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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

2017 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 with efforts of two newly hired SYs. Crossing to develop the Wild5 [Presidio/Oryza (O.) rufipogon (IRGC103404)] backcross population for blast tolerance was underway to obtain BC2F1 progeny. A total of 90 F1 seeds of the cross of a universal susceptible japonica rice variety Lijiangxintuanhegu (LTH) with ShuFeng 121 were produced, and 10 of them were grown in a greenhouse for producing F2 seeds for mapping blast resistance (R) genes to blast race IB33. A blast R gene Ptr(t) was identified as a Pi-ta independent R gene at the Pi-ta region near the centromere of chromosome 12. A blackhull awned weedy red rice PI653419 has resistance to IB33 and a genetic factor in PI653419 was mapped at Ptr(t) locus. Ptr (t) in weedy red rice PI653419 is the R gene to IB33 that will be verified in 2018. Two new methods of sheath blight evaluation were developed. One was involved in growing the fungus on the tips of toothpicks, and another was involved in wrapping fungal sclerotia on the sheath of tillers. Both methods will be examined with rice lines with different resistance Quantitative Trait Loci (QTL) to see which one is the best to determine minor resistance differences. The major sheath blight resistance QTL qSHB9-2 was fine mapped, and 160 lines of BC3F5 of LJ50 into Lemont containing qSHB9-2 are being evaluated for agronomic traits and sheath blight reactions in replicated field experiments in 2017. The effort to find new resistance from wild rice relatives was also progressed. The Wild4 [LaGrue/Oryza nivara (IRGC104443)] backcross population was evaluated for sheath blight disease reaction. Genotyping for QTL analysis will be in year 5, and sheath blight reaction will be evaluated in the field in 2018-19. As part of a USDA-National Institute of Food and Agriculture (NIFA) funded project with Kansas State University, a total of 1,022 rice blast collected from 1959 to 2015 were evaluated with 8 international rice differentials and 10 simple sequence repeat markers, and results demonstrated that rice blast population in the USA has become more dynamics, and virulent over the time. Progress was made on phenotyping traits associated with weed suppression including measuring photosynthesis, growth, weed biomass reduction, and root digital imaging of mapping parents (allelopathic PI 312777 X non-allelopathic U.S. cultivar) and diverse Recombinant Inbred Lines (RILs) from a mapping population. About 40 diverse RILs have been scanned for seedling root architecture in petri plates in a 2-D agar system, revealing that the RILs vary greatly for initial angle and spreading pattern of root growth, number and total area of roots, and length, number, and total area of root hairs. A field study to determine weed competition interactions on a subset of 45 RILs from the above population that are diverse for growth and weed suppression potential has been established. Effects of alternating wetting and drying (AWD) on 15 RILs diverse for root architecture or weed suppression are also being evaluated in a pilot AWD field study. Plant and root growth of eight diverse RILs are being measured in the greenhouse, and their photosynthesis response to light and CO2 levels indicates that some RILs respond differently to these environmental variables. Initial efforts to produce, isolate, and purify a momilactone allelochemical standard in-house was unsuccessful. Preliminary analyses to detect momilactone exuded from PI 312777 roots and absorbed by plastic microtubes in field soil are underway at an Iowa State University laboratory. A field experiment with red rice and rice under AWD and flood irrigation showed that a long grain rice and a strawhull red rice produced the greatest outcrossing, and that AWD can reduce this. A follow-up field study comparing the outcrossing rates for this long grain rice-strawhull red rice pair at three levels of AWD stress is ongoing. Photosynthesis, canopy temperature, and soil moisture are being measured to monitor the degree of stress imposed by each level of AWD. ARS scientists in Stuttgart, Arkansas, in cooperation with ARS-Office of International Research Programs (OIRP) and Taiwan Agricultural Research Institute (TARI) scientists in Taiwan, investigated Taiwan weedy red rice in comparison with U.S. red rice, finding that the phylogeny/genetic background and phenotypic traits of the two populations differed, and that most Taiwan red rice lines appear to have been derived from red-seeded landraces produced by farmers in Taiwan nearly a century in the past. The 3rd year of a 5-year field experiment in cooperation with ARS scientists in Beltsville, Maryland, is ongoing to test the hypothesis that yields of historical U.S. rice varieties will increase under present-day ‘elevated’ CO2 levels. Fine-map QTLs associated with early tiller production was also progressed. Potted BC2F1 plants were evaluated for tiller number, 27 progeny selected for high early tiller production were backcrossed producing BC3F1 seed. A set of 123 CSSL lines (aka TILs) have been evaluated in multi-year field trials for response to heat stress and response to reduced irrigation (AWD). The TILs are being resequenced and the data will be used to identify genomic regions associated with tolerance to heat and water stress. Mitigation of greenhouse gas research progressed. Phenological and anatomical traits linked to methane emissions including aerenchyma formation in rice roots and correlation with tiller number, root and shoot biomass were investigated. Research was also expended to determine the relationship of rice genetic variation for root-soil-microorganism interactions with methane emissions. The predominant microbes in the root microbiome among parents and their selected progenies based on root/shoot biomass are being characterized with a grant USDA ARS OIRP-PJ008710 in collaboration with Beltsville, Maryland, Gainesville, Florida, and scientists from the Rural Development Administration, South Korea, and the Cuu Long Delta Rice Research Institute, Vietnam. Progress was made on an organic project funded by USDA-Agriculture and Food Research Initiative (AFRI) grant in collaboration with Texas AgriLife where successful efforts have been made using green manure crops to increase soil fertility and reduce weed pressure. With this accomplished, a set of 10 rice varieties are being evaluated for yield potential under organic management in a replicated trial conducted in Arkansas and Texas. As a result of a USDA-AFRI grant with Cornell University a diversity panel of 150 historical and current U.S. varieties has been established and is being distributed through Genetic Stocks Oryza (GSOR). The set has been characterized using Genotyping By Sequencing (GBS), for several agronomic traits, and with images of the plants at heading and of the rough and brown rice. This will serve as a means for exploring genes within the U.S. southern breeding genepool for response to historic and projected changes in climate. A pilot study was conducted to determine the appropriate salt concentration to use when evaluating the wild Oryza species diversity panel for salt tolerance.

1. Losing control: Escape of herbicide resistant rice genes into weedy red rice populations through cross pollination. Herbicide resistant (HR) rice varieties, developed through mutation breeding, have dramatically improved the control of red rice, a common weed found on many farms in the southern USA. However farms with a history of heavy, repeated use of these herbicides have experienced persistent weed problems caused by cross pollination between HR rice and weedy red rice. In a National Science Foundation funded project, scientists with the University of Arkansas, in cooperation with ARS scientists in Stuttgart, Arkansas, collected numerous HR weedy rice populations from these farm fields, and through DNA testing, showed that all of the them carried the specific HR gene found in the commonly grown HR varieties, which confirmed that the resistance was acquired through cross pollination. Many of HR weedy rice accessions were similar to the rice varieties in terms of plant traits like height, days to flowering, and low seed dormancy. These crop-like traits may make it more difficult for farmers to identify visually, further complicating control of this weed problem.

2. Closing in on genes controlling sheath blight disease resistance in rice. Sheath blight disease of rice caused by the fungus Rhizoctonia solani causes major crop losses in high input-high yielding production systems. Management of this disease relies on expensive fungicides because no complete genetic resistance has been found. However, a major sheath blight resistance quantitative trait locus (QTL), qShB9-2, which confers approximately 25% of total resistance, was previously identified by ARS scientists in Stuttgart, Arkansas. Using further breeding techniques and DNA analyses, the genomic region containing qSHB9-2 was delimited to a much smaller region and 10 candidate genes were identified. Ultimately, developing DNA markers linked to the genes that control sheath blight resistance will improve breeding efficiency via a marker assisted selection.

3. Stacking genes for improved cold tolerance at the germination and seedling stages in rice. Farmers need the flexibility to be able to plant in the early spring when field conditions allow, however cool temperatures at this time can delay seedling emergence from the soil. Cold tolerance at the germination and seedling stages results in better plant survival which directly impacts crop yields. ARS scientists in Stuttgart, Arkansas, in collaboration with scientists at Marquette University in Milwaukee, Wisconsin, with support from an USDA-AFRI Foundational grant, evaluated over 200 rice varieties from around the world for cold tolerance at five different seedling timepoints. Based on the five assays and analyses with DNA markers, 27 chromosome regions were discovered that were linked to genes controlling cold tolerance at germination or the seedling stage, indicating both stages are controlled by many genes. This study lays the foundation for using the most tolerant varieties as parents in rice variety development programs and for using the identified genetic markers to combine cold tolerance at the germination and seedling stages into adapted rice varieties.

4. Unraveling the complexity of rice blast disease resistance. Rice blast disease caused by the fungus Magnaporthe oryzae is the most damaging disease of rice worldwide. The major blast resistance gene Pi-ta, found within a large region on chromosome 12, has been effectively deployed in USA rice varieties through breeding for over two decades. However, the actual genetic structure of this gene is not well characterized. ARS scientists at Stuttgart, Arkansas, identified Ptr(t) an additional independent blast resistance gene within a small genomic region close to Pi-ta on chromosome 12. The resistance function of Ptr(t) was confirmed by bombarding a resistant rice variety using fast neutrons as means of knocking out this specific gene and observing that it had become susceptible to blast disease. This research reveals the complexity of plant disease resistance and will give breeders better tools for developing new rice varieties to fight against the blast fungus.

5. Rice varieties that suppress weeds. Barnyardgrass is one of the most difficult weeds to control in rice production but some rice cultivars are known to suppress its growth. Scientists with ARS in Stuttgart, Arkansas, and College Station, Texas, showed that some varieties of rice are highly competitive with weeds whereas others require increased seeding rates to suppress weed growth. Varieties from the Indica genepool, largely found in southeast Asia, produced similar yields and tolerated weeds even at low seeding rates, whereas yields of U.S. varieties benefited from higher seeding rates to compete with weeds. This demonstrates that genepools of rice not found in the U.S. offer traits that can be used in breeding to develop new cultivars with improved weed suppression which may be particularly beneficial under reduced input cropping systems, like organic.

6. Strategic deployment of effective resistance genes to control rice blast disease. Rice blast disease caused by the fungus Magnaporthe oryzae is the most damaging rice disease worldwide. Major plant resistance (R) genes recognize avirulence (AVR) genes in specific pathogen strains that then results in a resistance response. However, pathogens can overcome disease resistance genes by evolving infection signals that escape plant detection. Scientists at ARS, Stuttgart, Arkansas, in collaboration with scientists at Hunan Hybrid Rice Research Center, Changsha, China, and Zhejiang Academy of Agricultural Sciences, Hangzhou, China, analyzed 182 field blast isolates from several ecological districts of rice production areas in Hunan province with rice varieties that possess known combinations of 24 major R genes. The findings suggest that major R genes, Pi9, Piz5, Pikh, and Pikm, are the most effective blast R genes for use in breeding for rice production areas in Hunan province.

7. Genetic signatures tell the story of weedy rice evolution. Weedy rice, is a persistent agricultural problem in rice fields and can lead to the serious reduction in rice production worldwide. Scientists with ARS in Stuttgart, Arkansas, along with researchers at the University of Massachusetts-Amherst, Washington University at St Louis, Chinese Academy of Sciences, Guangzhou, China; and Northeast Normal University, Changchun, China, analyzed the whole genome of 183 wild, cultivated, and weedy rice accessions. We found that relatively few genetic changes were required for the emergence of weediness traits. Weed strains likely evolved both early and late in the history of rice cultivation and represent an under-recognized component of the domestication process. This study illustrated that parallel evolution reshaped the weedy rice genome, which presents a unique challenge for weedy rice management worldwide.

8. Getting the red out – from rice fields. Weedy red rice competing with cultivated rice reduces yield and grain quality in rice production fields. Scientists with ARS in Stuttgart, Arkansas, along with researchers at the University of Massachusetts-Amherst, Washington University at St Louis, Sichuan Agricultural University, Yaan, China; Monash University, Selangor, Malaysia; and Chinese Academy of Sciences, Guangzhou, China, examined the rice Rc gene responsible for red pigmentation of the rice grain. This trait is found in most wild and weedy Oryza species and is associated with seed dormancy. The nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have non-pigmented pericarps. Phenotypic analysis of 52 Malaysian weedy rice accessions showed that most are characterized by the pigmented pericarp; however, some weedy rice biotypes have white pericarp suggesting close relationships to cultivated rice. These findings are useful for the development of effective genetic strategies to manage weedy rice in commercial rice fields worldwide.

Review Publications
Xing, J., Jia, Y., Peng, Z., He, Q., Shu, F., Zhang, W., Sun, P., Deng, H., Zhang, Z. 2016. Characterization of molecular identity and pathogenicity of rice blast fungus in Hunan province of China. Plant Disease. doi:10.1094.
Cui, Y., Song, B., Li, L., Li, Y., Huang, Z., Caicedo, A.L., Jia, Y., Olsen, K.M. 2016. Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice. G3, Genes/Genomes/Genetics. doi:10.1534/g3.116.035881.
Li, L., Li, Y., Jia, Y., Caicedo, A.L., Olsen, K.M. 2017. Signatures of adaptation in the weedy rice genome. Nature Genetics. doi:10.1038/ng.3825.
Shakiba, E., Edwards, J., Jodari, F., Duke, S.E., Baldo, A.M., Korniliev, P., Mccouch, S.R., Eizenga, G.C. 2017. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PLoS One. doi:10.1371/journalpone.0172133.
Singh, V., Singh, S., Black, H.L., Boyett, V., Basu, S., Gealy, D.R., Gbur, E.E., Pereira, A., Scott, R.C., Caicedo, A., Burgos, N.R. 2017. Introgression of Clearfield(TM) rice crop traits into weedy red rice outcrosses. Field Crops Research. 207:13-23.
Schlappi, M.R., Jackson, A.K., Eizenga, G.C., Wang, A., Chu, C., Shi, Y., Shimoyama, N., Boykin, D.L. 2017. Assessment of five cold chilling tolerance traits and GWAS mapping in rice using the USDA mini-core collection. Frontiers in Plant Science. doi:10.3389/fpls.2017.00957.
Huang, Z., Young, N.D., Hyma, K., Olsen, K.M., Jia, Y., Caicedo, A.L. 2017. All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza. Molecular Ecology. doi:10.1111/mec.14120.
Wang, X., Jia, Y., Wamishe, Y., Jia, M.H., Valent, B. 2017. Dynamic changes in the rice blast population in the USA over six decades. Molecular Plant-Microbe Interactions. https://doi:10.1094/MPMI-04-17-0101-R.