Location: Crop Genetics Research
2022 Annual Report
Objectives
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.
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.
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.
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.
4a. Identify and test molecular markers associated with traits that will enhance cotton host plant resistance.
4b. Combine into one elite line multiple traits that will enhance cotton host plant resistance.
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.
6. Identify cotton germplasm with tolerance or resistance to either the vector or the virus of insect-borne viral pathogens, with an initial focus on the cotton leafroll dwarf virus and develop relevant germplasm for the U.S. cotton belt.
Approach
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
The project 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. Growers also benefit from growing cultivars resistant to diseases or insect pests and objectives 4 and 6 concentrate on identifying sources of resistance to emerging cotton pest threats and developing cotton resistant to those threats. 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. This project began in April 2018 and is currently about one year behind schedule with 36-month milestones substantially met, but the 48-month milestones only fully met for objective 6.
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. This project is currently on hold as the scientist in charge of this research retired in FY2021 and there was no one to continue the project until the position is refilled.
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. Lines with high NGE were mated with high yielding cotton lines possessing superior fiber quality. Progeny from thirty of the matings between high NGE cotton and high quality cotton were evaluated and eighteen were ultimately chosen based on NGE and fiber quality. These lines are being grown in the field and screened for the nectariless (ne) trait. This ne trait makes the plants less desirable to damaging cotton insects. The fiber from these lines was harvested, but further evaluation for NGE and fiber quality is on hold. Leaf samples for DNA analyses were collected from 630 progeny and their parents. This part of the project is also on hold as the scientist in charge of this project retired and limited time in the Laboratory due to COVID-19 restrictions prevented the DNA analyses from being completed.
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, new lines are being selected and evaluated. In 2021, plants, selected from populations developed in the previous project, were tested in the field at two locations near Stoneville, Mississippi and evaluated for yield and fiber quality. In 2022, these plants were further tested in replicated field trials at Stoneville and Las Cruces, New Mexico.
In 2018, two soft funded projects, previously initiated to identify resistance to U.S. cotton disease threats, were expanded and formed the basis for Objective 4 in the current project. Research on cotton leaf curl virus (CLCuV) has progressed and advanced material has been developed with dual resistance to the two most prevalent strains of CLCuV. However, the project was temporarily delayed and is now one year behind schedule as marker assisted selection was delayed and it was not possible to send seed to Pakistan for field screening for CLCuV in 2021. We resumed genotyping and marker assisted selection for CLCuV in the summer of 2022 and we plan to send seed to Pakistan for screening in 2023.
Cotton blue disease (CBD) is caused by the cotton leaf roll dwarf virus (CLRDV) and research was initiated in 2016 at ARS Stoneville, Mississippi, to develop U.S. adapted cotton lines resistant to CBD. At that time, CBD had not been reported in the U.S.; however, in 2017, CBD-like symptoms were first observed in several southern Alabama fields. Using laboratory diagnostic tests and DNA sequencing, the virus was identified as an atypical form of CLRDV which is transmitted by cotton aphids (Aphis gossypii). In 2018, the virus was detected across the cottonbelt, and caused yield losses for growers. To combat this emerging disease threat, a Task Force of researchers, including one of the scientists on this project, was assembled. Symptomology for CLRDV was studied and a photo key of symptoms developed for other researchers and growers. In 2019, a collaborative multi-location field screening test of cotton cultivars and germplasm, confirmed that all the U.S. cultivars tested were susceptible to CLRDV, but there were a few germplasm lines that had no symptoms and tested negative for the virus. These lines are now being re-tested for the fourth year and additional new lines screened in 2022 at two locations in collaboration with a Task Force breeder from Auburn, Alabama. Five lines have consistently tested as resistant and a program was initiated to transfer the resistance from the potentially resistant lines to adapted cultivars. The program had to be downsized and only a few matings were made in 2020 and 2021 field seasons. Due to limited access to the lab, during the 2021 field season screening was limited to evaluating potential resistant lines for a third year or advancing to the F2 generation mapping population progeny. During the 2022 field season, new crosses and F2 mapping populations are being evaluated with DNA markers to conduct marker assisted selection and attempt to map the resistance trait.
Objective 5 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 2022 tests are being conducted in seven regions across the cotton growing area of the U.S and includes a Regional High Quality Test (RHQ) specifically to identify new lines with better quality fiber. Results for 2019 have been posted online, but 2020 and 2021 are not completed due to delays in fiber analyses in the ARS fiber testing lab. To ensure the availability and quality of the national standards seed, a seed distribution system was established with ARS Stoneville, Mississippi, obtaining enough seed of the eight national standards from their source companies for a three year cycle. Seed for the third year of the cycle were distributed to participants in 2022.
In 2020, new funds were appropriated by Congress to mitigate the effects of CLRDV and develop new resistant cultivars, resulting in an additional objective being added to this project. As part of the new Objective 6, cotton germplasm are being identified with tolerance or resistance to the virus or it’s insect vector and resistant/tolerant lines developed for U.S. cotton growers. The initial focus was on CLRDV resistant cotton for the U.S. cottonbelt, but in 2022 a germplasm evaluation for resistance to cotton leaf crumple virus (CLCrV) was initiated with a cooperator in Weslaco, Texas, where the virus is endemic. Objective 6 complements ongoing research under Objective 4 to mitigate the effects of CLCuV and CLRDV as well as develop resistant cotton cultivars.
Accomplishments
1. Using a new analysis method to improve simultaneous selection for cotton yield and fiber quality. In cotton breeding, selection for increasing fiber yield can be achieved by two approaches: 1) direct selection for fiber yield, or 2) indirect selection of yield components. The efficiency of the first approach is usually low due to the low heritability of yield. The efficiency of indirect selection may be higher if the desirable yield components can be identified and used. This approach requires an evaluation and quantification of each yield component’s contribution to fiber yield which had not been clearly documented due to the complicated interrelationships between yield and yield components. Traditionally, the exploration of relationships between fiber yield and fiber quality were based on a statistical method that used path coefficients. The deployment of this method required a priori knowledge of the fiber yield component’s effect on final fiber yield, which was not consistent due to the unknown genetic basis underlying relationships between final fiber yield and yield components. In this study, a statistical method called commonality analysis was used by ARS researchers in Stoneville, Mississippi. This method uses multiple regressions to calculate all possible combinations between fiber amount and yield components and classifies the total effects of yield components to total yield into direct and indirect effects. Using this method, we identified five single yield components and five multiple yield components with relatively large contributions to fiber yield. These were then used to select for increased yield. Among them, the multiple component composed of lint percentage and lint weight per fiber had the largest effect on yield increase and negligible negative associations between yield and fiber quality. This study is the first application of commonality analysis in cotton breeding and the results provide evidence for its feasibility to detect yield components that can be used for indirect selection for improved fiber yield.
Review Publications
Zeng, L. 2021. History, changes, impacts, and perspectives of the National Cotton Variety Test (NCVT): Sixty years of the program. Journal of Cotton Science. 25:205-202.
Bechere, E., Hardin, R.G., Zeng, L. 2021. Seed size, ginning rate, and net ginning energy requirements in upland cotton (Gossypium hirsutum L.). Journal of Cotton Science. 25:91-100.
Aslam, M.Q., Naqvi, R.Z., Asif, M., Akhter, K.P., Scheffler, B.E., Scheffler, J.A., Liu, S., Amin, I., Mansoor, S. 2022. Analysis of a tetraploid cotton line Mac7 transcriptome reveals mechanisms underlying resistance against the whitefly Bemisia tabaci. Gene. 820:146200. https://doi.org/10.1016/j.gene.2022.146200.
Restrepo-Montoya, D., Hulse-Kemp, A.M., Scheffler, J.A., Haigler, C., Hinze, L.L., Love, J., Percy, R.G., Jones, D.C., Frelichowski, J.E. 2022. Leveraging national germplasm collections to determine significantly associated categorical traits in crops: Upland and Pima Cotton as a case study. Frontiers in Plant Science. 13:837038. https://doi.org/10.3389/fpls.2022.837038.
