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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

2018 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 is the final report for this project, which concluded in April of 2018. It has been replaced by project 6066-21220-052-00D. The project addressed the need to improve cotton grower profits and make U.S. grown fiber more competitive in the global market. Growers would like higher yields and better quality fiber, however, previously there has always been a tradeoff. In order to get higher yields, the quality of the fiber decreased, or better fiber came at the expense of lower yields. From 2016 through 2018, ARS scientists at Stoneville, Mississippi, evaluated progeny derived using special crossing techniques to intermate diverse exotic cotton lines. The evaluation will continue in the next project, initiated in April 2018, and the study will be completed in 2020. Previous results showed that there were cotton lines that required less energy to gin. This could save the gins money and decrease the price producers must pay to have their cotton ginned. “Ginning Efficiency” was evaluated using two measurements: net ginning energy requirement and ginning rate. These two measurements are time consuming and expensive to complete. DNA markers associated with the two traits would allow these measurements to be estimated in earlier generations and at lower cost. A special plant population was developed to help researchers find the location of DNA markers associated with the net ginning energy trait. Two markers were identified on chromosomes 12 and 20. This information will be used in the next project as part of a marker assisted selection program to transfer the net ginning energy trait into high yielding cotton varieties. A second population developed for ginning rate is currently being analyzed to identify DNA markers associated with this trait. Concentrated on increasing the value of cotton seed as another way to improve grower income. The cotton plant and seed contain biochemical compounds (terpenoid aldehydes) which protect the cotton plant from pests and disease, but they also inhibit the growth of 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 2018, a three year evaluation of the improved elite lines was completed. The evaluation included fiber tests as well as chemical assays to measure the type and amount of the chemical compounds in the cotton lines. Starting in 2017, four of the elite lines are being used as parents in a project to combine (stack) two traits that improve host plant resistance into the same cotton line with the goal to develop cotton with multiple sources of resistance to diseases and insects. Some of the lines were also found to be resistant or tolerant to a disease caused by the cotton leaf curl virus pathogen. Fiber yield of cotton is determined by a number of factors, including the number of fibers initiated on each seed and how early in seed development this occurs. There are naturally occurring cotton mutants that lack fiber or produce only very short fibers. These can be compared to normal cotton using a number of new technologies to evaluate the mechanisms underlying fiber initiation and elongation. Sets of cotton lines were developed with the same genetic background except one had the mutant trait and one the normal version of the trait. These are called near isogenic lines (NILs) and they make the comparisons more effective as the two lines are nearly identical except for the mutant trait of interest. For example, a set of NILs was developed where one has normal fiber and the other has no fiber (fiberless). Several of these sets of NILs were sent to a collaborator to have their DNA sequenced. The sequences will be compared to identify differences underlying the cause of the mutation. Provided for a coordinated National Cotton Variety Test, an annual, multi-location test for breeders to evaluate new cotton material and provide a database of performance data across locations and years. The 2018 tests are being conducted at 24 locations with a total of 441 entries being tested at multiple locations. This includes a Regional High Quality Test at 9 locations to identify new lines with better quality fiber. Results for 2016 have been posted online and 2017 should be available by the end of 2018.


4. Accomplishments
1. DNA markers were identified that can help develop cotton that costs less to gin. Cotton lines that require less energy to gin would save the ginners money and decrease the price producers must pay to have their cotton ginned. “Ginning Efficiency” is traditionally evaluated using two measurements: net ginning energy requirement and ginning rate, but these two measurements are time consuming and expensive. DNA markers associated with the two traits would allow these measurements to be estimated in earlier generations and at lower cost. A special plant population was developed by ARS scientists at Stoneville, Mississippi, to help researchers find the location of DNA markers associated with the net ginning energy trait. Two markers were identified on chromosomes 12 and 20. This information is being used as part of a marker assisted selection program to transfer the net ginning energy trait into high yielding cotton varieties.

2. Lower cost HVI measurements are as efficient as higher cost AFIS measurements for breeding to improve fiber length and maturity. Currently, there are two instrument systems being used to measure cotton fiber quality. One system is called ‘High Volume Instrument’ (HVI), and the other system is ‘Advanced Fiber Information System’ (AFIS). HVI is about a third the cost of AFIS, but because HVI measures a bundle of fibers at one time while AFIS measures individual fibers, it was thought that the AFIS measurements would be more accurate in predicting lines with the longest fiber, the lowest short fiber content and best maturity ratings. From 2012 to 2016, plants in two breeding populations were measured with both HVI and AFIS by ARS scientists at Stoneville, Mississippi, and the selected plants evaluated in two subsequent generations. The objective was to evaluate the effectiveness of the two systems when used in a breeding program and provide recommendations to cotton breeders. Results indicated that the two systems are equally effective in selecting for fiber length and maturity, but different for short fiber content. These results will help the breeder make informed decisions on which tests to use in each generation of their breeding programs and they may opt to use only the lower cost HVI especially in early generations.


Review Publications
Zeng, L., Stetina, S.R., Erpelding, J.E., Bechere, E., Turley, R.B., Scheffler, J.A. 2018. History and current research in the USDA-ARS cotton breeding program at Stoneville, MS. Journal of Cotton Science. 22:24-35.

Fletcher, R.S., Turley, R.B. 2017. Employing canopy hyperspectral narrowband data and random forest algorithm to differentiate palmer amaranth from colored cotton. American Journal of Plant Sciences. 8:3258-3271.

Saski, C.A., Scheffler, B.E., Hulse-Kemp, A.M., Liu, B., Song, Q., Stelly, D.M., Scheffler, J.A., Jones, D.C., Peterson, D.G., Haigler, C., Schmutz, J., Chen, Z.J. 2017. Subgenome-anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Scientific Reports. 7:15274. https://doi:10.1038/s41598-017-14885-w.

Naqvi, R., Zaidi, S., Akhtar, K.P., Strickler, S., Woldemariam, M., Mishra, B., Mukhtar, M., Scheffler, B.E., Scheffler, J.A., Jander, G., Mueller, L.A., Asif, M., Mansoor, S. 2017. Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum. Scientific Reports. 7:15880. https://doi:10.1038/s41598-017-15963-9.

Bechere, E., Zeng, L., Auld, D. 2017. Registration of five upland cotton mutant germplasm lines with superior fiber length, strength, and uniformity. Journal of Plant Registrations. https://doi.org/10.3198/jpr2017.05.0024crg.

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. https://doi.org/10.3198/jpr2017.07.0043crg.

Zeng, L., Bechere, E. 2017. Correlated selection response of fiber properties measured by high volume instrument and advanced fiber information system in Upland cotton. Euphytica. 213:278. https://doi.org/10.1007/s10681-017-2061-7.

Bechere, E., Fang, D.D., Kebede, H.A., Hardin Iv, R.G., Islam, M.S., Li, P., Scheffler, J.A. 2017. Quantitative trait loci analysis for net ginning energy requirements in upland cotton (Gossypium hirsutum L.). Euphytica. 213:160-171. https://doi.org/10.1007/s10681-017-195-z.

Naoumkina, M.A., Bechere, E., Fang, D.D., Thyssen, G.N., Florane, C.B. 2017. Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (liy) in cotton (Gossypium hirsutum L.). Genomics. 109:320-329.

Ahmad, A., Ur Rehman M, Z., Hameed, U., Rao, A.Q., Ahad, A., Yasmeen, A., Akram, F., Bajwa, K.S., Scheffler, J.A., Nasir, I.A., Shahid, A., Iqbal, J., Husnain, T., Haider, M.S., Brown, J.K. 2017. Engineered disease resistance in cotton using RNA-interference to knock down cotton leaf curl kokhran virus-Burewala and cotton leaf curl Multan betasatellite. Viruses. https://doi.org/10.3390/v9090257.