Research Project: Development of Climate Resilient Germplasm and Management Tools for Sustainable Row Crop Production

Location: Plant Stress and Germplasm Development Research

2024 Annual Report

Objectives
1. Employ field and digital agronomy tools to identify quality, characterize and exploit traits that enhance stress tolerance and increase yield in row crops, such as cotton (NP301, C3, PS3A). 2. Determine genetic variability in plant environmental stress responses and exploit the diversity by designing and evaluating genotype-specific production schemes that recognize environmental limitations and interactions (NP301, C3, PS3A). Sub-objective 2A: Determine genetic variability on developing progeny-germplasm and mapping populations by evaluating genotype-specific responses to disease resistance (such as resistance to FOV4) and resilience to water-deficit stress. Sub-objective 2B: Exploit the genetic diversity on developed progeny-germplasm and mapping populations by evaluating genotype-specific approaches through whole genome sequencing, SNP biomarker-trait associations, and gene discovery associated with response to abiotic and biotic stress. Sub-objective 2C: Exploit the diversity of the causal mutation in heat sensitive (hs) sorghum mutants by mapping, cloning, and characterizing the function of identified genes. Sub-objective 2D. Recognize environmental limitations and interactions on heat responses of sorghum in reproductive tissues by characterizing and identifying genetic components critical for heat tolerance in sorghum. 3. Develop and implement crop management systems for water-limited and rainfed production environments by combining the strengths of climate-resilient new varieties with diverse local production practices (NP301, C3, PS3A). Sub-objective 3.A: Optimize the stay-green trait in grain sorghum for higher assimilate production and translocation to grain under stressful and favorable conditions. Sub-objective 3B: Characterizing cold tolerance in cotton by evaluating genetically diverse germplasm and the effect of planting dates on quantitative and qualitative yield. Sub-objective 3C: Characterize impact of elevated temperatures on cotton and peanut physiology and yield.

Approach
Widespread climate disruptions, increases in mean temperature, increased heat waves, altered rainfall patterns, and the emergence of new biotic (pests and diseases) stresses produced by increasing atmospheric greenhouse gas concentrations are threatening agricultural productivity in many regions of the world, notably semi-arid regions. Additionally, recent shifts in consumer demand and corporate values are prompting manufacturers and retailers to include sustainability goals into their buying practices. So, the development and adoption of climate-resilient germplasm and new management tools not only improves crop productivity and sustainability, but also provides a quantitative measure of inputs that can be used to improve practices, decrease carbon, and water footprints, and enhance marketability of the crop. The elucidation of how biological mechanisms control plant stress responses and disease resistance and how the environment, both natural and managed, defines, and restricts crop productivity, provide the foundation for the ability to improve agricultural production in low-input systems. The two approaches for improving future production in this project are: 1) development of germplasm that is better suited to the future production environment (less water, less fertilizer, sub- or supra-optimal temperature, altered biotic pressures), and 2) identification of management tools and approaches that optimize crop performance within a given environment. Genetic improvements will be derived from active, targeted selection of traits in diverse germplasm grown under relevant production scenarios. The successful completion of this project will provide the development of new remote sensing approaches for germplasm screening, crop management, maximizing crop value capture; fill the knowledge gap and design better traditional and molecular breeding strategies for developing resilient cotton, sorghum, and peanut varieties to water-deficit stress and diseases, and increase our understanding of plant response to environmental stress, having a direct impact on economic sustainability of agricultural production in semi-arid environments. The proposed research is relevant to the NP 301 Action Plan, Component 1. Crop Genetic Improvement: Problem Statement 1A, Trait discovery, analysis, and superior breeding methods and 1B, New crops, new varieties, and enhanced germplasm with superior traits; Component 2. Plant and microbial genetic resource and information management: Problem Statement 2A, Plant and microbial genetic resource and information management; Component 3. Crop Biological and Molecular Processes: Problem Statement 3A: Fundamental knowledge of plant biological and molecular processes; and Component 4. Information resources and tools for crop genetics, genomics, and genetic improvement: Problem Statement 4A, Information resources and tools for crop genetics, genomics, and genetic improvement.

Progress Report
Objective 1. Research continues in performing replicated variety trials with 6 of 14 previously evaluated commercial Upland varieties at 3 different planting dates (April – June), and trials having three different irrigation regimens (dry land-limited to regular irrigation) under sub-drip and pivot irrigation systems. Objective 2. These field evaluations also included more than 600 developed cross-combination progenies using Pima-S6, Upland TM-1, MD51ne, Fiber Max 832, Red Raider, Acala NemX, and PSSJ-FRU14 cultivars with diverse genetic backgrounds. Researchers created more than 600 progenies, about 500 of which will be increased in the greenhouse for subsequent field selections and evaluations. In addition, more than 200 cotton line-selections were planted in replicated trials in Lubbock, Texas, at 3 different planting dates (April – June) and using three different irrigation regimens (dry land-limited to regular irrigation) under sub-drip and pivot irrigation systems. Moreover, more than 6,000 research plots planted with selected breeding lines were evaluated for Fusarium wilt race 4 (FOV4) resistance/infection plant response in FOV4 infested fields at two locations in the El Paso, Texas, region. For genomic research, the whole genome assembly of the 26 cotton pseudo-chromosomes of Acala NemX and Pima-S6 cotton genotypes have been completed, and isolation of high molecular weight DNA is ongoing for the additional genotypes to sequence next. In addition, a gene-network was identified to be involved in Fusarium wilt diseases resistance, specifically FOV4, and genes/proteins in FOV4 infected roots and uninfected roots responding different between susceptible and resistant cotton were examined. Moreover, using Oxford Nanopore long read sequencing technology, we sequenced and released high quality genome assemblies of the fungus of Fusarium, two FOV4 and one Fusarium wilt race 1 (FOV1) fungus-isolates. Field-based phenotyping or field morphological characterization was performed for the first set of sorghum named ‘hs’ of the second generation (F2) populations and the corresponding hs mutant parental lines for heat tolerance traits after each of the major heat wave events in the experimental field in the 2023 season. The second set of research materials is ongoing for the 2024 season. In addition, from sampled tissues and isolated DNA from this material in 2023, a genetic analysis was performed of specific heat tolerance hs traits showing recessive/low gene trait-control. Sorghum seeds from control and heat treated BTx623 inbred line-panicles were collected at 8 different stages of seed development. Total RNA will be extracted after the growing season from these lines and will be sent for sequencing using RNAseq technology. Objective 3. Field experiments were conducted at multi-locations: College Station, Texas; New Deal, Texas; and ARS-Lubbock, Texas. A panel of more than 200 lines including 10 lines with a sliding-scale of dhurrin content were evaluated by aerial (UAV) and visual (ground truth) rating for staygreen. Because of post-flowering rains at College Station, Texas, and inconsistencies in subsurface drip irrigation at New Deal, data collection was unsuccessful. However, data collection for aerial and visual were successful at the ARS-Lubbock site in 2023. For the 2024 season, field experiments are ongoing for the 2024 season at ARS-Lubbock and New Deal sites. Initial stand plant-establishment and field base-line UAV flights were done 30 days after planting. Visual rating of stay-green and further UAV flights will be conducted 10 days prior physiological maturity. Furthermore, samples from some of the high stay-green rated lines will be collected for the high-performance liquid chromatography (HPLC) laboratory analysis of dhurrin content. For cotton early-season suboptimal temperature evaluation, twenty of the initial 32 cotton lines previously evaluated at two planting dates, early (March 27th, 2023) and standard (May 15th, 2023), under three Irrigation treatments, full (4ml/day), irrigated (1ml/day), and rainfed, were selected for varying degree of cold tolerance based on analyses of variability in seedling establishment, morphological, physiological, and end of season agronomic performances under early vs. standard planting dates and variable irrigation treatments. For the 2024 season, further evaluations are ongoing of the 20 lines plus 5 commercials entries. Germination, emergence, and vigor rating data have been collected. Within season and end-of-season physiological and agronomic traits will be measured to ascertained performances with respect to quantitative and qualitative yield penalties.

Accomplishments
1. Developing of a new set of cotton lines for breeding for Fusarium wilt race 4 resistance. Today, there is not a known Fusarium wilt race 4 (FOV4)-resistant or highly resistant Upland commercial variety in the United States. FOV4 has impacted cotton production in California’s San Joaquin Valley for two decades and more recently in New Mexico and the El Paso, Texas, region, causing plant wilt and death in commercial production fields. Recently, publicly released Upland cotton lines (PSSJ-FRU01 to PSSJ-FRU17) by USDA-ARS researchers at Lubbock, Texas, and university collaborators, with resistance to FOV4 were crossed with a diverse set of cotton lines that have different traits such as leaf types, plant and root morphology, and genetic backgrounds. These different cross-combinations will generate a new set of cotton breeding lines for continued breeding for FOV4 resistance. In addition, the lines will provide the needed source of FOV4 resistance to breeders of commercial seed companies to increase the genetic diversity in the Upland crop and reduce the vulnerability of the industry to this fungal pathogen.

2. The whole genome sequence and assembly of the source of Fusarium wilt race 4 resistance in cotton. Pima (Gossypium barbadense) cotton also known as long staple or sea island cotton, has long been recognized for its superior fiber quality and premium textile characteristics, compared to Upland (G. hirsutum) cotton. ARS scientists at Lubbock, Texas, and university cooperators sequenced the whole genome of Pima-S6 (PS6), the cultivar known to be the source of resistance for cotton against the fungus pathogen Fusarium wilt race 4 (FOV4). The information in this study describes the genome sequence of PS6, including the assembly of cotton chromosomes and identification of gene functions. This information will be used for researchers to reduce the vulnerability of cotton against this pathogen, assisting in breeding strong resistance to FOV4.

3. Gene-network involved in cotton resistance to Fusarium wilt disease. Fusarium wilt disease represents a continuing threat to cotton production. This plant-root fungal caused plant death and significant yield losses, specifically Fusarium wilt race 4 (FOV4). ARS scientists at Lubbock, Texas, with university cooperators identified and reported a gene-network involved in Fusarium wilt diseases resistance. Examined genes and proteins in FOV4 infected roots and uninfected roots responded differently between susceptible and resistant cotton. Resistant cotton plants were able to have fortified roots preventing less or no infection of FOV4. This is the first comprehensive report, and the information can be used by researchers involved in developing Pima or Upland resistant varieties to Fusarium wilt.

4. Fusarium wilt fungus genes involved in plant infection and disease. Many fungal pathogens produce small, infection-dependent proteins called ‘secreted in xylem’ (SIX) proteins. These proteins are secreted into the plant during the infection process and are thought to increase virulence or disease. Using a collection of Fusarium fungal isolates from across the U.S. (California State University, Fresno, California, and the USDA-ARS culture collection), ARS scientists at Lubbock, Texas, identified a gene specific to the Fusarium wilt (FOV) pathogen of cotton and reported that Fusarium wilt race 4 (FOV4) as well as a fungus from China, FOV race 7, share a common gene not found in less virulent strains. Information from this research will be of particular interest to scientists working in the fields of cotton disease and breeding, and Fusarium genetics.

5. Identifying heat tolerance sorghum mechanisms for heat stress tolerance. Sorghum is an ideal plant for uncovering the underlying mechanisms for heat tolerance. The first set of sorghum named ‘hs’ mutant plants that lost the function of heat tolerance in vegetative tissues were identified from the second generation of segregating populations and planted this year along with the corresponding hs mutant parental lines. Physical characteristics of these plants for heat-stress tolerance will be recorded after each of the major heat wave events during the growing season. In addition, sorghum seeds from control and heat-treated sorghum BTx623 inbred line-panicles were collected at 8 different stages of seed development, including at set days after flowering. Generated information will be used by researchers working in molecular biology to fill the knowledge gap to design better traditional and molecular breeding strategies for developing heat tolerant sorghum lines.

6. Alternative sources of stay-green in sorghum. The ability of sorghum to be productive under drought conditions depends on the level of before- and after-flowering drought tolerance. There are limited sources of the after-flowering drought tolerance trait known as stay-green, and many have poor agronomic traits for grain yield and quality. Dhurrin content has been linked to the stay-green trait and is being used to select sorghum lines containing this trait. ARS scientists at Lubbock, Texas, screened the sorghum association panel for the stay-green trait and identified ten lines with different concentrations of dhurrin. Field experiments were planted at three ARS locations (College Station, New Deal, and Lubbock, Texas), and on three planting dates (April 3rd, June 8th, and June 23rd, respectively). Virtual ratings of stay-green and sampling will be assessed 10 days prior to physiological maturity in all locations. Generated information will be used by researchers and breeders to evaluate the performance of sorghum lines and developed hybrids to determine the level of stay-greenness needed to obtain a significant increase in yield and grain protein under different target environments.

7. Identifying cotton germplasm with tolerance to sub-optimal temperatures. The cultivation of cotton in most temperate regions is constrained by a short production window with sub-optimal temperatures. Low temperatures at the beginning of the season will affect germination, emergence, stand, and vigor of plants. In addition, low temperatures at the end of the season will also affect boll formation and fiber yield and quality. Both phenomena effect the quality and quantity of upland cotton production in temperate regions. Using plant agronomy, morphology, and physiology tools that may uncover benefits or drawbacks of quality and quantity of yields in cotton, ARS scientists at Lubbock, Texas, evaluated a diverse set of cotton germplasms for tolerance to suboptimal temperatures based on varying planting dates. Using quality and quantity yield penalties, several best performing lines were selected. These lines will be suggested to breeding programs as parental sources for introgression of beneficial traits in breeding cotton varieties/hybrids suitable for early planting practices and end-of-season low temperature tolerance. Results from this research will also help to establish long-term production stability with a widespread understanding and adoption of early-planting practice by growers whenever possible. In addition, early planting will allow farmers to take advantage of early season moisture and reduce production costs for weed management before full crop development.

Review Publications
Jobe, T.O., Ulloa, M., Ellis, M.L. 2023. A high-quality whole-genome sequence, assembly, and gene annotation of Fusarium oxysporum f. sp. vasinfectum (FOV) race 1 from California. Microbiology Resource Announcements. 13(1). https://doi.org/10.1128/mra.00702-23.
Ojeda-Rivera, J., Ulloa, M., Najera Gonzalez, R.H., Roberts, A.P., Chavez Montes, R., Herrera-Estrella, L., Lopez-Arrendondo, D. 2024. Enhanced phenylpropanoid metabolism underlies resistance to Fusarium oxysporum vasinfectum f. sp. race 4 infection in the cotton cultivar Pima-S6 (Gossypium barbadense L.). Frontiers in Genetics. 14. https://doi.org/10.3389/fgene.2023.1271200.
Jobe, T.O., Ulloa, M., Ellis, M.L. 2023. Two De Novo genome assemblies from pathogenic fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) isolates from California. Microbiology Resource Announcements. 13(1). https://doi.org/10.1128/mra.00760-23.
Pugh, N.A., Young, A.C., Oijha, M., Emendack, Y., Sanchez, J., Xin, Z., Puppala, N. 2024. Yield prediction in a peanut breeding program using remote sensing data and machine learning algorithms. Frontiers in Plant Science. 15. https://doi.org/10.3389/fpls.2024.1339864.
Mendu, L., Jalathge, G., Dhillon, K., Singh, N., Balasubramanian, V., Fewou, R., Gitz, D.C., Chen, J., Xin, Z., Mendu, V. 2022. Mutation in Endo-ß-1,4-Glucanase (KORRIGAN) is responsible for thick leaf phenotype in sorghum. Plants. 11(24). https://doi.org/10.3390/plants11243531.
Chen, J., Laza, H., Burow, G.B., Hayes, C.M., Burke, J.J., Emendack, Y., Xin, Z. 2022. Registration of two novel grain sorghum nuclear male sterile mutants: BTx623ms9-1 and BTx623ms9-3. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20251.
Khan, A., Khan, N., Bean, S.R., Chen, J., Xin, Z., Jiao, Y. 2023. Variations in total protein and amino acids in the sequenced sorghum mutant library. Plants. 12(8). https://doi.org/10.3390/plants12081662.
Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Burke, J.J., Pugh, N.A., Ware, D. 2023. Registration of 252 sequenced sorghum mutants as a community reverse genetic resource. Journal of Plant Registrations. 17(3):599-604. https://doi.org/10.1002/plr2.20296.
Emendack, Y., Xin, Z., Hayes, C.M., Burow, G.B., Sattler, S.E., Bean, S.R., Smolensky, D. 2022. Registration of three new bmr12 sorghum mutants from an ethyl methane sulfonate–induced BTx623 mutant population. Journal of Plant Registrations. 16(2):453-458. https://doi.org/10.1002/plr2.20219.
Emendack, Y., Sawadogo, N., Ramadjita, T., Laza, H. 2023. Assessment of photoperiod sensitivity and the effect of sowing date on dry-season sorghum cultivars in Southern Chad. Agronomy Journal. 13(3). Article 932. https://doi.org/10.3390/agronomy13030932.
Chaudhuri, S., Roy, M., McDonald, L., Emendack, Y. 2023. Land degradation–desertification in relation to farming practices in India: An overview of current practices and agro-policy perspectives. Sustainability. 15(8). https://doi.org/10.3390/su15086383.
Laza, H., Acosta Martinez, V., Cano, A., Baker, J.T., Mahan, J.R., Gitz, D.C., Emendack, Y., Slaughter, L., Lascano, R.J., Tissue, D., Payton, P.R. 2023. Elevated [CO2] enhanced soil respiration and AMF abundance in a semiarid peanut agroecosystem. Agriculture, Ecosystems and Environment. 355. https://doi.org/10.1016/j.agee.2023.108592.
Somayanda, I.S., Bean, S.R., Ioerger, B.P., Hayes, C.M., Emendack, Y., Jagadish, K.S. 2023. Comparative assessment of grain quality in tannin versus non-tannin sorghums in the sorghum association panel. Cereal Chemistry. 100(3):663-674. https://doi.org/10.1002/cche.10643.
Chavez-Montes, R., Ulloa, M., Biniashvili, T., Zackay, A., Kfir, N., Lopez-Arrendondo, D., Herrera-Estrella, L. 2023. Assembly and annotation of the Gossypium barbadense L. 'Pima-S6' genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes. BMC Genomics. 24. Article 11. https://doi.org/10.1186/s12864-022-09102-6.
Mendu, L., Ulloa, M., Payton, P.R., Monclova-Santana, C., Chagoya, J., Venugopal, M. 2022. Lignin and cellulose content differences in roots of different cotton cultivars associated with different levels of Fusarium wilt race 4 (FOV4) resistance-response. Journal of Agriculture and Food Sciences. 10. Article 100420. https://doi.org/10.1016/j.jafr.2022.100420.
Ulloa, M., Hutmacher, R.B., Zhang, J., Schramm, T., Roberts, P.A., Ellis, M.L., Dever, J.K., Wheeler, T.A., Witt, T.W., Sanogo, S., Hague, S., Keely, M.P., Arce, J., Angeles, J., Hake, K., Payton, P.R. 2022. Registration of 17 upland cotton germplasm lines with improved resistance to Fusarium wilt race 4 and good fiber quality. Journal of Plant Registrations. 17(1):152-163. https://doi.org/10.1002/plr2.20258.
Ostmeyer, T.J., Somayanda, I.S., Bean, S.R., Dhillon, R., Hayes, C.M., Ritchie, G., Asebedo, A.R., Emendack, Y., Jagadish, K.S. 2023. Impact of in-season split application of nitrogen on intra-panicle grain dynamics, grain quality and vegetative indices that govern nitrogen use efficiency in sorghum. Plant and Soil. https://doi.org/10.1002/jpln.202200325.
Hayes, C.M., Emendack, Y., Sanchez, J., Burke, J.J., Pugh, N.A., Xin, Z., Rooney, W.L. 2023. Evaluation of diverse sorghum for leaf dhurrin content and post-anthesis (stay-green) drought tolerance. Crops. 3(3):241-250. https://doi.org/10.3390/crops3030022.
Triplett, E., Hayes, C.M., Emendack, Y., Longing, S., Monclova, C., Simpson, C., Laza, H. 2023. Leaf structural traits mediating pre-existing physical innate resistance to sorghum aphid in sorghum under uninfested conditions. Planta. 258. Article 46. https://doi.org/10.1007/s00425-023-04194-0.
Jiao, Y., Singh, D., Barry, K., Daum, C., Yoshinaga, Y., Khan, A., Lu, Z., Wang, X., Wei, X., Tello-Ruiz, M.K., Burow, G.B., Hayes, C.M., Chen, J., Mortimer, J., Ware, D., Xin, Z. 2023. A large sequenced mutant library- valuable reverse genetic resource that covers 98% of the genes in a Sorghum genome. Plant Journal. 117(5):1543-1557. https://doi.org/10.1111/tpj.16582.
Schwartz, R.C., Witt, T.W., Ulloa, M., Colaizzi, P.D., Baumhardt, R.L. 2024. Irrigation response, water use, and lint yield of upland cotton cultivars. Journal of the ASABE. 67(2):421-437. https://doi.org/10.13031/ja.15868.