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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

2016 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 lines 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 and 2016, ARS scientists evaluated progeny derived using special crossing techniques to intermate diverse exotic cotton lines. New methods using DNA markers are being used to track if the progeny have retained the traits of interest or were they lost from one generation to the next. This strategy allows the scientist to more accurately select the best lines and allow the development of higher yielding cultivars with better quality fiber. Increasing the value of cotton seed is another way to improve grower income. The cotton plant and seed contain biochemical compounds [terpenoid aldehydes (TA)] which protect the cotton plant from pests and disease, but they also inhibit the growth of monogastric animals 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 elite cotton lines. In FY 2016, the ARS scientist completed a three year evaluation of the improved elite lines. The evaluation includes fiber tests as well as ultra high performance liquid chromatography (UPLC) analyses to measure the TA 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. An important technique to identify what determines the length of cotton fiber, is to develop lines that are nearly identical except for the trait being evaluated (near isogenic lines – NILS). 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 three different laboratories, to study fiber development and determine which genes are important in fiber elongation. Two additional sets of NILs for fiber traits are on schedule to be available in FY 2017. Objective 3 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 2016 tests were conducted at 33 locations with a total of 74 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 to evaluate two new fiber testing instruments. The Cottonscope is a recent, small footprint instrument for measuring cotton fiber maturity, fineness, and ribbon width. Cottonscope maturity results have been shown to be more representative of the fiber’s actual maturity compared to the maturity results obtained from the often used Advanced Fiber Information System (AFIS) unit. Overall good linear agreement was observed between the maturity and fineness results for the two instruments. 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). However, 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.

4. Accomplishments
1. Saving energy and reducing ginning costs by improving ginning efficiency. To remain competitive, the American cotton grower needs to save on production and processing costs wherever he/she can. Cotton cultivars differ in how strongly fibers are attached to the seed, and cultivars with reduced fiber-seed attachment force have the potential to be ginned faster with less energy and fiber damage. ARS researchers at Stoneville, Mississippi, conducted a series of studies and identified conventional and transgenic cotton cultivars with lower net ginning energy (NGE) requirements and established an association between the (NGE) trait and fuzz percent (FZP) which estimates the amount of fiber remaining on the seed after ginning. A cross was made between high and low NGR parents to develop a population of progeny varying for NGE. These progeny were used to identify simple sequence repeat (SSR) DNA markers associated with NGE requirement. Two SSRs were identified on chromosomes 12 and 20. The low NGE progeny also had a lower FZP. Previous studies have localized the FZP trait to the same region on chromosome 12, further strengthening the association between the two traits. The SSR markers combined with the easy to measure FZP trait will allow breeders to quickly and accurately identify cotton lines with lower ginning energy requirements and develop cultivars that save energy at the gin as well as provide fiber less prone to damage. Longer unbroken fiber is highly desired by the textile mills.

5. Significant Activities that Support Special Target Populations:

Review Publications
Bechere, E., Zeng, L., Hardin IV, R.G. 2016. Combining ability of ginning rate and net ginning energy requirement in upland cotton (Gossypium hirsutum L.). Crop Science. 56:499-504.

Bechere, E., Zeng, L., Hardin IV, R.G. 2016. Relationships of lint yield and fiber quality with ginning rate and net ginning energy in upland cotton. Journal of Cotton Science. 20:31-39.

Zeng, L., Manning, R.O. 2016. Registration of cotton germplasm line md 10-5. Journal of Plant Registrations. 10:47-50. doi: 10.3198/jpr2015.08.0047crg.

Zeng, L., Campbell, B.T., Bechere, E., Dever, J.K., Zhang, J., Jones, A., Raper, T.B., Hague, S., Smith, W., Myers, G.O., Bourland, F. 2015. Genotypic and environmental effects on cottonseed oil, nitrogen, and gossypol contents in eighteen years Regional High Quality tests. Euphytica. 206:815-824.

Islam, M.S., Zeng, L., Thyssen, G.N., Delhom, C.D., Kim, H.J., Li, P., Fang, D.D. 2016. Mapping by sequencing in cotton (Gossypium hirsutum) line MD52ne identified candidate genes for fiber strength and its related quality attributes. Theoretical and Applied Genetics. 129:1071-1086.

Thyssen, G.N., Fang, D.D., Zeng, L., Song, X., Delhom, C.D., Condon, T.L., Li, P., Kim, H.J. 2016. The immature fiber mutant phenotype of cotton (Gossypium hirsutum) is linked to a 22-bp frame-shift deletion in a mitochondria targeted pentatricopeptide repeat gene. G3, Genes/Genomes/Genetics. 6:1627-1633.

Scheffler, J.A., Dowd, M.K., Romano, G.B., Pelitire, S.M. 2015. Cotton half seed selection strategy for gossypol and its plus isomer. Journal of Cotton Science. 19:279-289.

Mustafa, R., Shafiq, M., Mansoor, S., Briddon, R.W., Scheffler, B.E., Scheffler, J.A., Amin, I. 2016. Virus-induced gene silencing (VIGS) in cultivated cotton (Gossypium spp.) using Tobacco rattle virus (TRV). Molecular Biotechnology. 58:65–72. doi: 10.1007/s12033-015-9904-z.

Raza, A., Malik, H., Shafiq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Mansoor, S. 2016. RNA Interference Based Approach to Down Regulate Osmoregulators of Whitefly (Bemisia tabaci): Potential Technology for the Control of Whitefly. PLoS One. 11:e0153883.

Scheffler, J.A. 2016. Evaluating protective terpenoid aldehyde compounds in cotton (Gossypium hirsutum L.) roots. American Journal of Plant Sciences. 7:1086-1097.

Zaidi, S.S., Shafiq, M., Amin, I., Scheffler, B.E., Scheffler, J.A., Briddon, R.W., Mansoor, S. 2016. Frequent occurrence of tomato leaf curl New Delhi virus in cotton leaf curl disease affected cotton in Pakistan. PLoS One. doi:10.1371/journal.pone.0155520.