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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

2017 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, previously there has always been a tradeoff and in order to get higher yields, the quality of the fiber decreased or better fiber came at the expense of lower yields. During 2016 and 2017, ARS scientists addressed Objective 2 by evaluating progeny derived using special crossing techniques to intermate diverse exotic cotton lines. The evaluation will continue in 2018 and the study will be completed in 2019. Previous results from Objective 1A 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. Currently “Ginning Efficiency” is evaluated using two measurements: net ginning energy requirement and ginning rate. 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 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 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. The overall utility of incorporating “Ginning Efficiency” as a value added trait to enhance the value of U.S. cotton will be the subject of future economic analyses. Objective 1B targets 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 2016, 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. 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 line with the goal to develop cotton with multiple sources of resistance to diseases and insects. 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. Under Objective 2C, 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 was sequenced. The sequences will be compared to identify differences underlying the cause of the mutation. The gene(s) associated with the mutation play a role in the fiber development mechanism and their function will be studied further. Using a method that sequences all the genes that are active at a given timepoint, this project is comparing lines within each set of NILs to describe differences among the lines and identify those associated with fiber production. This study was delayed until next year as a freezer broke down, and the kit used to prepare the samples for sequencing was lost. Purchasing another kit was delayed due to insufficient funds. Objective 3 provides for a coordinated National Cotton Variety Test, a multi-location test for breeders to evaluate new cotton material and provides a database of performance data across locations and years. The 2017 tests are being conducted at 34 locations with a total of 79 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 2015 have been posted online and 2016 should be available by the end of 2017.


4. Accomplishments
1. Double and three-way hybrids can increase genetic diversity for lint yield in cotton. Cotton breeders are looking for ways to increase yield potential in their variety development programs and there is interest in using other crossing systems. The most common method used is the single cross (SC) where two parents are combined and the best progeny are selected. Other methods include the three way cross (TWC) where three parents are intercrossed and the double cross (DC) where progeny of two SC are combined. These methods were traditionally used in corn breeding programs. ARS researchers in Stoneville, Mississippi, evaluated the effectiveness of the three methods to improve yield potential. The study evaluated agronomic performance for yield and fiber quality in replicated field trials over three years. Results indicated increased genetic variability in TWC and DC progeny compared to SC progeny. When the performance of first generation progeny was compared to average performance of the parents, those from the TWC were more vigorous than those from the SC, suggesting that TWC lines might be developed as commercial hybrid cotton varieties or parents in a breeding program for yield improvement.


Review Publications
Yasmeen, A., Kiani, S., Butt, A., Rao, A.Q., Akram, F., Ahmad, A., Nasir, I.A., Husnain, T., Mansoor, S., Amin, I., Zubair, M., Tahir, M.N., Akhtar, S., Scheffler, J.A., Scheffler, B.E. 2016. Amplicon based RNA interference targeting V2 gene of cotton leaf curl Kokhran virus-Burewala strain can provide resistance in transgenic cotton plants. Molecular Biotechnology. doi:10.1007/s12033-016-9980-8.

Zeng, L., Wu, J., Bechere, E. 2017. Comparative genetic analysis of lint yield and fiber quality among single, three-way, and double crosses in upland cotton. Crop Science. 57:192-201. doi:10.2135/cropsci2016.06.0499.

Fletcher, R.S., Reddy, K.N., Turley, R.B. 2016. Spectral discrimination of two pigweeds from cotton with different leaf colors. American Journal of Plant Sciences. 7:2138-2150.

Santiago Cintron, M., Hinchliffe, D.J., Montalvo Jr, J.G., Von Hoven, T.M., Rodgers III, J.E., Thyssen, G.N., Zeng, L., Madison, C.A. 2016. Infrared imaging of cotton fiber bundles using a focal plane array detector and a single reflectance accessory. FIBERS. 4(27):1-11. doi:10.3390/fib4040027.

Islam, M.S., Thyssen, G.N., Jenkins, J.N., Zeng, L., Delhom, C.D., McCarty Jr, J.C., Deng, D.D., Hinchliffe, D.J., Jones, D.C., Fang, D.D. 2016. A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genomics. 17:903. doi:10.1186/s12864-016-3249-2.

Malik, H.J., Raza, A., Amin, I., Scheffler, J.A., Scheffler, B.E., Brown, J.K., Mansoor, S. 2016. RNAi-mediated mortality of the whitefly through transgenic expression of double-stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants. Scientific Reports. 6. doi:10.1038/srep38469.

Hinze, L.L., Hulse-Kemp, A., Wilson, I., Zhu, Q., Llewellyn, D., Taylor, J., Spriggs, A., Fang, D.D., Ulloa, M., Burke, J.J., Giband, M., Lacape, J., Van Deynze, A., Udall, J., Scheffler, J.A., Hague, S., Pepper, A., Frelichowski, J.E., Lawley, C., Jones, D., Percy, R.G., Stelly, D. 2017. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. Biomed Central (BMC) Plant Biology. 17:37.

Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Mattison, C.P., Naoumkina, M.A. 2017. A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and membrane anchoring of F-actin resulting in dwarf, lintless Li1 cotton plants. Plant Journal. 90:111-121. doi:10.1111/tpj.13477.

Mustafa, R., Hamza, M., Kamal, H., Mansoor, S., Scheffler, J.A., Amin, I. 2017. Tobacco rattle virus (TRV) based silencing of cotton enoyl-CoA reductase (ECR) gene and the role of very long chain fatty acids in normal leaf development and resistance to wilt disease. Molecular Biotechnology. doi:10.1007/s12033-017-0014-y.

Zubair, M., Zaidi, S., Shakir, S., Farooq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Mansoor, S. 2017. Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton. Scientific Reports. 7:article number 680. doi:10.1038/s41598-017-00727-2.