Skip to main content
ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Research Project #425080

Research Project: Using Genetic Approaches to Reduce Crop Losses in Rice Due to Biotic and Abiotic Stress

Location: Dale Bumpers National Rice Research Center

2016 Annual Report

The long-term objective of this project is to seek a better understanding of the genetic and molecular bases of rice response to biotic and abiotic stresses in an effort to maintain high yields, improve crop resilience to changes in climate and cultural management practices, and to reduce reliance on pesticides for crop protection. Obj. 1: Evaluate novel sources of disease resistance to develop closely linked genetic markers for breeding, and elucidate plant-pathogen interactions. 1A: Develop new genetic markers associated with genes that control resistance response to rice blast disease 1B: Explore new genetic resources that possess novel alleles for major and minor genes that convey resistance to the sheath blight pathogen Obj. 2: Identify and genetically map traits associated with weed suppression in indica rice germplasm. 2A: Develop methods to quantify alleleopathy chemicals and other weed suppressive traits using greenhouse, laboratory, and field assays 2B: Characterize relative contribution of agronomic traits and allelopathy to weed suppression effective under reduced-irrigation systems or reduced-pesticide/organic systems 2C: Validate and fine-map QTLs associated with early tiller production for development of genetic markers suitable for breeding for weed suppression in US genetic backgrounds 2D: Identify QTLs associated with weed suppression using RIL mapping population derived from an allelopathic weed suppressive/non-suppressive tropical japonica cross Obj. 3: Explore rice genetic resources for use in adapting to climate change and mitigating greenhouse gas emissions. 3A: Identify genetic resources that can be used in breeding to adapt to extremes in temperature at the seedling and flowering stage 3B: Identify genetic resources that can be used to mitigate methane emissions in rice production Obj. 4: Investigate the use of genetic resources for production under irrigation systems that use less water. 4A: Discover chromosomal regions linked to yield potential under reduced water use systems 4B: Develop genetic resources that can be used in saline soils where water is limited

Wild rice accessions will be evaluated for blast disease resistance and sources with novel genes will be used in a backcrossing program to both map the novel QTL and develop germplasm with improved resistance. A major gene that provides resistance to a blast race that is virulent on all sources of resistance commonly used in the USA will be finely mapped. Closely linked DNA markers will be used for its introgression using marker assisted selection into improved germplasm for use by breeders. The interaction and evolutionary dynamics of genes involved in blast resistance in both rice and the pathogen will be examined. The genetic identity of contemporary and historical field isolates will be determined using genomic techniques and international differentials. Small differences in resistance response to sheath blight disease will be evaluated and used to identify the location of quantitative resistance QTL. Newly introduced wild accessions of rice and diverse global cultivars will be evaluated for novel sheath blight resistance alleles which will be incorporated to US germplasm for use by breeders. A major sheath blight resistant QTL will be finely mapped so that DNA markers and improved germplasm can be developed. Rice root imaging, plant growth patterns, early tillering, and allelopathic activity associated with weed suppression will be determined and used in mapping studies. Weed suppression traits effective under reduced-irrigation systems or reduced-pesticide/organic systems will be characterized. Cold temperature tolerance at the seedling stage and high temperature stress at the flowering stage will be assessed using diversity panels and mapping populations. A greenhouse study will be conducted using rice cultivars demonstrated to differ in methane emissions under field conditions to determine plant traits that may explain these differences. Best nitrogen fertilizer management practices for minimizing greenhouse gas emissions will be identified using intermittent flood and genetic resources previously shown to differ in methane emissions. The key components including best cultural management techniques and agronomic and phenological traits associated with greenhouse gas reduction relevant to southern US germplasm will be identified. Genetic markers that are linked to key phenotypic traits associated with productivity under intermittent flood will be identified for ultimately developing cultivars that can be grown under reduced water use. Genetic resources and markers that demonstrate genetic differences for salinity tolerance at the seedling stage will be identified to develop improved germplasm and cultivars for US rice production. The outcome of this research will result in genetic markers linked to traits that can be incorporated into new cultivars that are resilient to disease, weed pressure, salinity, extremes in temperatue, and can be grown under production practices that use less water and have reduced greenhouse gas emissions.

Progress Report
ARS in-house and grant supported research have progressed and two scientific positions that have been vacant since the inception of the project were filled. Five microsatellite (SSR) markers spanning a major quantitative trait locus (QTL) for sheath blight disease resistance (qSHB9-2) were used to genotype BC4F2 progenies from a cross. Molecular recombinants were verified with these SSR markers and progenies were phenotyped with a newly developed greenhouse sheath blight inoculation method. The progeny are being advanced for disease resistance validation in replicated field trials. The Wild4 [LaGrue/O. nivara (IRGC104443)] backcross population of BC2F2 families was generated and reaction to sheath blight disease will be conducted in the greenhouse in year 4. A pilot study was conducted to adapt the methodology for evaluating salt tolerance to the Oryza species in preparation for evaluating a wild species diversity panel for salt tolerance in year 4. To identify a major gene conferring resistance to the most virulent blast race, IB33, a new cross was made and 250 progeny were generated for phenotypic and genotypic analyses. A critical rice gene Ptr(t) required for blast disease resistance of the Pi-ta/Pita2 gene was identified. Sequence analysis of Ptr(t) in ten selected rice germplasm lines revealed DNA polymorphisms determine resistance specificity to different blast isolates. As part of a USDA-NIFA funded project with Kansas State University a total of 800 USA blast isolates, including 100 isolates collected in 2015, were examined for race identity, avirulence (AVR) gene, SSR profiles, and pathogenicity towards known blast resistance genes using a set of International Rice Research Institute (IRRI) monogenic lines. Five effective blast resistance genes were identified and new DNA markers for the Pi9 and Pita/Pita2 genes were developed for marker assisted breeding to improve disease resistance in USA rice. Resistance spectra of these blast resistance genes are being determined with further pathogenicity tests using selected isolates and germplasms. Two blast races, IB1 and IB17, were determined to be the two most commonly found isolates from 2012 to 2015 in the southern USA. Genome wide association analysis of selected rice germplasm is being conducted to identify effective resistance genes to these two most commonly found blast isolates. Progress was made on phenotyping traits associated with weed suppression including measuring photosynthesis, growth, seedling digital imaging, and deploying polydimethylsiloxane microtubes in field plots to capture allelochemicals of mapping parents (allelopathic X non-allelopathic US cultivar) and some of their offspring. In addition, a preliminary laboratory procedure was developed for the extraction and quantification of the momilactone allelochemical. The photosynthetic productivity and water use of parents of a weed suppressive mapping population and of barnyardgrass in intermittent flood systems (AWD) were measured in the greenhouse and field. Progress was made in a separate QTL mapping effort for early tiller production in rice which creates weed-suppressing shade under field conditions. Newly generated population of BC1F2 progeny was used to more precisely map the QTLs on chromosomes 2 and 5 that are associated with early tiller production. Marker and phenotypic data were used to select 62 BC1F1 plants which were backcrossed generating BC2F1 seed to further efforts to introgress alleles for increased tillering ability from Zhe733, a cultivar from China, into the US cultivar Presidio. A two-year study showed limited benefits to rice emergence, yield, and weed suppression from using seed pre-treatments. Progress was made to identify QTLs for adaptation to alternate wetting and drying (AWD). The TeQing X Lemont introgression (TIL) population was used to map QTLs for yield performance under contrasting flooded and AWD conditions, and lines have been identified with superior yield under AWD. The third year of a field experiment comparing mapping parents and elite cultivars at four varying levels of soil saturation was established. Photosynthesis, canopy temperature, and soil moisture were measured and will be associated with plant yield under different levels of water stress. A second year of field testing the TIL population for tolerance to heat stress at the flowering stage was implemented with the objective of conducting QTL mapping. Field experiments in cooperation with ARS scientists in Beltsville, MD are underway to test the hypothesis that yields of historical U.S. rice varieties will increase under present-day ‘elevated’ CO2 levels (~400 ppm) compared with the same varieties grown at the lower levels of CO2 (~350 ppm) present in the 1960s. A growth chamber experiment in cooperation with ARS scientists in Beltsville, MD is currently ongoing to understand CO2 effect on rice grain protein content. Two nearly isogenic cultivars, Cypress and a mutant of Cypress with high protein content, are being grown under ambient CO2 (400 ppm) and 1.5X elevated CO2 (600 ppm). To unravel a holistic view of CO2 effect on protein synthesis during grain development, transcriptomics, metabolomics, and proteomics studies will be conducted using grain samples from R6 and R7 plant growth stages. Seven rice cultivars previously shown to differ in CH4 emissions will be examined for anatomical and physiological traits (aerenchyma volume, root exudates, tiller numbers) along with CH4 emissions using favorable and unfavorable soil conditions for methanogens in a controlled greenhouse experiment. The study will be conducted under field conditions in year 4 to validate differences and understand further environmental effects. Scientists with ARS at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas, along with researchers from the University of Arkansas-Fayetteville, Institute of Plant Breeding and Phytogenetic Resources-Thermi, Thessaloniki, Greece, Aberystwyth University-Ceredigion, UK, and Rothamsted Research-Harpenden, Hertfordshire, UK conducted a review of key effects of climate change on crop cultivars and weeds. Rice, a C3 plant, is expected to yield better under increased carbon dioxide (CO2), but may suffer serious yield losses under the higher temperatures that are projected for the future. Moreover, C3 weeds are likely to respond more positively than C4 weeds to CO2 increases through biomass and leaf area increases, and could become more of a problem in tropical regions. Temperature increases will probably expand the geographical range of C4 weeds and some invasive weed species, thus making weed management more challenging. The first year of establishing an organic rice field testing site was completed as part of a USDA-NIFA-OREI grant with Texas A&M University and University of Arkansas-Stuttgart and Pine Bluff. A winter green manure crop was planted and harvested in the spring demonstrating excellent production of crimson clover and very poor production of winter wheat. As compared to the non-planted area, there was 47% more biomass produced in the area planted to the green manure crop. Following the spring plowdown, the soil in the green manure crop area had 27% soil nitrate as compared to 12% in the non-planted area. Planting of preliminary rice yield trial at the site, revealed additional cultural practices would be needed to control water tolerant weeds like nutsedge in the organic system.

1. Molecular markers more closely linked to a new rice blast disease resistance gene are developed. Rice blast disease is the most damaging rice disease worldwide. Molecular markers are useful for the identification of genes that control important traits in agricultural crops, and for the utilization of these genes in crop improvement using marker assisted selection (MAS). ARS scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas along with researchers at the University of Massachusetts, Amherst, Massachusetts, and Washington University in St. Louis, Missouri developed three molecular markers for a newly identified blast resistance gene Pi66(t). These new genetic markers were validated in a diverse USDA-ARS core germplasm collection. These markers are useful for rice breeders using an MAS approach to improve blast resistance in new rice cultivars.

2. Increasing temperatures that are projected under higher carbon dioxide (CO2) levels negate yield benefits in rice. Researchers are examining which varieties of important cereal crops, such as rice, respond best to rising CO2 levels and the basis for such a response. Evaluating genetically diverse rice varieties at current and projected CO2 concentrations under four different temperature environments, scientists with ARS at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas and at the Crops Systems and Global Change Laboratory in Beltsville, Maryland, along with researchers at Cornell University-Ithaca, New York, showed that rice grown under projected increases of CO2 was more sensitive to high temperature stress compared with rice grown at current CO2 levels, suggesting that rising temperatures associated with global warming might generally negate CO2 increases in rice yield, and for certain varieties, could even reduce yield relative to current conditions. These data are important for developing strategies to mitigate and adapt to the anticipated effects of climate change on rice productivity.

3. Rice cold tolerance at the seedling and reproductive stages. Improving cold tolerance at germination allows rice to be planted earlier in the growing season, thus avoiding high temperature stress during the reproductive phase that is commonly observed in tropical rice growing areas. Improving cold tolerance at the reproductive stage is important in temperate regions where cool night temperatures can reduce grain yield. ARS scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas in collaboration with researchers at the University of Arkansas and at the California Rice Research Foundation surveyed a diverse collection of 420 rice accessions and identified 91 accessions with excellent germination under cold temperatures and eight accessions with improved cold tolerance at the reproductive phase. Molecular analysis revealed 34 possible genes controlling cold tolerance at germination and 19 possible genes controlling tolerance at the reproductive stage. The numerous genes identified associated with cold tolerance underscores the complexity of the trait and the importance of developing molecular markers to tag the most important genes so that breeders can incorporate improved cold tolerance into new varieties.

4. The trade-off of disease resistance versus productivity. Resistance to rice blast disease could result in poor yield production if the resistance response requires expenditure of energy by the plant. Scientists with ARS at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas, along with researchers at the University of Arkansas, Stuttgart, Arkansas and Arkansas State University, Jonesboro, Arkansas found that molecular markers associated with a blast resistance gene were also associated with yield related traits. Most noticeable, taller plants were correlated with blast susceptibility, and rice germplasm carrying a major blast resistance gene Pi-ta were associated with lower seed weights. These findings are useful for developing strategies for combining high yield and blast resistance in new rice cultivars via genomic and marker assisted selection.

5. First report of multiple races of the rice blast fungus in Puerto Rico. The rice breeding nursery located in southwestern Puerto Rico has been used by U.S. rice breeders for the past 43 years to expedite the process of developing new varieties. ARS scientists at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas identified multiple races of blast from the nursery that are similar to isolates commonly found in the US southern rice growing area. They also demonstrated that rice varieties which possess the major blast resistance gene Pi-ta is effective for preventing infections from these isolates. These findings suggest that the Puerto Rico winter nursery serves rice breeders by offering an opportunity to select for blast disease resistance as well as other agronomic traits.

6. Sexuality of rice blast fungus identified. Sexual reproduction may occur when two opposite mating types of a pathogen meet which can lead to an increase in genetic diversity making it more difficult to control the disease in rice. The sexuality of the rice blast pathogen is controlled by the MAT gene and has two mating types, MAT1-1 and MAT1-2. Scientists with ARS at the Dale Bumpers National Rice Research Center, Stuttgart, Arkansas along with researchers at the Yunnan Academies of Agricultural Sciences, Kunming, China and Japanese International Research Center for Agricultural Sciences, Ishigaki, Okinawa, Japan collected blast isolates from two large rice growing regions in Yunnan Province of China to examine the genetic diversity, mating type, and pathogenicity. There was no evidence of sexual recombination between MAT1-1 and MAT1-2 populations but the latter was more genetically diverse suggesting it has the capability to adapt over a broader range of environments in Yunnan province. This study demonstrated that the rice blast pathogen is highly diverse enabling it to cause disease on all known resistance genes in rice even without sexual recombination.

7. Weedy red rice biotypes are genetically diverse in competiveness with cultivated rice. Weedy red rice is a major weed pest in the southern USA that is known for its aggressive competitiveness against rice crops. In a greenhouse study, relative competitive abilities were determined between a common commercial rice variety and two predominant and genetically diverse weedy red rice biotypes (strawhull or blackhull) from the southern USA. Scientists with ARS at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas and researchers at the Federal University of Pelotus, Rio Grande do Sul, Brazil, showed that both the strawhull and blackhull red rice biotypes grew aggressively, easily out-competing the commercial rice variety, and the blackhull biotype was more competitive than the strawhull biotype. Thus, the red rice biotypes were predominantly susceptible to competition from each other, and not from the commercial rice. These results highlight the need for diligent identification and aggressive management of red rice in USA rice fields and subsequent rotational crops.

8. Useful blast resistance genes validated. Minor blast resistance genes also referred as quantitative trait loci (QTL) are commonly identified using phenotypic data from replicated field plot experiments. However, because of the relatively minor effect of these genes the data are often are not reliable due to variability in uncontrolled field environments. Scientists with ARS at the Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, along with researchers at the University of Arkansas-Fayetteville and Hunan Hybrid Rice Research Center, Changsha, China validated previously identified QTL for minor blast resistance genes using a greenhouse method. This study demonstrated identification of minor blast resistance genes under a controlled environment are reliable, and DNA markers closely linked to these QTL are useful for breeding for improved blast resistance with marker assisted selection.

9. Carry-over seed from hybrid rice cultivars reduce grain yield and quality in subsequent rice crops. Seed from hybrid rice varieties that survive from the previous cropping seasons, called volunteers, may differ in their grain physical and chemical traits from those of cultivated rice, and thus, may reduce the quality and consumer value of harvested rice grain. From field surveys and laboratory analyses, scientists with ARS at the Dale Bumpers National Rice Research Center in Stuttgart, Arkansas, along with researchers at the University of Arkansas-Fayetteville and the University of Massachusetts-Amherst, showed that rice fields with a cropping history that included hybrid rice cultivars in the previous two years had higher volunteer rice infestations (20%) compared with fields planted previously with inbred cultivars (5.6%), and that the total yield of rice was reduced 0.4% for every 1% increase in volunteer rice density. Volunteer rice density of 7.6% and above negatively impacted milling yields, and protein and amylose contents of rice were adversely affected at volunteer rice infestations above 30%. Thus, rice cropping systems that have persistent hybrid rice volunteers are predicted to more negatively impact grain yield and quality in subsequent crops than systems without hybrid rice.


Review Publications
Pinson, S.R., Jia, Y. 2016. QTLs for early tiller production and relationships with rapid seedling growth and increased panicle number in rice. Crop Science. 56:505-519. doi: 10.2135/cropsci2014.09.0667.
Xing, J., Jia, M.H., Correll, J.C., Yuan, L., Deng, H., Jia, Y. 2015. Confirming and identifying new loci for rice blast disease resistance using magnaporthe oryzae field isolates in the US. Crop Science. 55:2620-2627. doi: 10.2135/cropsci2015.02.0077.
Liu, Y., Jia, Y., Gealy, D.R., Goad, D.M., Caicedo, A.L., Olsen, K.M. 2016. Marker development for rice blast resistance gene Pi66(t) and application in USDA rice mini-core collection. Plant Science. 56:1-8. doi: 10.2135/cropsci2015.07.0422.
Li, J., Li, L., Jia, Y., Wang, Q., Fukuta, Y., Li, C. 2016. Characterization of field isolates of Magnaporthe oryzae with mating type, DNA fingerprinting, and pathogenicity assays. Plant Disease. 100(2):298-303.
Wang, X., Jia, M.H., Ghai, P., Lee, F.N., Jia, Y. 2015. Genome-wide association of rice blast disease resistance and yield-related components of rice. Molecular Plant-Microbe Interactions. 28(12):1383-1392.
Jia, Y., McClung, A.M. 2016. First report of multiple races of the rice blast fungus Magnaporthe oryzae in Puerto Rico. Plant Disease. doi: 10.1094/PDIS-12-15-1391-PDN.
Jia, Y., Zhou, E., Lee, S., Bianco, T.A. 2016. Coevolutionary dynamics of rice blast resistance gene Pi-ta and Magnaporthe oryzae avirulence gene AVR-Pita 1. Phytopathology. 106(7):676-683. doi: org/10.1094/PHYTO-02-16-0057-RVW.
Pinson, S.R., Wang, Y., Tabien, R.E. 2016. Registration of TIL:383.13, TIL:625 and TIL:634, three long grain tropical Japonica Rice (Oryza sativa L.) germplasm lines containing novel Indica Alleles that increase tiller production and grain yield. Journal of Plant Registrations. 10:171-176.
Nohatto, M.A., Agostinetto, D., Gealy, D.R., De Avila, L.A., Da Silva, B.M., Westendorff, N. 2016. Relative competitive ability of rice with strawhull and blackhull red rice biotypes. Científica: Revista de Ciências Agrárias. 4:176-184. doi: org/10.15361/1984-5529.2016v44n2p176-184.
Korres, N., Norsworthy, J.K., Tehranchian, P., Gitsopoulos, T.C., Loka, D.A., Oosterhuis, D.M., Gealy, D.R., Moss, S.R., Miller, R.M., Palhano, M. 2016. Effects of climate change on crops and weeds: scope for developing cultivars better adapted to both abiotic stress and an ability to suppress weeds . Agronomy for Sustainable Development. 2016. 36:12.