Location: Plant Stress and Germplasm Development Research
2023 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: Even though the project plan was recently approved and certified, 12 replicated variety trials were planted this season with 14 commercial Upland varieties at 4 different planting dates (April – June), and trials will have 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 and new F1-F3 progeny previously created. In addition, more than 300 cotton line-selections from diverse-cross combinations were planted within some of these replicated trial sites in Lubbock, Texas, as well as at two locations in the El Paso, Texas, region in FOV4 infested fields, representing more than 6,000 research plots. For genomic research, the whole genome sequences of Acala NemX and Pima-S6 cotton genotypes were completed, and DNA sequences of these genotypes have been assembled in the 26 cotton pseudo-chromosomes. In addition, isolation of high molecular weight DNA is ongoing for additional genotypes to sequence next. The first set of sorghum heat sensitive (hs) F2 sorghum populations and the corresponding hs mutant parental lines were planted in May of 2023, and the phenotyping for heat tolerance traits will be performed after each of the major heat wave events during the growing season. In addition, sorghum seeds from control and heat treated BTx623 inbred line-panicles were collected at 8 different stages of seed development, including at set days of post-anthesis. Total RNA will be isolated or extracted from control and inbred lines after the growing season and will be sent for sequencing (RNAseq). Objective 3: Ten lines with a sliding-scale of dhurrin content were identified from the sorghum association panel. Field experiments were planted at multi-locations: ARS College Station, New Deal, and Lubbock, Texas on April 3rd, June 8th, and June 23rd, 2023, respectively. Virtual rating of staygreen and sampling will be assessed at 10 days prior to physiological maturity in all locations. In addition, thirty-two cotton genotypes germplasm lines from USDA-ARS Lubbock, Texas AgriLife and Texas Tech University, were planted in a randomized complete block design. The early planting was done on March 27th and the standard planting on May 15th. Germination, emergence, and vigor rating data have been collected. Irrigation treatments, full (4ml/day), irrigated (1ml/day), and rainfed will be implemented at first square, and lines will further be evaluated during the season.
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 cotton 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 ARS scientists in Lubbock, Texas, and university collaborators publicly released Upland cotton lines (PSSJ-FRU01 to PSSJ-FRU17) with resistance to the Fusarium fungus FOV4. The PSSJ-FRU01-FRU17 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 eventually provide the needed source of FOV4 resistance to breeders of commercial seed companies to increase the genetic diversity in the Upland cotton and reduce the vulnerability of the industry to this fungal pathogen.
2. Identifying heat tolerant sorghum mechanisms for heat stress tolerance. Sorghum is an ideal plant for uncovering the underlying mechanisms for heat tolerance as it possesses a superior tolerance to high temperatures. The first set of sorghum heat sensitive (hs) mutant plants that lost the function of heat tolerance in vegetative tissues were identified by ARS scientists in Lubbock, Texas, 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 knowledge gap to design better traditional and molecular breeding strategies for developing heat tolerant sorghum lines.
3. 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 a sliding-scale of dhurrin content. Field experiments were planted at three locations (College Station, New Deal, and ARS Lubbock, Texas) and at three planting dates (April 3rd, June 8th, and June 23rd, respectively). Virtual rating of stay green and sampling will be assessed at 10 days prior physiological maturity in all locations. Generated information will eventually 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.
