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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

2018 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
This is the final report for project 6028-21220-005-00D, which has been replaced by new project 6028-21000-011-00D. For additional information, see the new project report. Toward the long-term goal of improving understanding of genetic and molecular bases of rice response to biotic and abiotic stresses, 50+ peer reviewed research articles were published as part of this project plan and associated grant-funded studies. One significant accomplishment was the cloning of Ptr, an atypical rice blast resistance (R) gene, and the new knowledge that Ptr acts by broadening the race specificity and increasing the disease resistance conferred by the classical R gene Pi-ta. New breeder-useful DNA markers for Ptr and for other R genes, Pi-9, Pid2, Pit and Pi66(t) were developed for marker assisted selection (MAS). A total of 42 improved genetic stocks combining blast-resistance with appropriate medium grain rice quality and agronomics was developed as genetic stocks. Most blast R genes originated from indica rice, however, weedy red rice, which coexists with U.S. commercial rice, can be a new source for disease resistance. Adapted mechanisms and whole genomes of weedy rice were evaluated, revealing that the two major biotypes, blackhull (BH) and strawhull (SH), can use different strategies to acquire weedy traits and biotic stress tolerance. Weedy red rice AR-1994-10A was identified as the most blast-resistant among 60 weedy rice accessions exposed to 14 blast races/isolates, and was even resistant to the most virulent race, IB-33. Also, U.S. weedy blast R genes were mapped to four R-gene clusters in genomic regions not previously known to contain R genes. Sheath blight (SB) is another disease that significantly reduces U.S. rice production. Ten R quantitative trait loci (QTLs) including the major effect QTL qShB9-2 were identified and validated from adapted U.S. rice germplasm. Due to lack of complete resistance to SB, our validation and fine mapping of qShB9-2 to a 145 kb region significantly improves the ability to use this resistance in breeding. A mapping population derived from the adapted U.S. varieties Lemont and Jasmine 85 was developed to identify QTLs and useful DNA markers for blast and SB R, and grain aroma. To determine if disease resistance may cause a yield penalty, 151 accessions were evaluated for disease reactions and yield components. Twenty-one simple sequence repeat (SSR) markers were associated with blast resistance, and 16 SSR markers were associated with seed weight, heading date, and plant height. Most notably, the resistance Pi-ta region was associated with lighter seed and suggested a complex relationship between disease resistance and yield-related traits. Characterization of genetic identity of blast fungus from commercial fields can help direct future breeding efforts. To facilitate rapid genomic analysis of the blast fungus, an efficient method for isolation of DNA from fungus stored on filter paper was developed. Pathogen avirulence (AVR) genes determine efficacies of cognate R genes. Six AVR genes in 1169 U.S. field blast isolates collected over six decades were analyzed. The disappearances of AVR-Pita and AVR-Pik correlated with deployed cognate R genes over 6 decades suggests that the host plays a role in directing pathogen genetic changes. This study demonstrated that continued search for new R genes is essential for securing stable rice production. Rice wild relatives (Oryza species) are another source of novel alleles. Earlier screening of wild Oryza accessions for SB and blast R, revealed four SB R accessions that were used in advanced backcrossing (ABC) mapping populations to incorporate these R alleles into cultivated rice. Mapping in ABC populations from two different O. nivara accessions identified three SB R QTL and two blast R QTL. Mapping in a third population with O. meridionalis revealed a SB R QTL which mapped to the aforementioned qShB9-2, suggesting O. meridionalis as a progenitor source of qShB9-2. Another population using a third O. nivara accession was screened in the greenhouse for SB and will be used in the next project plan. Currently, a fifth ABC population developed with a blast R, O. rufipogon, donor, is being advanced to the BC2F2 generation with screening and mapping to follow in the new project plan. The mechanisms of yield gain in hybrid rice due to heterosis are not fully understood. Many genes involved in epigenetic regulation in an F1 hybrid were mapped to 71 QTLs associated with yield related traits. This provides a starting point to better understanding the genetic basis of heterosis. To genetically map traits associated with weed suppression in indica germplasm, rapid seedling growth and production of tillers at early growth stages were analyzed. Eleven QTLs for increased tiller number (TN) at early and later growth stages were identified in three mapping populations. Three TN QTLs identified in all three populations included one residing near the sd1 semidwarf locus which alters hormones that potentially also impact tiller production. However, mapping this TN QTL in our population that did not segregate for sd1 indicates this TN locus is independent from sd1, and thus will be useful in increasing TN and yield in both Sd1 (tall) and sd1 (semidwarf) varieties. Seven TN QTLs were backcrossed into U.S. adapted cultivars to make them more useful to U.S. breeders, introgression of 3 more QTLs and development of associated markers is in the next project plan. Natural outcrossing between weedy red rice and indica germplasm was shown to increase with flowering synchronization. Alternative wetting and drying (AWD) reduced outcrossing between rice and weedy red rice, suggesting that this irrigation system will help alleviate weedy red rice problems. Outcrossing has resulted in herbicide resistance being discovered in weedy red rice on farms, further complicating its management. Weedy red rice was shown to be substantially more competitive than cultivated rice, and biotypes of the weed vary in competitiveness. Elevated temperatures and CO2 levels resulted in weedy red rice being more aggressive, indicating that red rice weed control is likely to be even more challenging under future climatic conditions. Methods which can measure rice root characteristics revealed indica cultivars exhibit superior surface root proliferation, total root length, and root hair production compared with conventional U.S. cultivars, explaining why indica rice has better weed suppression traits. Indica cultivars were also more productive in low input systems using reduced seeding rates and/or agricultural chemicals (e.g. organic production). Five mapping parents (PI312777, Saber, Rondo, Zhe733, and TeQing) were identified as having useful agronomic traits and potential of harboring QTL/genes for superior performance under deficit (drip) irrigations. A mapping population (TeQing-into-Lemont introgression lines, a.k.a. the TILs) was screened under AWD irrigation management for multiple years. Based on field experiments and greenhouse validations for two years, three TILs were selected for a focused field study in 2017/2018 using flowmeters to quantify water use efficiency. High temperature during the flowering stage can severely affect yield and grain quality. Minghui-63, Saber, and TILs: TIL390, TIL486 and TIL112 were identified as useful germplasm for heat stress tolerance. From this work, mapping populations involving Minghui 63 with M202, Cybonnet with Saber, and the TILs were selected for candidate QTL/gene identification and for fine mapping of heat tolerant genes in the new project plan. In addition, the TILs were resequenced, and efforts to identify genomic regions providing tolerance to abiotic stress (heat and water) is being completed and will be used in the new project plan. Weed-suppressive indica rice, PI312777, crossed with U.S. variety, Katy, was used to produce a mapping population. A 2017 field test comparing 45 Recombinant Inbred Line (RILs) from the this population identified lines with both weed suppression and high yield. One of these RILs was found to be as tolerant to AWD stress as PI312777. Additional RILs with these traits will be studied further in the new project plan. Field studies determined weed suppression and yield under modern, elevated CO2 levels as compared with previous, lower levels. In an AWD test with four levels of irrigation, outcrossing between rice and red rice was lowest at high levels of AWD stress, confirming our earlier findings. Mitigation of greenhouse gas research has been completed. The study using the five rice cultivars (Francis, CLXL745, Sabine, Jupiter, and Rondo) found that genetic variation exists in methane emissions, and further demonstrated root biomass to be a major agricultural trait affecting these emissions. These results were verified in a subsequent study with nine RILs and their parents, Francis and Rondo, segregating for root biomass. About 100 O. rufipogon accessions were screened for seedling salt tolerance and genome wide analysis will be completed once the SNP genotypic data is available.

1. Characterization of a new rice blast disease resistance (R) gene, Ptr, Rice blast disease is a significant disease of rice worldwide. The major blast R gene, Pi-ta, is a classical R gene with nucleotide binding sites and a leucine rich repeat domain has been effectively deployed in U.S. rice varieties for over two decades. Pi-ta was known to require another rice gene Ptr to produce a full resistance response, however, the structural and functional relationship of Ptr was unknown. ARS researchers at Stuttgart, Arkansas, in collaboration with university researchers in Arkansas, Pennsylvania, Ohio, California, and Kansas, with support from a USDA-AFRI Integrated Grant, found that Ptr is required for broad spectrum disease resistance and has an atypical R gene structure. Using fast neutron technology as a rice mutagen, a two-base pair deletion within the Ptr coding region created a smaller protein leading to susceptibility. A targeted mutation of Ptr in a resistant variety led to blast susceptibility, thus further verifying this gene’s resistance function. These findings will aid in understanding molecular basis of disease resistance and in developing broad spectrum blast resistant rice varieties.

2. Release of improved high yielding rice germplasm with QTLs for increased tiller production. Rapid seedling vigor and production of many tillers at early growth stages can increase weed competitiveness by producing shade that blocks light interception by neighboring weeds. ARS researchers at Stuttgart, Arkansas, in collaboration with university researchers in Arkansas, and Texas, identified 11 QTLs associated with increased rice tiller number (TN) at early and later growth stages in three mapping populations. Three TN QTLs were identified in all three populations, including one that resides near the well-known sd1 semidwarf locus on chromosome 1. However, the identification of this TN QTL also in the mapping population that did not segregate for sd1 showed that the TN QTL near sd1 is not dependent on hormonal alterations known to be associated with sd1. Thus, this TN QTL can be used in both Sd1 (tall) and sd1 (semidwarf) rice varieties to increase yield. Ten of the 11 alleles for high TN originated from the indica parents of these crosses and they were associated with chalkiness and poor grain cooking quality. Seven of the indica TN alleles were made available to U.S. rice breeders through the creation and release of three new germplasms with improved tiller production backcrossed into an adapted U.S. rice variety. The increased tiller production in these germplasms was also coupled with increased panicle number and grain yield, and was associated with rapid canopy development that can contribute to weed suppression. Markers linked to these QTLs can facilitate Marker Assisted Selection (MAS) to incorporate these new tillering genes into U.S. cultivars.

3. Weed suppressive rice tolerates weeds under a reduced-irrigation system. Conventional flood irrigation systems for rice production are used to control weeds but have contributed to severely depleted irrigation water resources in many areas of the southern U.S. Some rice varieties are naturally weed-suppressive and could be beneficial to farmers interested in using water-saving irrigation systems such as “alternating wetting and drying” (AWD). ARS researchers at Stuttgart, Arkansas, showed that weed-suppressive indica rice varieties from southeast Asia can tolerate weed pressure from barnyardgrass, reduce its growth, and also maintain rice yields better than traditional U.S. varieties when grown under the water-saving, but potentially more stressful conditions of AWD systems. This demonstrates that rice germplasm from other countries may be good sources of traits that would enable U.S. farmers to maintain production of high yielding rice while using less irrigation water.

4. Root biomass affects methane emissions from rice cultivars. Agriculture is recognized as a significant contributor to greenhouse gas emissions (GHGE) globally. Methane is an important greenhouse gas (GHG) that is 25 times more potent than CO2 and is the primary GHG emitted from flooded rice fields wherein growth conditions are ideal for the anaerobic bacteria that produce methane. Because of the extensive global rice acreage, reducing methane emissions as a result of rice production would have a significant impact on global warming. ARS researchers at Stuttgart, Arkansas, in collaboration with ARS researchers at Jonesboro, Arkansas, have shown that the amount of methane emitted from paddy-grown rice can vary by cultivar, indicating that genetic improvement is one method to pursue for reducing GHG emissions, and further determined that root biomass is a major means for affecting methane emissions. Improved understanding of the relationship between root biomass and methane emissions will assist breeders in developing high yielding rice cultivars with reduced methane emissions.

5. Water-saving irrigation systems have an added benefit of reducing outcrossing between weedy red rice and cultivated rice. Flooded paddies are used in rice production as a means of controlling weeds however this irrigation system has helped deplete water resources in the southern USA over time. New water-saving irrigation systems such as “alternating wetting and drying” (AWD) are being implemented by farmers in an attempt to reverse this trend, but their potential effects on interactions between weedy red rice and commercial herbicide-resistant rice varieties are unknown. ARS researchers at Stuttgart, Arkansas, and Beltsville, Maryland, showed that AWD, and the moisture stress that accompanied it, reduced rice yields minimally, but provided added benefit of reducing outcrossing rates with one of two weedy red rice biotypes tested. This indicates that, for certain biotypes of weedy red rice, AWD has the potential to reduce outcrossing with rice, which will help reduce the production of herbicide-resistant rice-weed hybrids that can contaminate fields making weed management more difficult.

6. Enhanced disease resistance through synergistic interaction of two major rice blast resistance (R) genes. Rice blast disease is important worldwide and breeders deploy resistance genes through new varieties. Individual major blast R genes are known to be effective in preventing disease due pathogen strains that contain the corresponding avirulence genes. However, no information is available on how resistance may be impacted by interaction between major R genes. ARS researchers at Stuttgart, Arkansas, in collaboration with researchers at China Agricultural University and University of Arkansas, examined blast reactions of 243 recombinant inbred lines (RILs) derived from the cross of two U.S. rice varieties, one with Pi-ta and another having Pi-b R genes, when challenged with 10 differential isolates of blast under greenhouse conditions. Enhanced disease resistance was observed in RILs that contained both Pi-ta and Pi-b. These findings suggest that Pi-ta interacts synergistically with Pi-b, which will encourage breeders to stack major blast R genes in developing disease resistant rice varieties.

7. Integrated Pest Management (IPM) strategies improve profitability of organic rice. Organic crop production can have high risks because of the lack of access to agricultural chemicals that increase yields and decrease pest pressures. ARS researchers at Stuttgart, Arkansas, collaborated with university researchers in Texas, and Arkansas, to develop IPM practices that decrease risks and increase returns of organic rice. Cover crops decreased disease pressure and weed infestations while indica type varieties had robust plant growth and high yields. These new IPM strategies will increase stability of production and increase economic returns of organic rice producers.

8. Identification of blast susceptible rice growth stages. Rice blast is one of the most serious diseases of rice. Older rice leaves are known to be more resistant to blast disease than younger rice leaves. However, it is not known at which plant growth stage the plants begin to resist disease infection. If the timing of blast scouting is not correct, then susceptible varieties may be mis-classified as resistant causing them to not receive appropriate fungicide applications. ARS researchers at Stuttgart, Arkansas, in collaboration with researchers at China Agricultural University, with support from the China Scholarship Council, characterized blast reactions in two blast susceptible rice varieties, M202 and Nipponbare, from plant emergence through grain maturity in the greenhouse. Vegetative growth stages were documented as V1 to V10 based on the number of leaves present on the main stem; grain-filling stages from were denoted R1 to R8. Both rice varieties were susceptible to blast from V1 to V4 but this was measurably reduced at V5, and even stronger levels of resistance were observed in later growth stages. These findings suggest that field scouting of commercial fields for rice blast disease should begin before the V5 growth stage to properly manage the disease. The results will be useful for further research on the genetic basis of adult plant resistance and for managing rice blast disease in the field.

9. Weed suppressive rice allows economical crop production in combination with reduced herbicide inputs. Some varieties of rice are naturally weed-suppressive, and could be economically beneficial for farmers interested in growing rice with if they could be grown in combination with reduced herbicide inputs. ARS researchers at Stuttgart, Arkansas, and researchers at the University of Arkansas showed that some weed-suppressive rice varieties from the genepool of indica rice in southeast Asia can be produced economically when grown under reduced herbicide rates, whereas traditional U.S. varieties generally were not economically viable under these reduced-input conditions due to heavy yield losses from weed competition. This demonstrates that genepools of rice from other parts of the world offer traits that can be used in the development of new cultivars with better weed suppression that can be beneficial for reduced-input rice systems in the U.S.

10. Identification of rice germplasm with enhanced tolerance for reduced irrigation in tropical japonica background. Conventional rice production in the U.S. requires a tremendous amount of irrigation resources. The rate of aquifer depletion is greater than the recharging rate, which makes season-long flooding of rice an unsustainable cropping system in the USA. ARS researchers at Stuttgart, Arkansas, in collaboration with researchers at the University of Arkansas, identified rice varieties with useful agronomic traits and potential for harboring QTL/genes for superior performance under deficit (drip) irrigation. Using a mapping population derived from a cross using one of these varieties, ARS researchers identified 14 progenies that exhibited enhanced tolerance to water deficits compared to the parental varieties when grown using reduced water. Identification of these rice lines will help breeders develop new varieties that produce more yield with less water.

Review Publications
Mulaw, T., Wamishe, Y., Jia, Y. 2018. Characterization and in plant detection of bacteria that cause bacterial panicle blight disease of rice. American Journal of Plant Sciences.
Vigueira, C.C., Qi, X., Song, B., Li, L., Caicedo, A.L., Jia, Y., Olsen, K.M. 2017. Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia. Evolutionary Applications.
Zhao, H., Wang, X., Jia, Y., Minkenberg, B., Wheatley, M., Fan, J., Jia, M.H., Famoso, A., Edwards, J., Wamishe, Y., Valent, B., Wang, G., Yang, Y. 2018. The rice blast resistance gene Ptr encodes an atypical protein required for broad spectrum disease resistance. Nature Communications.
Chen, X., Jia, Y., Jia, M.H., Pinson, S.R., Wang, X., Wu, B. 2018. Functional interactions of major rice blast resistance genes Pi-ta with Pi-b and minor blast resistance QTLs. Phytopathology.