Location: Genetics and Sustainable Agriculture Research
2019 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
Completed development of 598 Recombinant Inbred Lines from random mated population involving race lines and cultivars. Completed seed increase of these 598 lines to use in yield trials and collected leaves for genomic genotyping. Completed official germplasm release for a new random mated population involving four tetraploid species of cotton. Completed official germplasm release of four cotton germplasm lines that are high in oleic acid in seed oil in cooperation with ARS scientist New Orleans, Louisana. These lines have >33% oleic acid in seed oil whereas commercial varieties have about 17 % oleic acid. Oils with high levels of oleic acid are considered to be healthier and have improved oxidative stability at elevated temperature making them preferred for some cooking and frying applications. These high oleic acid germplasm lines are also resistant to root knot and reniform nematodes. Completed yield trials for 180 recombinant Inbred Lines from a random mated population involving 18 chromosome substitution lines from Gossypium barbadense crossed with three cultivars. Grew field plots for seed increase of 1378 day neutral derived lines from the accession collection that we have previously converted to day-neutral status. Planted the 2019 Regional Breeders Test for evaluation for resistance to cotton bollworm. We have several lines being evaluated in Alabama in a blue disease nursery. We have 180 recombinant lines being evaluated in the Fusarium wilt race 4 nursery in Clint, Texas. At this time in the season several lines have not been killed by the wilt and appear to be resistant. Final determinations on resistance or susceptibility will not be made until plants are examined for the presence of the fungus in the root and stem. In cooperation with ARS scientists in New Orleans, Louisiana we identified and cloned the first root knot nematode gene in cotton. Structure/function analysis allowed us to form a new hypothesis as to how the resistance is attained and identification of the gene has allowed us to design a gene-specific marker to use on the germplasm collections to help find new sources of resistance. We have initiated the first known research on cotton with Meloidogyne enterolobii (Guava Root-knot nematode) which is a new nematode on cotton in North Carolina. We have received Animal and Plant Health Inspection Service and Mississippi State Department of Agriculture permits to work with this nematode under confined and quarantine conditions. The major host where it has been found is sweet potato, but it is also a pest on cotton where it occurs. All our currently root knot nematode lines are susceptible to this new species of nematode. We are searching for genes for resistance to this nematode that could become a major pest of cotton. Research is underway with chromosome substitution lines to search for resistance to 2,4-Dichlorophenoxyacetic acid (2-4D) herbicide and to tarnished plant bugs. Preliminary results are encouraging.
Accomplishments
1. Genetic base for upland cotton breeding has been broadened. ARS researchers at Mississippi State, Mississippi, have utilized G. hirsutum and chromosome substitution lines from cultivated tetraploid species G. barbadense and two wild tetraploid species (G. mustelinum and G. tomentosum) in the development of a random mated population that has recombined the alleles and genes from these four tetraploid species into a germplasm population that has solved the interspecific incompatibility problems. A germplasm release was written and approved for this random mated population of cotton, named Random Mated Barbadense Hirsutum Mustelinum Tomentosum Upland Population (RMBHTM-UP), that has recombined the alleles and genes from four species of cotton. These four species are upland cotton varieties of Gossypium hirsutum, 3-79 a variety of cultivated species G. barbadense, wild species G. mustelinum native to Brazil, and wild species G. tomentosum native to Hawaii. The germplasm population has agronomic and fiber properties similar-to upland cotton but has recombined many genes from the four tetraploid species of cotton. This germplasm offers an expanded genetic base for upland cotton breeding. Seed of this population have been made available to all public and private cotton breeders for their use in cultivar development. This germplasm provides the means for upland breeders to use many of the genes and alleles from the three non- upland tetraploid species of cotton in upland cotton breeding. This germplasm will be useful for many years in upland cotton breeding
2. Germplasm lines of cotton developed and released with double the amount of oleic acid in the cottonseed oil. ,Seed oil with higher levels of oleic acid is considered to be a healthier oil, has greater oxidative stability at elevated cooking temperature, and is thus preferred for some cooking and frying applications. ARS researchers at Mississippi State, Mississippi and New Orleans, Louisiana, have developed four germplasm lines of upland cotton with 31-34% oleic acid in their seed oil; whereas commercial cultivars have only 17% oleic acid in their seed oil. A germplasm release was written and approved for these four high oleic acid lines. In addition, these high oleic acid lines also have genes for resistance to root knot and reniform nematodes and fiber and agronomic properties are essentially equal to the average commercial cultivar. These germplasm lines are available to public and private upland cotton breeders who can use these germplasm lines as parental lines to develop commercial cultivars of upland cotton with high levels of oleic acid in seed oil. This could create a new market opportunity for cotton seed oil and add economic value to both the cotton growers and the seed industry companies.
Review Publications
McCarty Jr, J.C., Deng, D.D., Jenkins, J.N., Geng, L. 2018. Genetic diversity of day-neutral converted landrace, Gossypium hirsutum L., accessions. Euphytica. 214:173. https://doi.org/10.1007/s10681-018-2264-6.
Jenkins, J.N., McCarty Jr, J.C., Deng, D.D., Geng, L., Hayes, R.W., Jones, D.C., Mammadova, R. 2018. Introgression of Gossypium barbadense L. into Upland cotton germplasm RMBUP-C4S1. Euphytica. 214:118. https://doi.org/10.1007/s10681-018-2200-9.
Thyssen, G.N., Jenkins, J.N., McCarty, J.C., Zeng, L., Campbell, B.T., Delhom, C.D., Islam, M.S., Li, P., Jones, D.C., Condon, B.D., Fang, D.D. 2018. Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.). Journal of Theoretical and Applied Genetics. 132:989-999. https://doi.org/10.1007/s00122-018-3254-8.
Naoumkina, M.A., Thyssen, G.N., Fang, D.D., Jenkins, J.N., McCarty, J.C., Florane, C.B. 2019. Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population. BMC Genomics. 20:112. https://doi.org/10.1186/s12864-019-5427-5.
Miao, Q., Deng, P., Saha, S., Jenkins, J.N., Hsu, C., Abdurakhmonov, I.Y., Buriev, Z.T., Pepper, A., Ma, D. 2017. Genome-wide identification and characterization of microRNAs differenytially expressed in fibers in a cotton phytochrome A1 RNAi line. PLoS One. 12(6):e0179381.
Kushanov, F., Buriev, Z.T., Shermatov, S.E., Turaev, O.S., Norov, T., Pepper, A.E., Saha, S., Ulloa, M., Yu, J., Jenkins, J.N., Abdukarimov, A., Abdurakhmonov, I.Y. 2017. QTL mapping for flowering-time and photoperiod insensitivity of wild cotton Gossypium darwinii Watt. PLoS One. https://doi.org/10.1371/journal.pone.0186240.
Read, J.J., Adeli, A., McCarty Jr, J.C., Feng, G.G. 2018. Cotton response to residual poultry litter: leaf area, nitrogen removal, and yield. Agronomy Journal. 110(6):2360-2368. https://doi.org/10.2134/agronj2018.05.0348.
Wu, J., Jenkins, J.N., McCarty Jr, J.C. 2019. Revealing GE interactions from trial data without replications. Open Journal of Statistics. 9:407-419. https://doi.org/10.4236/ojs.2019.93027.
Martinez, G.K., Abdelraheem, A., Darapuneni, M., Jenkins, J.N., McCarty Jr, J.C., Zhang, J. 2019. Evaluation of a multi-parent advanced generation inter-cross (MAGIC) introgressed line population for Verticillium wilt resistance in Upland cotton. Euphytica. 214:197. https://doi/10.1007/s10681-018-2278-0.
