on cottonseed macronutrients. Plants. 10(6):1-13.
Bellaloui, N., Turley, R.B., Stetina, S.R. 2021. Cottonseed protein, oil, and minerals in cotton (Gossypium hirsutum L.) lines differing in curly leaf morphology. Plants. 10(3):525.
Park, S., Scheffler, J.A., Ray, J.D., Scheffler, B.E. 2021. Identification of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) that are associated with nectariless trait of Gossypium hirsutum L.. Euphytica. 217:78.