Location: Crop Genetics Research
2024 Annual Report
Objectives
1. Characterize the genetic mechanisms for controlling nematode resistance for diploid cotton species.
1.A. Genetic characterization of reniform nematode resistance for selected G. arboreum germplasm accessions.
2. Transfer novel nematode resistance identified for diploid cotton species to tetraploid upland cotton.
2.A. Introgression of reniform nematode resistance from G. arboreum germplasm accessions into upland cotton cultivars.
3. Determine environmental influences on nematode infection, development, and reproduction on cotton lines.
3.A. Determine soil temperature effects on nematode infection, development, and reproduction on cotton lines.
3.B. Determine soil moisture effects on nematode infection, development, and reproduction on cotton lines.
Approach
Develop populations by crossing resistant accessions with one or more Gossypium (G.) arboreum accessions classified as susceptible or highly susceptible to determine the inheritance of the resistance. Ovule culture will be used to introgress resistance from G. arboreum accessions into G. hirsutum varieties. Gossypium accessions with high levels of resistance to reniform nematode will be evaluated in growth chamber experiments to measure the effects of soil temperature and soil moisture stress on the number of infections, rate of development of females after infection, and production of eggs.
Progress Report
Reniform nematode is a threat to cotton production. Growing resistant cotton cultivars provides an environmentally friendly season-long approach to manage reniform nematode. However, resistance to reniform nematode is not found naturally in widely grown upland cotton [scientific name Gossypium (G.) hirsutum], so resistance from related species needs to be identified and transferred to upland cotton. The goals of this project are to identify and characterize the resistance, determine if its durability is maintained across a range of environmental conditions, and transfer it to upland cotton. The following is a summary of progress made during the past year towards achieving these goals.
Reniform nematode resistance has been found in related cotton species. Genetic characterization of the resistance found in the species G. arboreum and G. herbaceum is the goal of Objective 1 of this project. We worked with both species over the past year.
To study the genetic mechanism of resistance of G. arboreum to reniform nematode, 65 crosses were made in 2023 between seven resistant (R) accessions (A2-190, A2-272, A2-354, A2-514, A2-690, A2-737, and A2-995) and three susceptible (S) accessions (A2-20, A2-40, and A2-101). The crosses included R x R, R x S, and S x S types of crosses. The F1 seed harvested from the crosses last fall were planted in the field for producing F2 seed during the 2024 growing season. The F2 generations of these crosses will be evaluated for resistance/susceptibility to reniform nematode, and to identify markers that can be used to support selection of improved lines in breeding programs using these materials.
Gossypium arboreum accession A2-711 is resistant, and accession A2-101 is susceptible to reniform nematode. These two accessions were used as parents to produce a F2 population. The two parental lines, the F1 progenies, and 261 F2 plants from this population were scored for resistance to reniform nematode. Seeds from individual F2 plants were harvested and planted as a F2:3 row in the field in 2024. This summer, DNA will be extracted from each F2:3 row and sequenced. The resistance scores and DNA sequence data will be analyzed to determine which regions of the DNA are associated with the resistance, and to develop genetic markers associated with these regions that can be used by cotton breeders to help them rapidly select the best plants for further development and testing.
Gossypium herbaceum also was evaluated as a source of genes for resistance to reniform nematode. A total of 51 G. herbaceum lines were tested for resistance to reniform nematode. Nineteen lines (37%) were resistant, and 25 lines (49%) were moderately resistant to reniform nematode. Thirteen lines had better resistance than the resistant control used in the test. Analysis of the DNA from these lines identified 15 genetic markers distributed across nine chromosomes that were associated with the number of female nematodes developing on plant roots. Eleven disease resistance genes were found adjacent to some of the markers we identified on four chromosomes. The findings of this research were presented at the 2024 Plant and Animal Genome Conference, and a manuscript is in preparation.
Potentially useful levels of resistance in G. arboreum and G. herbaceum will not help growers combat reniform nematodes unless that resistance can be successfully transferred into upland cotton. Both of these species are diploid (have 2 sets of chromosomes). Because upland cotton is tetraploid (has 4 sets of chromosomes), traditional crosses to diploid plants typically result in sterile triploid plants (with 3 sets of chromosomes) that do not successfully produce seed. As such, movement of the resistance is exceptionally challenging and requires manipulating the number of sets of chromosomes the plants possess. Developing ways to successfully move the resistance into G. hirsutum is the goal of Objective 2 of this project. Work on this component of the project resumed in 2023 when a new geneticist was hired to fill a vacancy created when the previous geneticist retired in 2021.
Four G. hirsutum varieties (MD10-5, MD25-87, MD51ne, and SureGrow 747) were crossed with four resistant G. arboreum lines (A2-354, A2-690, A2-737, and A2-995) in the 2023 field season. Hundreds of young embryos from each cross were cultured in the laboratory on five media to try and generate plants. Some embryos grew to the size of a regular cotton seed, but none germinated. However, for two crosses a few seeds developed on the plants in the field. Six triploid seeds of the cross SG747 x A2-354, and four triploid seeds of the cross MD10-5 x A2-354 were harvested. Two plants from each cross are growing in the greenhouse, but these are expected to be sterile. To successfully transfer the resistance from these plants into a fertile upland cotton line will require a complicated and lengthy process known as bridge crossing. First, these plants will be treated with a chemical to double their chromosome number, then they will be crossed to another diploid species. The chemical treatment was applied to the plants in 2024 as the first step in this process.
Another approach used this year was to cross two resistant G. arboreum lines together to combine their resistance genes. Seedlings from 5 crosses involving resistant G. arboreum lines (A2-690 x A2-190; A2-690 x A2-272; A2-737 x A2-190; A2-737 x A2-354; and A2-737 x A2-514) were grown in the greenhouse and treated with a chemical to double their chromosome number from 2 to 4. Next, the treated plants were crossed with upland cotton. Three of the treated plants produced seed when pollinated with pollen from upland cotton. The progenies will be tested for resistance to reniform nematodes.
There are many challenges to transfer resistance from related Gossypium species into G. hirsutum, so it is important to choose sources with resistance that is resilient in the face of a wide range of environmental conditions. Current research being conducted for Objective 3 of this project is assessing the durability of the resistance under a range of soil temperatures. Nematode infection and development on resistant G. barbadense accessions GB713 and TX110 are being compared with that on susceptible G. hirsutum cultivar Deltapine 16 included as a control. The goal for this reporting period was to complete the growth chamber testing at a soil temperature of 28ºC, which is the temperature used for our germplasm screening work and is defined as the normal temperature in this series of experiments. Following that, tests were to be initiated at a higher than normal soil temperature. Unfortunately, there were two failed attempts due to growth chamber malfunctions before we successfully repeated the normal temperature test. As a result, we are slightly behind schedule in the testing sequence, so the tests at higher soil temperatures will not begin until later this year.
This project includes a congressionally mandated subordinate project (6066-22000-094-001S). Research on this subordinate project during the past 12 months focused on determining the impact of naturally occurring reniform nematode populations on nematode reproduction and cotton yield of three USDA reniform resistant cotton lines, three commercial Phytogen reniform nematode resistant varieties, and three commercial reniform susceptible cotton varieties in the field. During the 2023 field season, the second run of this experiment was conducted. Soil samples were collected at planting, midseason and post-harvest for nematode quantification, and data were analyzed. The third and final year of the field trial was successfully established in May of 2024. A growth chamber test evaluating the same materials under more controlled conditions was established in June of 2024 to further verify nematode responses.
Accomplishments
1. Differentially expressed genes identified in resistant Gossypium accessions challenged by reniform nematode. Reniform nematode is a threat to United States cotton production and causes hundreds of millions of dollars in loss each year. Current control practices using pesticides and crop rotation do not provide season-long suppression of the reniform nematode population, and growing resistant cultivars is a more economical and effective way to control this important parasite. However, resistance to reniform nematode has not been found in the widely grown upland cotton (Gossypium hirsutum) but is found in its relatives, Sea Island cotton (G. barbadense) and Asiatic cotton (G. arboreum). Two resistant lines each of Sea Island cotton and Asiatic cotton were used by ARS researchers in Stoneville, Mississippi, to study what genes were activated in these lines in response to infection by reniform nematodes. Two genes previously reported to provide resistance to a different nematode species, along with other genes that have potential roles in plant defense, were identified. This work adds to our basic knowledge about how the resistant plants react to the nematode. The findings will help scientists develop genetic markers for the resistance genes that cotton breeders can use to develop resistant cultivars for cotton growers.
Review Publications
Gupta, S., Lekshmy, V.S., Reddy, K., Stetina, S.R., Bheemanahalli, R. 2023. Resilience of cotton cultivars to chilling stress during germination. Plant Physiology Reports. 28. https://doi.org/10.1007/s40502-023-00746-4.
Feng, C., Stetina, S.R., Erpelding, J.E. 2024. Transcriptome analysis of resistant cotton germplasm responding to reniform nematodes. Plants. 13:958. https://doi.org/10.3390/plants13070958.
Abdelraheem, A., Zhu, Y., Zeng, L., Stetina, S.R., Feng, C., Wheeler, T., Zhang, J. 2024. Identification of new genetic sources of resistance to bacterial blight race 18 in diploid Asiatic cotton and resistance transfer to tetraploid cotton (Gossypium hirsutum). Euphytica. 220:85. https://doi.org/10.1007/s10681-024-03342-1.
Abdelraheem, A., Zhu, Y., Zeng, L., Stetina, S.R., Zhang, J. 2024. A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum. Molecular Genetics and Genomics. 299:30. https://doi.org/10.1007/s00438-024-02130-9.
