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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

2011 Annual Report

1a. Objectives (from AD-416)
The long-term objective of this project is to better understand rice responses to pests, pathogens, and weather stress in the environment, and to use that information to enhance pest protection and production efficiency for a more sustainable U.S. rice production. Over the next 5 years we will focus on the following objectives: Objective 1: Map rice genes associated with resistance to sheath blight and blast diseases and identify sources of resistance to kernel and false smut diseases. Sub-objective 1.A. Map candidate genes for sheath blight resistance in rice. Sub-objective 1.B. Develop high-resolution genetic maps of Rhizoctonia solani phytotoxin. Sub-objective 1.C. Elucidate recognition mechanisms of the rice blast resistance gene, Pi-ta, to the pathogen avirulence gene AVR-Pita. Sub-objective 1.D. Identify sources of resistance to grain quality reducing diseases: false smut and kernel smut. Objective 2: Identify the physiological, environmental, and genetic factors associated with tillering and seedling vigor under cold temperatures in rice. Sub-objective 2.A. Identify environmental and cultural factors that induce early tillering in indica germplasm and identify early tillering QTL in mapping populations. Sub-objective 2.B. Identify genomic regions associated with cold temperature stress at the seedling stage. Objective 3: Develop chromosome segment substitution lines (CSSLs) and advanced backcross mapping populations using selected Oryza wild species to study the chromosomal location of grain shape, pest resistance, and domestication traits. Sub-objective 3.A. Introgress novel sheath blight resistance genes into U.S. rice cultivars using Oryza wild species accessions. Sub-objective 3.B. Exploring transgressive variation in rice. Objective 4: Identify growth factors associated with changes in weed species populations in response to the use of herbicide–resistant rice cultivar technology and other non-conventional cultural management practices. Sub-objective 4.A. Determine the efficacy of weed-suppressive rice in reduced input rice production systems. Sub-objective 4.B. Quantify gene flow of herbicide resistance genes in commercial rice production.

1b. Approach (from AD-416)
Genetic markers associated with QTLs linked to sheath blight resistance, sheath blight toxin sensitivity, and tillering will be identified in various mapping populations. Sequence diversity for the Pi-ta blast resistance gene in several species of rice and of the avirulence gene in the pathogen will be determined. Interactions of predicted host and pathogen proteins will be used to identify critical amino acid residues important for disease resistance. Cultivars and parents of existing mapping populations will be evaluated to identify sources of resistance to kernel and false smuts. The impact of different tillage methods, fertilizer rates, and crop rotation systems on incidence of smut will be determined to give cultural management recommendations to farmers. To identify QTL underlying tillering in rice, we will identify growth conditions including include soil temperature, planting depth, and fertilizer rates, sources, and timing that maximize the phenotypic differences between high- and low-tillering genotypes. Germplasm lines will be evaluated for coleoptile emergence under cold temperatures (11oC) to identify sources that can be used to develop mapping populations. Novel sources of sheath blight resistance identified in wild species of rice (i.e. O. meridionalis, O. nivara, O. rufipogon) will introgressed into a susceptible Southern U.S. cultivar through backcrossing. Putative sheath blight resistance QTL will be verified using inoculated field tests and greenhouse toxin assays. The O. rufipogon wild species of rice and several O. sativa sub-populations will be used to identify adapted gene complexes responsible for positive transgressive variation. Chromosome segment substitution lines and near isogenic lines (NILs) will be used to systematically explore the relationship between diversity and transgressive variation. In addition, lines containing O. rufipogon introgressions that alter flowering time, grain size and weight, and number of grains per plant will be analyzed to determine the impact of the introgressions on agronomic traits. High-tillering indica rice lines and commercial hybrids will be evaluated to determine if they have sufficient weed-suppression capabilities when coupled with low rates of herbicide and/or alternative production systems that result in effective weed control. Competitive interactions between rice and barnyardgrass (C4 weed species) will be assessed using 13C isotope depletion analyses of roots extracted from soil core samples. Alternative cultural practices including early planting, reduced irrigation, and decreased seeding rates will be evaluated for their savings in water use and impact on weed control. Reciprocal outcrossing rates between commercial hybrid rice cultivars and common U.S. red rice biotypes will be investigated to determine the likelihood of herbicide resistance gene flow. Putative outcrosses will be verified using herbicide screening when herbicide resistant cultivars serve as the male or assessment of unique plant characteristic and genetic markers when non-herbicide resistant rice serves as the male.

3. Progress Report
Four germplasm lines possessing quality trait loci (QTL) for resistance to sheath blight and blast diseases were released, and these were crossed with commercial cultivars as part of a breeding effort. Ten genes were found to be expressed by the sheath blight pathogen during the initial stages of disease development. In addition, the phytotoxin produced by the sheath blight pathogen was found to be carbohydrate-based unlike other plant toxins, which are proteins. Although one chromosomal region has been identified associated with a necrotic response to the toxin, efforts to identify the genetic control of a chlorotic response will be stopped due to a scientific vacancy. Results of these studies will lead to a better understanding of the molecular and chemical mechanisms of plant-pathogen interactions. Germplasm accessions possessing major genes for resistance to rice blast disease were identified, and chromosomal regions associated with resistance were determined through QTL analysis of a mapping population. Analysis of genetic variation in the AVR-Pita1 gene of the rice blast pathogen demonstrated that mutations within this gene allow the pathogen to overcome resistance in rice cultivars. Field trials were conducted to evaluate genetic diversity and cultural management factors that influence crop susceptibility to false and kernel smut diseases. Resistant cultivars have been identified, and reducing nitrogen inputs can also limit incidence of these diseases. An evaluation of previously genotyped mapping populations for variation in seedling vigor under cold temperatures was not successful. However, another population that was increased in the field as part of a collaboration with a university partner was determined to vary for this trait. This population will be analyzed for seedling tolerance to cold and salt next year. The first year of a field study was conducted using different fertility managements and cultivars to determine if these factors can mitigate the effects of greenhouse gas emissions. Other studies demonstrated that out-crossing was increased at elevated CO2 levels, suggesting that problems associated with geneflow to weedy species of rice may occur with climate change. Progress was made in the development of four sets of chromosome segment substitution lines using wild species of rice as the donor genome. Two other sets currently in the BC1 stage of development are being obtained from a Korean collaborator because crossing efforts in the USA were unsuccessful. Previous research had resulted in the development of germplasm that had higher yield as a result of wild species introgressions. Further backcrossing of these lines to reduce the number of introgressions resulted in a decrease in yield. This indicates that the yield improvement may be due to multiple genes and genetic interactions. Some rice cultivars that are naturally weed-suppressive were found to have larger root systems and elevated allelopathic activities. These traits may eventually be incorporated into new rice varieties to help control weeds.

4. Accomplishments
1. Using genetic markers to reveal the ancestry of weedy red rice in rice production fields. Red rice is a bane to rice production in the U.S.A. and throughout the world where commercial fields are directly seeded. There are many biotypes of this weed that can intercross with each other or with cultivated rice because they are all of the same species, thus increasing the complexity of rice-weed problems and complicating management strategies. In this research, ARS and University of Arkansas scientists in Stuttgart, Arkansas, used molecular analyses to show that an unusual, but widespread biotype of weedy red rice in the southern U.S.A. was likely descended from previous intercrossing between major weedy red rice types (awned and awnless). This information provides us with a better understanding of the biology, genetic backgrounds, and history of the diverse red rice biotypes presently infesting farm fields, and increases our ability to predict the development of new weedy rice types and how to identify and manage them.

2. Rice cultivars suppress weed root mass. A new 13C stable isotope method developed for use in flooded rice fields was used to evaluate the distribution and mass of roots of rice and barnyardgrass, a common weed in rice fields. ARS and University of Arkansas scientists at Stuttgart, Arkansas, are studying the value of using weed-suppressive rice cultivars as compared to conventional rice varieties. They used 13C analysis in combination with a recently developed mathematical formula that corrects for inaccuracies arising from unwanted soil contamination to demonstrate that barnyardgrass root mass was twice as high in plots of non-suppressive rice as compared to weed-suppressive rice plots. Weed-suppressive rice also provided much greater weed control and had less yield loss than the non-suppressive cultivars. Having a sensitive method that can evaluate distribution of rice and weed roots under field conditions irrespective of soil contamination in samples will help in the development and understanding of how some rice cultivars can suppress weeds, which will ultimately provide farmers with additional tools to manage weeds.

3. Identification of new sources of resistance to rice blast disease. The blast resistance gene Pi-z(t) in rice confers resistance to a wide range of races of the rice blast fungus, one of the most threatening rice diseases in the world. ARS scientists in Stuttgart, Arkansas, with cooperators at the University of Arkansas, surveyed 117 rice accessions using DNA markers and a blast disease response test. Among the accessions surveyed, 81 were found to carry the Pi-z(t) gene. The remaining 36 accessions were found to have resistance to additional blast races not covered by the Pi-z(t) gene, suggesting the presence of additional resistance genes. This study demonstrated the power of resistance gene identification and verification using DNA markers and disease screening assays. These characterized rice accessions can be used for genetic studies and marker-assisted breeding for improving blast resistance in rice.

4. Identification of the bioactive component of the toxin that causes sheath blight disease in rice. A phytotoxin is produced by the fungus Rhizoctonia solani during the infection process and results in disease lesions that can reduce rice yield. The component of the toxin that causes plant cell death has been unclear. ARS scientists in Stuttgart, Arkansas, with cooperators at Southern China Agriculture University, investigated an array of extraction methods for identification of the major bioactive component of the toxin. A simple and reliable bioassay system was developed to evaluate the phytotoxicity of the isolated component, which was determined to be carbohydrate-based and not an amino acid or protein like some other toxins. Identification of the major bioactive components of this phytotoxin will help develop more effective control methods to manage rice sheath blight disease.

5. Analysis of agronomic and grain traits reveal early domestication efforts by man in rice. A diverse collection of genetically pure rice accessions has been developed for genetic studies to dissect the molecular and biochemical basis of important traits related to yield, grain quality, and stress resistance. ARS and University of Arkansas researchers in Stuttgart, Arkansas, collaborated with scientists at Cornell University on a project funded by the National Science Foundation to select accessions for this collection and determine the range in trait diversity. Cultivars in this "Rice Diversity Panel" were characterized for their geographic origin, the ancestral subpopulation that they were derived from, and 18 agronomic and grain traits. Results suggest that during rice domestication, man selected for unique types of rice in various growing regions of the world. This collection of rice accessions will be used to determine the chromosomal location of genes controlling these important agronomic and grain traits. Ultimately this information will be used by rice breeders to develop improved rice cultivars and rice hybrids.

6. Understanding the genetic control of complex agronomic, grain, and stress resistance traits in cultivated rice. ARS researchers in Stuttgart, Arkansas, collaborated with researchers at Cornell University, Stanford University, University of Arkansas, University of Aberdeen, U.K., and Bangladesh Agricultural University, Bangladesh, on a project to identify genetic markers linked to important agronomic traits. The project was primarily funded by the National Science Foundation, with additional funds from the National Institute of Health and the government of the United Kingdom. Over 400 rice cultivars, originating from 82 different countries, were evaluated for 34 plant traits and with 44,100 DNA markers, called single nucleotide polymorphism (SNP) markers. Using newly developed mathematical models, DNA markers were identified that were associated with the 34 agronomic, morphological, grain, and stress resistance traits. The chromosomal SNP marker location enables researchers to identify specific genes controlling these traits. Subsequently the biochemical pathways controlling these traits can be dissected, thus increasing our understanding of the genetic and physiological processes that are important for yield, grain quality, and tolerance to environmental stress.

7. Development of new DNA marker technology for rice and other self-pollinated crop plants. Recent advancements make it possible to more quickly dissect DNA from crop plants like rice, into the four nucleic acids that compose DNA (adenine, thymine, guanine, and cytosine). The order of these nucleotides within the DNA strands allows them to be used as genetic markers called single nucleotide polymorphisms (SNPs). Because millions of SNPs occur within the rice genome, new genotyping and statistical tools are required to identify and utilize these markers effectively in breeding. ARS researchers in Stuttgart, Arkansas, collaborated with researchers at Cornell University, Stanford University, University of Arkansas, International Rice Research Institute, Philippines, and the National Institute of Agrobiological Sciences, Japan, on a project funded by the National Science Foundation and USDA National Institute for Food and Agriculture to develop new genotyping platforms that could assay up to 1 million SNP markers. In addition, a statistical method was developed that allowed the SNP markers to be accurately identified in self-pollinating crop plants like rice. Development of these new SNP platforms and the new statistical analysis method will allow genotypic data to be more quickly and accurately determined and will ultimately help breeders develop improved rice cultivars.

8. Reintroducing agronomically important traits lost during the domestication of cultivated rice. In ancient times, cultivated rice was domesticated from wild species of rice (Oryza species) but only about 60% of the variation present in the wild donors was transferred into cultivated rice. Research has shown that these wild donors possess traits such as pest resistance, drought tolerance, tolerance to acid soils, larger panicles, and more seed per panicle. In order to recover and utilize the genetic variation in the Oryza species that was lost during the domestication process, crosses are made to reintroduce these traits into cultivated rice. ARS researchers in Stuttgart, Arkansas, collaborated with researchers at the University of Arkansas, University of Arizona, International Center for Tropical Agriculture, Colombia, and Huazhong Agricultural University, P.R. China, with support from the National Science Foundation, National Natural Science Foundation of China, and the Generation Challenge Program, to demonstrate worldwide efforts to incorporate wild donors into the background of cultivated rice by developing either chromosome segment substitution lines (CSSLs) or backcross inbred lines (BILs). Both CSSLs and BILs have the background of an adapted rice cultivar with small chromosomal segments from a wild Oryza donor species. Across a set of CSSLs or BILs, the complete wild donor genome is represented. These CSSLs and BILs provide a platform for discovering new genes and tools for conducting basic studies to dissect the function of genes controlling agronomically important traits. In addition, these genetic resources can be used by rice breeders to easily incorporate desirable traits into new rice cultivars, thus broadening the rice gene pool.

Review Publications
Wang, X., Fjellstrom, R.G., Jia, Y., Yan, W., Jia, M.H., Scheffler, B.E., Wu, D., Shu, Q., McClung, A.M. 2010. Characterization of Pi-ta Blast resistance gene in an international rice core collection. Plant Breeding. 129(5):491-501.

Brooks, S.A., Anders, M.M., Yeater, K.M. 2011. Influences from long-term crop rotation, soil tillage and fertility on the severity of rice grain smuts. Plant Disease. 95(8):990-996.

Costanzo, S., Jackson, A.K., Brooks, S.A. 2011. High-resolution mapping of Rsn1, a locus controlling sensitivity of rice to a necrosis-inducing phytotoxin from Rhizoctonia solani AG1-IA. Theoretical and Applied Genetics. 123(1):33-41.

Liakat Ali, M., McClung, A.M., Jia, M.H., Kimball, J.A., McCouch, S.R., Eizenga, G.C. 2011. A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution. Crop Science. 51(5):2021-2035. doi: 10.2135/cropsci2010.11.0641

Zhao, K., Tung, C., Eizenga, G.C., Wright, M.H., Ali, M., Price, A., Norton, G., Islam, R.M., Reynolds, A., Mezey, J., McClung, A.M., Bustamante, C.D., McCouch, S.R. 2011. Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa. Nature Communications. 2:467. doi: 10.1038/ncomms1467.

Ali, M., Sanchez, P.L., Yu, S., Lorieux, M., Eizenga, G.C. 2010. Chromosome segment substitution lines: A powerful tool for the introgression of valuable genes from wild species of rice (Oryza spp.). Rice. 3:218–234.

McCouch, S.R., Zhao, K., Wright, M., Tung, C., Ebana, K., Thomson, M., Reynolds, A., Wang, D., DeClerck, G., Ali, M., McClung, A.M., Eizenga, G.C., Bustamante, C. 2010. Development of genome-wide SNP assays for rice. Journal of Breeding Science. 60:524-535. doi:10.1270/jsbbs.60.524.

Jia, Y., Liu, G. 2011. Mapping quantitative trait loci for resistance to rice blast. Phytopathology. 101(2):176-181.

Yang, Y., Yang, M., Li, M., Jia, Y., Zhou, E. 2011. Isolation and characterization of a phytotoxin from Rhizoctonia solani, the causal agent of rice sheath blight. Asian Journal of Chemistry 23(8):3500-3508.

Tung, C., Zhao, K., Wright, M.K., Ali, M., Jung, J., Kimball, J.A., Tyagi, W., Thomson, M.J., McNally, K., Leung, H., Kim, H., Ahn, S., Reynolds, A., Scheffler, B.E., Eizenga, G.C., McClung, A.M., Bustamante, C.D., McCouch, S.D. 2010. Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice. 3:205–217.

Last Modified: 06/28/2017
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