Location: Genetics and Sustainable Agriculture Research
2022 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
Sub objective 1.1. Develop and evaluate recombinant inbred lines (RILs) from random mated populations of primitive accessions (RM-PAP), develop random mated population of G. barbadense, G. hirsutum, G. mustelinum, G. tomentosum (RM-BHMT) and evaluate RILs and evaluate RILs from random mated population barbadense Upland (RM-BUP).
Grew 200 RM-PAP RILs at two locations to collect a second year of agronomic and fiber trait data. Grew 124 RM-PAP RILs for agronomic and fiber evaluations. 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.
Seed were increased for the first 200 RILs developed from RM-BHTM population. These 200 RILs are currently being grown at two field locations for agronomic and fiber data collection. A second cohort of 200 RM-BHT RILs are currently being grown for seed increase. This seed will be used in future years for field evaluation studies. We have developed 750 RILS from RM-BHTM with a few remaining to be harvested from the greenhouse.
Evaluated 28 entries as part of a regional breeders testing network for agronomic, fiber quality, and tobacco budworm resistance.
Sub-objective 1.3. Identify new genes for reniform and root-knot nematode resistance. First-tier RKN-resistance screening was performed on (98) RM-BHMT RILs. Three RILs showed reduced root galling compared to the susceptible control ‘SureGrow747’. Another 100 RILs will be evaluated by the end of FY 2022. RKN resistance was confirmed in the Gossypium barbadense accession CIR1348 from CIRAD (France). Crosses were made between CIR1348 and TM-1 during spring 2022 and the F1 seed from this cross is currently being selfed in the greenhouse to produce a bulked F2 population.
Sub-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.
Two years of yield and fiber quality data has been collected on two RILs that carry reniform and root-knot nematode resistance. Seed is being increased this summer in preparation for germplasm release.
Sub-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.
The 48-month milestone was not met because collaborator was not able to perform necessary lab work due to pandemic restrictions.
Sub-objective 2.2. Identify specific genes and signaling pathways required for GB-713 derived RN resistance.
The 48-month milestone was not met because collaborator was not able to perform necessary lab work due to pandemic restrictions.
Accomplishments
Review Publications
Kushanov, F.N., Turaev, O.S., Khusenov, N.N., Tulanov, A.A., Amanboyev, R.S., Saha, S., Yu, J., Abdurakhmonov, I. 2021. Application of marker-assisted breeding technology in cotton (Gossypium spp). Frontiers in Plant Science. 12:779386. https://doi.org/10.3389/fpls.2021.779386.
Bellaloui, N., Saha, S., Tonos, J.L., Scheffler, J.A., Jenkins, J.N., McCarty Jr, J.C., Stelly, D.M. 2021. Effects of interspecific chromosome substitution in upland cotton on cottonseed macronutrients. Plants. 10(6):1-13. https://doi.org/10.3390/plants10061158.
Wang, M., Qi, Z., Thyssen, G.N., Naoumkina, M.A., Jenkins, J.N., McCarty, J.C., Xiao, Y., Li, J., Zhang, X., Fang, D.D. 2022. Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton. Communications Biology. 5:60. https://doi.org/10.1038/s42003-022-03022-7.
Reddy, K.R., Bheemanahalli, R., Saha, S., Lokhande, S.B., Read, J.J., Jenkins, J.N., Raska, D.A., De Santiago, L., Hulse-Kemp, A.M., Vaughn, R.N., Stelly, D.M. 2020. High-temperature and drought-resilience traits among interspecific chromosome substitution lines for genetic improvement of Upland cotton. Plants. 9:1747. https://doi.org/10.3390/plants9121747.
Zhu, Y., Thyssen, G.N., Abdelraheem, A., Teng, Z., Fang, D.D., Jenkins, J.N., Mccarty Jr, J.C., Wedegaertner, T., Hake, K., Zhang, J. 2022. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance. Theoretical and Applied Genetics. 135:2297-2312. https://doi.org/10.1007/s00122-022-04113-z.
Tewolde, H., Buehring, N., Way, T.R., Feng, G.G., He, Z., Sistani, K.R., Jenkins, J.N. 2021. Yield and nutrient removal of cotton-corn-soybean rotation systems fertilized with poultry litter. Agronomy Journal. 113:5483-5498. https://doi.10.1002/agj2.20857.
Hulse-Kemp, A.M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D.D., Frelichowski, J.E., Giband, M., Hague, S., Hinze, L.L., Kochan, K., Riggs, R., Scheffler, J.A., Udall, J.A., Ulloa, M., Wang, S., Zhu, Q., Bag, S.K., Bhardwaj, A., Burke, J.J., Byers, R.L., Claverie, M., Gore, M.A., Harker, D.B., Islam, M.S., Jenkins, J.N., Jones, D.C., Lacape, J., Llewellyn, D.J., Percy, R.G., Pepper, A.E., Poland, J.A., Rai, K., Sawant, S.V., Singh, S., Spriggs, A., Taylor, J.M., Wang, F., Yourstone, S.M., Zheng, X., Lawley, C.T., Ganal, M.W., Van Deynze, A., Wilson, L.W., Stelly, D.M. 2015. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.). Genes, Genomes, Genetics. 5:1187-1209. doi:10.1534/g3.115.018416.
