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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

2020 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 twenty-four month milestones fully 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. 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 currently on hold due lack of access to the lab during the COVID-19 work restrictions. 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 2020, these selected lines are being tested in the field at two locations near Stoneville, Mississippi and being evaluated for yield and fiber quality. In a second study under Objective 3, progeny from matings between Delta lines with high yield and Pima cotton lines with high quality fiber, are being grown in field tests at Stoneville, Mississippi and will be 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 on schedule and advanced material has been developed with dual resistance to the two most prevalent strains of CLCuV. However, the project is temporarily on hold due to COVID-19 work restrictions and Milestones for 2021 will likely need to be modified to reflect this delay. 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, virus-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 this 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, the program was downsized and only a few matings made due to the COVID-19 restrictions. 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 2020 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 and 2019 should be available by the end of 2020. This year two major changes were made to the NCVT with the number of national standards increased to eight and regional standards were eliminated in all regional tests except RHQ. To ensure the availability and quality of the national standards seed, a new 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 first year of the cycle are distributed to participants and seeds of the next two years are stored in a coldroom at Stoneville for distribution over the next two years. ARS Stoneville has also joined the Partnership for Data Innovation program led by ARS New Orleans, Louisiana. Under the program, the historic NCVT information will be converted to a standardized format and uploaded into a centralized database that can be readily accessed by interested stakeholders. Cotton fiber neps and seed coat neps are impurities in cotton raw fibers that reduce yarn quality and cause flecks in cotton fabrics. A study conducted under Objective 5 showed it was possible to successfully select for fewer fiber neps and seed coat neps without sacrificing fiber yield. 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. New sources of improved cotton fiber. Recent advances in spinning technologies require longer and stronger cotton fibers to manufacture high-quality textiles with minimal waste from short or immature fibers. Only modest gains in fiber quality have been reported over the last few decades of intensive plant breeding, probably due to the overreliance on a relatively few elite and genetically similar cultivars for use as parents in most cultivar development programs. Sources of parents with unique fiber traits have been limited; however, modifying cotton using chemical mutagenesis offers a new source of genetic variation. Mutagenesis of seed from regionally adapted cultivars followed by screening and conventional breeding techniques resulted in plants with heritable fiber traits better than their parents, including improved fiber length and/or strength. These lines were released to the cotton community to be used as parents in breeding programs to develop better cotton cultivars.

2. Decreasing neps in cotton fabric. Cotton fiber neps and seed coat neps are impurities in raw cotton fibers that reduce yarn quality and cause white flecks in dyed cotton fabrics. Genetic improvement for fewer neps in cotton cultivars via selection has proven an effective approach. However, as fiber yield is always the top priority for cotton breeding programs, selection for fewer neps should not decrease yield. Through a program that simultaneously selected for fewer neps and high yield, cotton lines were identified with fewer neps, while maintaining fiber yield. This study provided the first evidence that cotton neps could be decreased without a yield penalty. Cultivars with fewer neps will allow the cotton grower to deliver higher quality cotton fiber to the textile mills and results in less subsequent loss due to rejection of fabrics with white undyed flecks.

Review Publications
Zeng, L., Boykin, D.L., Zhang, J., Bechere, E., Dever, J.K., Campbell, B.T., Raper, T.B., Meeks, C., Smith, W., Myers, G.O., Bourland, F.M. 2019. Analysis of testing locations in regional high quality tests for cotton fiber quality traits. Journal of Cotton Science. 23:284-291.
Bechere, E., Auld, D.L., Smith, W.C., Cantrell, R.G., Hequet, E.F., Ritchie, G.L., Pabuayon, I., Mishra, D., Hendon, B.R., Brown, N., Kelly, B.R. 2020. Registration of six upland cotton germplasm lines with improved fiber quality through ethyl methane sulfonate treatments and selection. Journal of Plant Registrations.
Hussain, S., Farooq, M., Malik, H., Amin, I., Scheffler, B.E., Scheffler, J.A., Liu, S., Mansoor, S. 2019. Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species. BMC Genomics. 20:507.
Fang, D.D., Naoumkina, M.A., Thyssen, G.N., Bechere, E., Li, P., Florane, C.B. 2020. An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the liy short fiber phenotype in cotton. Journal of Theoretical and Applied Genetics. 133(1):271-282.
Kim, H.J., Delhom, C.D., Fang, D.D., Zeng, L., Jenkins, J.N., Mccarty Jr, J.C., Jones, D.C. 2020. Application of the cottonscope for determining fiber maturity and fineness of an upland cotton MAGIC population. Crop Science. 60(5):2266–2279.
Gaudin, A.G., Wallace, T.P., Scheffler, J.A., Stetina, S.R., Wubben, M. 2020. Effects of combining Renlon with Renbarb1 and Renbarb2 on resistance of cotton (Gossypium hirsutum L.) to reniform nematode (Rotylenchulus reniformis Linford and Oliveira). Euphytica. 216:67.
Turley, R.B., Stetina, S.R., Bellaloui, N., Molin, W.T. 2019. Comparison of growth, yield and fiber quality of the obsolete SA30 yellow leaf with four sets of modern yellow and green leaf near isogenic cotton (Gossypium hirsutum L.) lines. Journal of Cotton Science. 23(3):253-261.