Research Project: Improvement of Cotton through Genetic Base Diversification and Enhancement of Agronomic, Fiber, and Nematode Resistance Traits

Location: Genetics and Sustainable Agriculture Research

2023 Annual Report

Objectives
1. Discover genes from tetraploid landraces of Gossypium (G.) hirsutum and related tetraploid Gossypium species for nematode resistance, improved agronomic traits, and fiber properties, and use them to develop and release diverse cotton germplasm lines with enhanced yield and quality. 1.1. Develop and evaluate recombinant inbred lines (RILs) from random mated population of primitive accessions (RM-PAP), develop random mated population of G. barbadense, G. hirsutum, G. mustelinum, G. tomentosum (RM-BHMT), and evaluate RILs from random mated population barbadense Upland (RM-BUP). 1.2. Evaluate chromosomes 04, 17, and 18 from G. barbadense, G. hirsutum, G. mustelinum, and G. tomentosum. 1.3. Identify new genes for reniform (RN) and root-knot (RKN) nematode resistance. 1.4. Identify SNPs associated with RN resistance in the MT2468 Ren 1 germplasm line and incorporate this resistance with known RKN and RN resistance QTLs in germplasm with improved agronomic and fiber properties. 2. Develop improved foundational molecular knowledge of nematode resistance mechanisms, nematode biology, and fiber properties. 2.1. Fine-mapping of RKN resistance QTLs on chromosomes 11 and 14 and functional characterization of candidate genes within the respective mapping intervals. 2.2. Identify specific genes and signaling pathways required for GB-713 derived RN resistance.

Approach
Approach to objective 1: Random mated populations will be developed introgressing genes from three wild tetraploid species via chromosome substitution lines crossed with upland cultivars. Recombinant Inbred Lines (RIL) development will begin for this population. In the prior cris project we developed three random mated populations from Upland varieties (RMUP), Gossypium barbadense (RMBUP), and land race primitive accession (RMPAP) crossed with cultivars. RIL have also been developed from these three random mated populations. These RIL will be evaluated and used for association of markers with fiber quality traits. Chromosome Specific Recombinant Inbred Lines (CSRIL) will be developed by crossing individual chromosome specific chromosome substitution lines from three wild tetraploid species with a common parent (TM-1). Comparison of chromosome substitution lines for specific chromosomes from tetraploid species will be made. Molecular markers will be associated with resistance to root knot and reniform nematodes, as well as fiber quality traits. Approach to objective 2: Fine-mapping of resistance QTLs on chromosomes 11 and 14 should allow the development of more efficient molecular markers for marker assisted selection. Identification of genes underlying the activity of each QTL will enhance our understanding of how the resistance works. In the previous cris project we developed 550 RIL from a random mated population that included a root knot nematode resistant parent as one of the parents. These RIL and parents have been sequenced and will be used to select lines showing recombination between known QTL mapping intervals for chromosome 11 and 14 which contain QTL for root knot nematode resistance. We will evaluate these selected recombination lines in growth chambers to discover the sequences responsible for resistance. We will then identify functional characteristics of candidate genes in these sequence regions. Knowledge of the putative function of the resistance gene should allow us to construct hypotheses of how these genes are mediating resistance. We have developed isolines for two genes responsible for resistance to reniform nematode. Transcriptome profiling of susceptible and resistant isolines in response to reniform nematode infection will be used to identify signaling pathways involved in resistance and should provide a list of candidate genes that can be functionally characterized. Gene silencing technology will be used to confirm candidate genes and their contribution of candidate gene to resistance.

Progress Report
This is the final report for this project. New project is pending completion of researh review. Five Year Summary: There were 13 germplasm lines and one random Mated population developed, released, and registered with Journal of Plant Registrations during the life of this project. Of the 13 germplasm lines, 2 had improved fiber micronair, 7 had improved fiber length and strength, and 4 had twice the normal level of oleic acid in the seed oil. The random mated population released involved 32 chromosomes from three tetraploid species of Gossypium barbadense, G. mustilinum, and G. tomentosum crossed with G. hirsutum and random mated for 5 generations. We have provided 400 RIL from this random mated population to a collaborator to evaluate for stress and drought tolerance and for susceptibility to verticillium wilt. Fiber from 5 Recombinant Inbred Lines (RIL,) from a random mated population developed during an earlier research project, were discovered that can be made into nonwoven cloth that is naturally fire retardant. Fiber from several other RIL were discovered that can be made into nonwoven cloth that has various desirable water retention or dissipation properties. These lines have the potential to expand into new markets for cotton fiber and cottonseed. Industry has taken notice of these new potential markets for cotton fiber and cottonseed. Research was begun with a new nematode pest in cotton, Meloidogyne enterolobii (guave nematode). The genes that are responsible for resistance to root-knot nematode and reniform nematode do not confer resistance to this nematode. We have begun evaluation of all our RIL, and other sources, for resistance to M. enterolobii. Multiple advanced generation intercrossing (MAGIC) population sequencing and virus-induced gene silencing identify Gh_D02G0276 as a novel root-knot nematode resistance gene on chromosome 14 in Upland cotton. FY23 Progress: Objective 1.1. Develop and evaluate RILs from random mated population, RM-PAP. Develop RM-BNMT and RILs, and evaluate RIL from RMUP. Grew 164 RM-PAP RILs at two locations to collect a second year of agronomic and fiber trait data. This completes two years and two locations per year of data collection for 484 RM-PAP RILs. In addition, 112 RM-PAP RILs were grown at two location and evaluated for agronomic and fiber traits. Preliminary data analyses indicate a wide range exist for agronomic and fiber properties. Fiber length and strength for several RILs exceeded the commercial parents of the population. Grew 200 RM-BHMT RILs at two locations to collect a second year of agronomic and fiber data. Grew 144 RM-BHMT RILs at two field location to collect the first year of agronomic and fiber data. Fiber and agronomic data analyses are not complete, but a wide range of genetic diversity exist. Seed were increased for the third cohort of 200 RILs developed from the RM-BHTM population. This seed will be used in future years for field evaluation studies. We have developed approximately 800 RILS from RM-BHTM. Evaluated 20 entries as part of a regional breeders testing network for agronomic, fiber quality, and tobacco budworm resistance. Objective 1.2. Evaluate chromosome 04, 17, and 18 from G. barbadense, G. hirsutum, G. mustelinum, and G. tomentosum. No progress made on this objective: Scientist died in 2021 and replacement was not on board until February 2023. Objective 1.3. Identify new genes for reniform and root-knot nematode resistance. First-tier RKN-resistance screening has been performed on (298) RM-BHMT RILs. Seven RILs showed reduced root galling compared to susceptible checks. These seven RILs will be evaluated in a second-tier experiment during summer 2023. An additional 200 RILs will be evaluated in first-tier screening by the end of FY 2023. RKN resistance was confirmed in the Gossypium barbadense accession CIR1348 from CIRAD (France) and crosses were made between CIR1348 and TM-1 during spring 2022. F1 seed from this cross was selfed during fall 2022 to produce a bulked F2 population. F2 plants that flower in the field during summer 2023 will be selfed to create F2:3 families that will be evaluated for RKN resistance. Objective 1.4. Identify SNPs associated with RN resistance in the MT2468 Ren 1 germplasm line and incorporate this resistance with known RKN and RN resistance QTLs in germplasm with improved agronomic and fiber properties. SNPs associated with MT2468 Ren1 resistance were identified on chromosome A02. A molecular marker(s) is in development that can be used to track the resistance in segregating populations. Objective 2.1. Fine-mapping of RKN resistance QTLs on chromosomes 11 and 14 and functional characterization of candidate genes within the respective mapping intervals. Genomic sequence data from related projects became available that may be useful in narrowing the chromosome 11 QTL interval and reducing the number of candidate resistance genes. Objective 2.2. Identify specific genes and signaling pathways required for GB-713 derived RN resistance. In previous years, RNA-Seq data identified a handful of candidate resistance genes on chromosome 21. Functional analysis of these genes and development of a molecular marker was severely hampered by Covid restrictions and is still ongoing.

Accomplishments
1. Expanding markets for cotton fiber products increases profits to cotton producers and provides expanded product choices for consumers. Cotton cloth does not have natural fire retarding properties. ARS researchers in Starkville, Mississippi, and New Orleans, Louisiana, have developed recombinant inbred lines of cotton that produce fibers that can be used to produce a nonwoven cloth that has natural fire-retardant properties. In flammability test, cloth from these lines self-extinguish naturally. This has a huge potential to open new markets for cotton producers and offer new cotton flame resistant products to consumers. ARS researchers are increasing seed of these lines for a germplasm release to the cotton seed breeding industry.

2. Expanding food markets for cottonseed oil would increase profits to cotton producers and ginners as well as providing a healthy food grade oil to health-conscious consumers. Cottonseed oil is a desirable oil for deep frying because of its unique fatty acid composition; however, consumers would benefit from a cottonseed oil that has a higher content of Oleic acid and a lower linoleic acid profile. ARS researchers in Starkville, Mississippi, and New Orleans, Louisiana, have developed several lines of cotton that produce cottonseed oil that has 50-55% oleic acid and yet have 20-25% linoleic acid which contributes to excellent flavor for deep frying as well as other uses as a cooking oil, and as a salad oil. This has the potential to open new markets for cotton producers and to offer an improved healthy food grade cottonseed oil to consumers.

3. Cotton fibers are a sustainable and environmentally responsible raw material for the production of nonwoven textiles. There has been little attempt to correlate cotton fiber quality and fluid handling and moisture management properties of nonwoven textiles for personal hygiene and disposable applications. This includes potential end-use in diapers and incontinence products as well as disposable textiles for use in clinical settings. ARS researchers in Starkville, Mississippi, and New Orleans, Louisiana, have used selected recombinant inbred lines from their Multiple Advanced Generation Intercross population to determine the relationship of fiber quality properties and moisture management properties of nonwoven textiles made from these fibers. Results show that fiber that is normally subject to a discount sales price because of fiber quality can be effectively used for these nonwoven textiles to replace synthetic fiber currently being used for these products. This expands the market for cotton and is a winning combination for cotton producers, consumers, and the environment.

Review Publications
Hu, J., Miles, D.M., Adeli, A., Brooks, J.P., Podrebarac, F.A., Smith, R.K., Lei, F., Li, X., Jenkins, J.N., Moorehead Ii, R.J. 2023. Effects of cover crops and soil amendments on soil CO2 fluxes in Mississippi corn cropping system on upland soil. Environments. 10(2):19. https://doi.org/10.3390/environments10020019.
Gaudin, A.G., Wubben, M., Mccarty Jr, J.C., Jenkins, J.N. 2023. Virulence of two isolates of Meloidogyne enterolobii (guava root-knot nematode) from North Carolina on cotton lines resistant to southern root-knot nematode (M. incognita) and reniform nematode (Rotylenchulus reniformis). Journal of Nematology. 55:0021. https://doi.org/10.2478/jofnem-2023-0021.
Saha, S., Tewolde, H., Jenkins, J.N., Mccarty Jr, J.C., Stelly, D.M. 2023. Chromosome substitution lines with improved essential mineral nutrients and fiber quality traits in Upland cotton. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-023-01628-2.
Fang, D.D., Thyssen, G.N., Wang, M.C., Jenkins, J.N., Mccarty Jr, J.C., Jones, D.C. 2022. Genomic confirmation of Gossypium barbadense introgression into G. hirsutum and a subsequent MAGIC population. Molecular Genetics and Genomics. 298:143-152. https://doi.org/10.1007/s00438-022-01974-3.
Thyssen, G.N., Condon, B.D., Hinchliffe, D.J., Zeng, L., Naoumkina, M., Jenkins, J.N., Mccarty,J.C., Sui, R., Madison, C., Li, P., Fang, D.D. Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population. PLOS ONE. 18:e0278696.2023. https://doi.org/10.1371/journal.pone.0278696.
Jenkins, J.N., Mccarty Jr, J.C., Hayes, R.W., Wubben, M., Fang, D.D., Thyssen, G.N., Zeng, L., Campbell, B.T., Jones, D.C. 2021. Registration of seven recombinant inbred lines of Upland cotton with improved fiber length or strength. Journal of Plant Registrations. 16:94-99. https://doi.org/10.1002/plr2.20193.
Tewolde, H., Way, T.R., Buehring, N., Jenkins, J.N. 2022. Fertilizer value of poultry litter applied by subsurface band vs. surface broadcast in corn production. Journal of Plant Nutrition. 46(9):2044-2059. https://doi.org/10.1080/01904167.2022.2118133.
Adeli, A., Brooks, J.P., Miles, D.M., Todd, M., Feng, G.G., Jenkins, J.N. 2022. Combined effects of organic amendments and fertilization on cotton growth and yield. Agronomy Journal. 2022;1-12. https://DOI.org/10.1002/agj2.21178.
Hron, R.J., Hinchliffe, D.J., Thyssen, G.N., Condon, B.D., Zeng, L., Santiago Cintron, M., Jenkins, J.N., Mccarty Jr, J.C., Sui, R. 2023. Interrelationships between cotton fiber quality traits and fluid handling and moisture management properties of nonwoven textiles. Textile Research Journal. https://doi.org/10.1177/00405175221132011.
Hinchliffe, D.J., Thyssen, G.N., Condon, B.D., Zeng, L., Hron, R.J., Madison, C.A., Jenkins, J.N., Mccarty Jr, J.C., Delhom, C.D., Sui, R. 2023. Interrelationships between cotton fiber quality traits and tensile properties of hydroentangled nonwoven fabrics. Journal of Industrial Textiles. https://doi.org/10.1177/15280837231171312.
Fuller, M.G., Saha, S., Stelly, D.M., Jenkins, J.N., Tseng, T.P. 2021. Assessing the weed-suppressing potential of cotton Chromosome Substitution Lines using the Stair-Step Assay. Plants. 10:2450. https://doi.org/10.3390/plants10112450.