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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

2019 Annual Report

Objective 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. Objective 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. Objective 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. Objective 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. Sub-objective 4a. Identify and test molecular markers associated with traits that will enhance cotton host plant resistance. Sub-objective 4b. Combine into one elite line multiple traits that will enhance cotton host plant resistance. Objective 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.

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 twelve month milestones fully met. The project continues and expands upon objectives from 6066-21000-051-00D and 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 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. 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. Cotton variants (mutations) can be found occurring naturally or created through chemical mutagenesis. Using the chemical mutagen ethyl methane sulfonate (EMS), a new cotton line with extremely short fiber was identified. It is caused by a single gene located on chromosome A07 and different from other naturally occurring variants. Because of its known chromosome location and single gene inheritance, it will provide a useful model system to study fiber elongation and development. 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. Identified lines were mated with high yielding cotton lines possessing superior fiber quality. Progeny from 30 crosses between High NGE cotton and high quality cotton were evaluated and eighteen were ultimately chosen based on NGE and fiber quality. These are being grown in the field and will be further evaluated for NGE and fiber quality. 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, a new line was developed and released in 2018. Cotton line MD16-1 had 9% to 16% higher fiber yield than the four high yield checks when evaluated in replicated yield trials at 13 locations across the cotton growing region. MD16-1 was the top yielder across the 13 locations and also had above average fiber quality. MD16-1 is being used by ARS researchers at Stoneville and has been requested by U.S. public and private cotton breeders. Currently there are two major methods used to measure cotton fiber properties, the High Volume Instrument (HVI) and the Advanced Fiber Information System (AFIS). The HVI is simpler to use and much less expensive to run per sample, but it was not known if the results were as accurate as those from AFIS. Using two populations developed for a normal breeding program under Objective 3, fiber samples were divided into two sub-samples and analyzed using both methods. Selections were made based on the results of each method independently in generation three of the breeding program and then the progeny of those selections were analyzed again in generations 4 and 5. The results using either method were highly correlated for fiber length and maturity suggesting that the cheaper and quicker HVI analysis method could be used to select for these traits. During 2017, virus-like symptoms were observed in fields of six counties of southern Alabama. In 2018, more virus-like symptoms were observed in Georgia, Florida, Alabama and Mississippi. Using laboratory diagnostic tests and DNA sequencing, a virus was identified as an atypical form of cotton leafroll dwarf virus (CLRDV) which is transmitted by cotton aphids (Aphis gossypii) and causes cotton blue disease (CBD). This emerging virus was most often observed in late planted cotton and caused extensive yield loss. To combat this emerging disease threat, Cotton Inc. assembled a Task Force of researchers, including one of the scientists on this project. As part of Objective 4, this project will support and accelerate some key parts of the Task Force activities. Plants with symptoms typical for CBD or related viruses are being collected from an observation plot planted in an area where the virus was found in 2018 and also from farmers’ fields. Laboratory diagnostic testing will be conducted to confirm the presence of the virus. A collaborative replicated field screening test of cotton cultivars and germplasm is also being conducted by this project and university partners to identify cotton lines resistant to the new virus. Under Objective 4, a breeding program to combine genes for resistance to cotton leaf curl disease into one cotton line is progressing with the first cotton lines containing both sources of resistance to the Burewala strain of cotton leaf curl virus currently being evaluated in Pakistan. Reducing the number of testing locations in multi-location tests can decrease costs as long as vital information is not lost. As part of Objective 5, National Cotton Variety Test (NCVT) data was collected from 2005 to 2013 for seed quality traits from tests at twelve locations across the cotton growing region and used to create a series of datasets where two or three locations were omitted in various combinations and the loss of detecting ability of the resulting data assessed. The results indicated that up to three locations could be omitted and similar results obtained. Based on these results, the number of seed samples analyzed was decreased with a considerable cost savings for the NCVT program.

1. A new short-fiber mutant of cotton was created using chemical mutagenesis. Currently, there are two naturally occurring dominant fiber mutant lines, Ligon- lintless-1 (Li1 chromosome D04) and Ligon-lintless-2 (Li2, chromosome D13), and one dominant man-made fiber mutant, Ligon-lintless-x (Lix, chromosome A04) previously developed by an ARS researcher at Stoneville, Mississippi. All these fiber mutants exhibit extremely short lint fibers. In collaboration with University partners, the ARS researcher at Stoneville, Mississippi, has created a fourth cotton fiber mutant line using ethyl methane sulfonate (EMS) chemical mutagenesis. Unlike the other three, this lintless mutant (liy) is recessive and located on chromosome A07. This set of four lintless mutants provides cotton researchers with an excellent system to study fiber growth and development. During the past two decades, a number of advancements in understanding fiber development were achieved through comparative analysis of fiber mutants to wild type cotton lines. With the availability of new technologies such as transcriptome analysis and genotyping by sequencing, this mutant and the other three are allowing researchers to expand upon earlier studies into the mechanisms of fiber initiation and development.

Review Publications
Hendon, B.R., Bechere, E., Witt, T.W., Kelly, B.R., Mishra, D., Auld, D. 2019. Genetic improvement of naked-tufted seed mutants in upland cotton (Gossypium hirsutum L.). Euphytica. 215:81.
Janga, M.R., Pandeya, D., Campbell, L.M., Konganti, K., Toinga, S., Puckhaber, L.S., Pepper, A., Stipanovic, R.D., Scheffler, J.A., Rathore, K. 2018. Genes regulating gland development in the cotton plant. Plant Biotechnology Journal. 16:1-12.
Bechere, E., Manning, R.O. 2018. Registration of cotton germplasm USDA MD 16-1 and USDA MD 16-2 with enhanced lint yield and fiber quality. Journal of Plant Registrations. 12(2):241-245.
Zeng, L., Bridges, W., Bourland, F. 2019. Testing locations in regional high quality tests for cotton seed quality traits. Journal of Cotton Science. 23:48-58.
Shakir, S., Zaidi, S., Farooq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Nawaz-Ul-Rehman, M., Mansoor, S., Atiq, U. 2019. Non-cultivated cotton species (Gossypium spp.) act as a reservoir for cotton leaf curl begomoviruses and associated satellites. Plants. 8:127. .