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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Research Project #425112

Research Project: Enhancing Fiber and Seed Quality Traits Through Conventional and Molecular Approaches, and Conducting the National Cotton Variety Testing Program to Improve Cotton Competitive Ability

Location: Crop Genetics Research

2015 Annual Report

1a. Objectives (from AD-416):
Objective 1 - Develop and release superior cotton germplasm or genetic stocks that incorporate improved lint yield, combined with value added traits such as longer fiber, improved ginning efficiency, nectariless, or high leaf Terpenoid Aldehydes, with accompanying DNA markers and improved methods for effective selection. Sub-objective 1A - Identify and evaluate lines with improved ginning efficiency using conventional and molecular methods. Sub-objective 1B - Identify and introgress into adapted cotton lines, natural variants that improve host plant resistance (HPR) to pests. Objective 2 - Use genetics, genomics, and molecular approaches to determine interrelationships among these genetic and agronomic traits and how they are controlled, as well as develop strategies to reduce undesirable linkages between traits. Sub-objective 2A – Broaden the genetic base of Upland cotton and improve efficiency of trait transfer by evaluating genetic and genomic relationships and the interactions that occur during intermating and introgression of fiber traits. Sub-objective 2B - Develop and compare strategies to reduce undesirable linkages between lint yield and fiber traits. Sub-objective 2C - Use the rapidly expanding arsenal of molecular techniques to develop and evaluate near isogenic lines with phenotypic variants for fiber and leaf trichomes. Objective 3 - Conduct a regional and national cotton variety testing program to generate supporting data that can be applied in a diverse set of situations to develop genetic and/or production strategies to improve the cotton crop. Sub-objective 3A - Test annually new germplasm and varieties for yield, fiber and seed quality and maintain a database of the evaluation. Sub-objective 3B - Compare and validate effects of changing the source or method of fiber quality analyses or seed assays.

1b. Approach (from AD-416):
Use a coordinated approach to develop new germplasm and tools to improve cotton fiber and seed, as well as maintaining a regional and national cotton testing program relevant to the needs of the cotton community. Use 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 processes 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. Evaluate the feasibility of using cotton genotypes with low attachment strengths to improve ginning efficiency and decrease fiber damage during the ginning process. 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 improve the levels of protective compounds in the plant and the nectariless trait that decreases the plant’s attractiveness to insects. 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. Evaluate the potential of new fiber quality measurements compared to existing measurement methods.

3. Progress Report:
This project was initiated in April of 2013 to address the need to improve cotton grower profits and make U.S. grown fiber more competitive in the global market. Objectives 1 and 2 are addressing these needs by searching more widely for unique cotton and finding novel ways to generate new cotton lines with higher yield and improved fiber and seed traits. Growers would like higher yields and better quality fiber; however, there is a negative correlation between better cotton fiber and high yield. During 2015, ARS scientists evaluated progeny derived using special crossing techniques to intermate diverse exotic cotton lines. New methods using DNA markers are being developed to track if the progeny have retained the traits of interest or they were lost from one generation to the next. This strategy allows the development of plants with unique combinations of yield and fiber properties and provides improved methods for the scientist to more accurately identify and select the best lines. Increasing the value of cotton seed is another way to improve grower income. The cotton plant and seed contain several toxic compounds (gossypol, hemigossypolone and heliocides) which protect the cotton plant from pests and disease, but also inhibit the growth of monogastric animals (pigs, chickens, fish) and humans that eat the cotton seed. There are wild cottons that contain modified less toxic compounds and the trait responsible for the less toxic compounds was previously transferred into adapted cotton lines. In 2015, the ARS scientist completed the second year of a three year evaluation of these improved elite lines. The evaluation includes yield and fiber tests as well as high performance liquid chromatography (HPLC) analyses of toxic compound levels. These elite lines could be used in breeding programs to develop cultivars where the seed as well as the fiber can provide income for the grower. Important tools to identify what determines the length of cotton fiber, are near isogenic lines (NILs). NILs are lines that are nearly identical except for the trait being evaluated. An ARS scientist has developed NIL’s for a trait called Ligon lintless which has very short fiber. One NIL has normal fiber and the other very short fiber. These NILs are currently being used by two different laboratories, to study fiber development and determine which genes are important in fiber elongation. Project plan Objective 3 provides for a coordinated National Cotton Variety Test (NCVT), a multi-location test for breeders to evaluate new cotton material, as well as provide a database of field performance test data across locations and years. The 2015 tests were conducted at 35 locations with a total of 82 entries being tested at multiple locations. This includes a Regional High Quality Test (RHQT) at 9 locations to identify new lines with better quality fiber. Objective 3 also has a component that covers testing new methods of evaluating fiber quality. In 2014 and 2015, fiber samples from the NCVT were provided to the Cotton Structure & Quality Research Unit in New Orleans, LA, to evaluate two new fiber testing instruments. The Cottonscope is a new, small footprint instrument for measuring cotton fiber maturity and fineness. Cottonscope and Fiber Information System (AFIS) instrument measurements were made on 187 samples (both Pima and Upland cotton) from the NCVT to compare CottonScope and AFIS maturity and fineness measurements. Overall good linear agreement was observed between the maturity and fineness results for the two instruments. However, Cottonscope maturity results were shown to be more representative of the fiber’s actual maturity compared to the maturity results obtained from the more commonly used AFIS. Approximately 200 additional samples are currently being analyzed using the Cottonscope in order to expand the database and validate the results. Samples from multiple years of the NCVT program were also tested using a Fibrotest instrument. In general, good agreement was found between Fibrotest results and the industry standard High Volume Instrument (HVI). The Fibrotest did not correlate well with the Stelometer measurements, which had previously been used for the NCVT as a standard measurement of fiber strength. The Fibrotest instrument was found inadequate to measure short fiber content on samples with extreme fineness or very low maturity. Work is underway with the manufacturer to resolve the deficiencies that have been identified.

4. Accomplishments
1. U.S. Department of Agriculture (USDA) researcher releases cotton resistant to cotton leaf curl virus, a Top 20 threat to U.S. agriculture. Although cotton leaf curl virus (CLCuV) disease has not yet been reported in the U.S., the USDA has ranked it among the top 20 potential threats to U.S. agriculture and funded a multinational partnership project to proactively develop resistant cotton varieties. The goal is to be prepared before the disease comes to the U.S. by screening for CLCuV in Pakistan, where the disease is endemic and causes losses of a million or more bales of cotton each year. An ARS scientist at Stoneville, Mississippi, developed a series of lines that were then screened resistance to CLCuV for two years in Pakistan. The best two resistant lines (GVS8, GVS9) have been made available to breeders through USDA-ARS germplasm release P.0063.14 for use in breeding programs to develop CLCuV resistant varieties.

2. Eighteen years of National Cotton Variety Test data confirm environment affects cotton seed quality traits. Environment is often a critical factor affecting plant traits. This study evaluated if environment played an important role in determining the amount of oil, protein, or the anti-nutritional compound gossypol in cotton seed. The National Cotton Variety Test (NCVT) is a system that provides data from yield trials at locations across the U.S. Cottonbelt. Data from 18 years of NCVT trials covering 1996 to 2013 were analyzed to determine genetic and environmental effects for the three cotton seed quality traits. Across years, the heritable genetic portion of the total variation observed averaged 87% (oil), 71% (protein) and 75% (gossypol). Although all three traits were highly heritable, results showed cultivars consistently varied across locations, indicating that multiple location trials were needed to successfully evaluate these traits. This information will help cotton breeders improve oil, protein or gossypol as part of their breeding programs to improve cotton seed quality.

Review Publications
Bechere, E., Zeng, L. 2014. Genetics correlation and path coefficient analysis of cotton yield with some contributing quantitative and qualitative traits in Upland Cotton (Gosspypium hirsutum L.). Journal of Crop Improvement. 28(6):852-870.

Said, J.I., Song, M., Fang, D.D., Zhang, J. 2014. A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum interspecific populations and Gossypium hirsutum x Gossypium barbadense populations. Molecular Genetics and Genomics. DOI 10.1007/s00438-014-0963-9.

Zeng, L., Pettigrew, W.T. 2015. Combining ability, heritability, and genotypic correlations for lint yield and fiber quality of Upland cotton in delayed planting. Field Crops Research. 171:176-183.

Stetina, S.R., Turley, R.B., Bellaloui, N., Boykin Jr, J.C. 2014. Yield and fiber quality of five pairs of near-isogenic cotton (Gossypium hirsutum L.) lines expressing the fuzzless/linted and fuzzy/linted seed Phenotypes. Journal of Crop Improvement. 28:680-699.

Bellaloui, N., Stetina, S.R., Turley, R.B. 2015. Cottonseed protein, oil, and mineral status in near-isogenic cotton (Gossypium hirsutum) lines expressing fuzzy/linted and fuzzless/linted seed phenotypes. Frontiers in Plant Science. 6:137.

Bechere, E., Auld, D.L. 2014. Registration of a tufted-naked seed upland cotton germplasm. Journal of Plant Registrations. 8(1):63-67.

Zeng, L., Bechere, E., Boykin, D.L. 2014. Commonality analysis and selection of parents for with-in boll yield components in Upland cotton. Euphytica. 199:339-348.

Percy, R.G., Hendon, B., Bechere, E., Auld, D. 2015. Quantitative genetics and utilization of mutants. Book Chapter. doi:10.2134/agronomogr57.2013.0042.

Hulse-Kemp, A.M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D.D., Frelichowski, J.E., Giband, M., Hague, S., Hinze, L.L., Kochan, K., Riggs, R., Scheffler, J.A., Udall, J.A., Ulloa, M., Wang, S., Zhu, Q., Bag, S.K., Bhardwaj, A., Burke, J.J., Byers, R.L., Claverie, M., Gore, M.A., Harker, D.B., Islam, M.S., Jenkins, J.N., Jones, D.C., Lacape, J., Llewellyn, D.J., Percy, R.G., Pepper, A.E., Poland, J.A., Rai, K., Sawant, S.V., Singh, S., Spriggs, A., Taylor, J.M., Wang, F., Yourstone, S.M., Zheng, X., Lawley, C.T., Ganal, M.W., Van Deynze, A., Wilson, L.W., Stelly, D.M. 2015. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.). Genes, Genomes, Genetics. 5:1187-1209. doi:10.1534/g3.115.018416.

Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Naoumkina, M.A. 2014. Next Generation Genetic Mapping of the Ligon-lintless-2 (Li2) Locus in Upland Cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 127:2183-2192.

Kim, H.J., Hinchliffe, D.J., Triplett, B.A., Yeater, K.M., Moon, H.S., Gilbert, M.K., Thyssen, G.N., Turley, R.B., Fang, D.D. 2015. Phytohormonal networks promote differentiation of fiber initials on pre-anthesis cotton ovules grown in vitro and in planta. PLoS One. 10(4):e0125046.

Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Naoumkina, M.A. 2015. Mapping-by-sequencing of Ligon-lintless-1 (Li1) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (Gossypium hirsutum L.). Journal of Theoretical and Applied Genetics. 128:1703-1712.

Percy, R.G., Frelichowski, J.E., Arnold, M., Campbell, B.T., Dever, J., Fang, D.D., Hinze, L.L., Main, D., Scheffler, J.A., Sheehan, M., Ulloa, M., Yu, J., Yu, J. 2014. The U.S. National Cotton Germplasm Collection – its Contents, Preservation, Characterization, and Evaluation. In: Abdurakhmonov, I. Editor. World Cotton Germplasm Resources. Rijeka, Croatia: InTech. 167-201. Available:

Bellaloui, N., Turley, R.B., Stetina, S.R. 2015. Water stress and foliar boron application altered seed nutrition in near-isogenic cotton lines expressing fuzzy and fuzzless seed phenotypes. PLoS One. 10(6):e0130759.