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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

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.

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

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.

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.

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.

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.

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

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.

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.

Last Modified: 10/15/2017
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