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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

2013 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:
Rice production around the globe faces challenges from stresses such as plant disease, weed competition, pest damage, and environmental impacts. This 5-year project achieved significant progress in the areas of: understanding and managing devastating diseases such as sheath blight, blast and kernel smut; identifying and determining precise chromosomal locations of key genes or groups of genes influencing these diseases; testing damage and limitations caused by chilling temperatures; and improving cropping system practices. These efforts created useful new tools and expanded scientific knowledge for the rice industry. Rice sheath blight and blast disease research focused on creating true-breeding mapping populations (each population is a set of diverse individual progeny lines obtained from a cross between two parents, one parent being resistant and the other susceptible), and mapping the genes responsible for the resistance. Using cutting edge methods such as DNA microarray and serial analysis of gene expression, we found 27 genes from the rice cultivar Jasmine85 that are turned on by the sheath blight fungus. The most promising genes from this group were used to develop genetic (DNA) markers which can be used by breeders to improve sheath blight resistance. Related research on blast disease produced similar successes with a number of DNA markers and genes (e.g. Pi-ta on chromosome 12) associated with blast resistance being discovered. On-going studies will broaden our understanding of how to combat this disease by combining the benefits of these newly discovered genes with previously known resistance genes. These results illustrate the successful development of genetic markers and validate their potential application in the rice industry. Other mapping populations from crosses between the rice wild ancestral species, such as Oryza rufipogon, and cultivated rice were made to genetically map and exploit important chromosomal regions for improvement of disease resistance and grain quality. In research to minimize stress impacts on crop development, we have also investigated important genetic controls for stem production (tillering) and growth, vigor, yield, and weed competitiveness through increased tillering at early rice growth stages. Creation of similar mapping populations allowed us to map some important crop productivity and disease resistance traits with even greater precision (fine-mapping). We have developed a new high quality rice cultivar that suppresses weed growth. Carbon isotope technology was used to show that some weed-suppressive rice lines produce an unusually large number of roots near the soil surface. Other studies identified several rice lines that withstand reduced amounts of irrigation and fewer herbicide applications, offering promising gains in conserving resources and improving crop sustainability. Our research results are published and were presented at a number of regional, national, and international conferences, which promoted additional collaboration in national and international research projects. Continuation of this work is incorporated into the new ARS project #6225-21220-005-00D.

4. Accomplishments

Review Publications
Gealy, D.R., Duke, S.E., Moldenhauer, K. 2013. Root distribution and potential interactions between allelopathic rice, sprangletop (Leptochloa spp.), and barnyardgrass (Echinochloa crus-galli) based on 13C isotope discrimination analysis. Journal of Chemical Ecology. 39:186-203.

Xing, J., Jia, Y., Correll, J.C., Lee, F.N., Cartwright, R., Cao, M., Yuan, L. 2013. Analysis of genetic and molecular identity among field isolates of the rice blast fungus with an international differential system, rep-PCR and DNA sequencing. Plant Disease. 97:491-495.

Wang, J., Jia, Y., Wen, J., Liu, W., Liu, X., Li, L., Jiang, Z., Zhang, J., Guo, X., Ren, J. 2013. Identification of rice blast resistance genes using international monogenic differentials. Crop Protection. 45:109-116.

Liu, G., Jia, Y., McClung, A.M., Oard, J., Lee, F., Correll, J. 2013. Confirming QTLs and finding additional loci responsible for resistance to rice sheath blight disease. Plant Disease. 97:113-117.

Chodavarapu, R.K., Feng, S., Ding, B., Simon, S.A., Lopez, D., Jia, Y., Wang, G., Meyers, B.C., Jacobsen, S.E., Pellegrini, M. 2012. Transcriptome and methylome interactions in rice hybrids. Proceedings of the National Academy of Sciences. 109:30-36.

Hongmei, Y., Jia, M.H., Jia, Y., Venus, R., Wang, Z., Sun, C., Wang, G. 2013. Molecular mapping of four blast resistance genes using recombinant inbred lines of 93-11 and nipponbare. Journal of Plant Biology. 56:91-97.

Pinson, S.R., Shahjahan, A., Rush, M.C., Groth, D.E. 2010. Bacterial panicle blight resistance QTL in rice (Oryza sativa L.) and their association with resistance to other diseases. Crop Science. 50:1287-1297.

Jia, Y., Wang, X., Costanzo, S., Lee, S. 2009. Understanding the co-evolution of the rice blast resistance gene Pi-ta and Magnaporthe oryzae avirulence gene AVR-Pita. In: Wang, X., Valent, B., editors. Advances in Genetics, Genomics and Control of Rice Blast Disease. Springer, Berlin. p. 137-148.

Brooks, S.A., Yan, W., Jackson, A.K., Deren, C. 2008. A natural mutation in rc reverts white-pericarp-rice to red and results is a new, dominant, wild-type allele Rc-g. Theoretical and Applied Genetics. 117:575-580.

Correll, J.C., Boza, E.J., Seyran, E., Cartwright, R.D., Jia, Y., Lee, F.N. 2009. Examination of the rice blast pathogen population diversity in Arkansas, USA – Stable or Unstable? In: Wang, X., Balent, B., editors. Advance in Genetics, Genomics, and Control of Rice Blast Disease. Springer, Berlin. p. 217-228.

Bryant, R.J., Yeater, K.M., Miller, H.B. 2012. The effect of induced yellowing on the physicochemical properties of specialty rices. Journal of the Science of Food and Agriculture. 93(2):271-275.

Gealy, D.R., Agrama, H., Jia, M.H. 2012. Genetic analysis of atypical U.S. red rice phenotypes: indications of prior gene flow in rice fields? Weed Science. 60:451-461. DOI: 10.1614/WS-D-11-00159.1.

Gealy, D.R., Yan, W. 2012. Weed suppression potential of 'Rondo' and other indica rice germplasm lines. Weed Technology. 26:517-524.

Miller, H.B., Miller, G.H., Moldenhauer, K.A. 2011. Utilizing the genetic diversity within rice cultivars. Planta. 235:641-647.

Jia, Y., Valent, B. 2009. Molecular aspects of rice blast disease resistance: Insights from structural and functional analysis of the Pi-ta and AVR-Pita gene pair. In: Datta, S., editor. Rice Improvements in the Genomic Era. Boca Raton, FL: CRC Press, Taylor & Francis Group. p. 207-236.

Sharma, A., McClung, A.M., Pinson, S.R., Kepiro, J.L., Shank, A.R., Tabien, R.E., Fjellstrom, R.G. 2009. Genetic mapping of sheath blight resistance to QTLs within tropical Japonica rice cultivars. Crop Science. 49:256-264.

Lee, S., Costanzo, S., Jia, Y. 2012. The structure and regulation of genes and consequences of their genetic mutations. In: Shu, Q.-Y., Forster, B.P., Nakagawa, H. editor. Plant Mutation Breeding and Biotechnology. CAB International:Cambridge. p. 33-47.

Pinson, S.R., Liu, G., Jia, M.H., Jia, Y., Fjellstrom, R.G., Sharma, A., Wang, Y., Tabien, R.E., Li, Z. 2012. Registration of a rice gene-mapping population consisting of 'TeQing'-into-'Lemont' backcross introgression lines. Journal of Plant Registrations. 6(1):128-135. doi: 10.3198/jpr2011.02.0066crmp.

Ziska, L.H., Tomecek, M.B., Gealy, D.R. 2010. Competitive interactions between cultivated and red rice as a function of recent and projected increases in atmospheric carbon dioxide. Agronomy Journal. 102:118-123.

Boyette, C.D., Gealy, D.R., Hoagland, R.E., Vaughn, K.C., Bowling, A.J. 2012. Hemp Sesbania (Sesbania exaltata) control in rice (Oryza sativa) with the bioherbicidal fungus Colletotrichum gloeosporioides f. sp. aeschynomene formulated in an invert emulsion. Biocontrol Science and Technology. 21 (12):1399-1407.

Wang, Y., Pinson, S.R., Fjellstrom, R.G., Tabien, R.E. 2011. Phenotypic gain from introgression of two QTLs, qSB9-2 and qSB12-1, for rice sheath blight resistance. Molecular Breeding. 30:293-303.

Jia, Y., Liu, G., Park, D., Yang, Y. 2013. Inoculation and scoring methods for rice sheath blight disease caused by Rhizoctonia solani. In: Yang, Y., editor. Rice Protocols. Methods in Molecular Biology Book Series, Volume 956. Humana Press. p. 257-268.

Zhao, G., Jia, Y., Deren, C.W., Yan, Z., Jia, M.H., Dai, L. 2012. Establishment and application of an efficient, economic, and rapid rice DNA extraction method. Chinese Journal of Rice Science. 26(4):495-499.

Ziska, L.H., Gealy, D.R., Tomecek, M.B., Jackson, A.K., Black, H.L. 2012. Recent and projected increases in atmospheric CO2 concentration can enhance gene flow between wild and genetically altered rice (Oryza sativa). PLoS One. 7(5). DOI:10.1371/Journal.Pone.

Ziska, L.H., Bunce, J.A., Shimono, H., Gealy, D.R., Baker, J.T., Newton, P.C., Reynolds, M.P., Jagadish, K.S., Zhu, C., Howden, M., Wilson, L.T. 2012. Food security and climate change: On the potential to adapt global crop production by active selection to rising atmospheric carbon dioxide. Proceedings of the Royal Society of London B. 279:4097-4105.

Lisko, K.A., Hubstenberger, J.F., Phillips, G.C., Miller, H.B., McClung, A.M., Lorence, A. 2013. Ontogenetic changes in vitamin C in selected rice varieties. Plant Physiology and Biochemistry. 66:41-46.

Gealy, D.R., Moldenhauer, K., Jia, M.H. 2013. Field performance of STG06L-35-061, a new genetic resource developed from crosses between weed-suppressive indica rice and commercial southern U.S. long-grains. Plant and Soil. 370(1):277-293.

Venu, R.A., Sreerekha, M., Nobuta, K., Madhav, S.M., Jia, Y., Meyers, B.C., Wang, G. 2013. Deep transcriptome sequencing reveals the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways in rice. Journal of Plant Biology. 56:216-231.

Thurber, C.S., Jia, M.H., Jia, Y., Caicedo, A. 2013. Similar traits, different genes? Examining convergent evolution in related weedy rice populations. Molecular Ecology. 22:685-698. doi: 10.1111/mec.12147.

Eizenga, G.C., Prasad, B., Jackson, A.K., Jia, M.H. 2013. Identification of rice sheath blight and blast quantitative trait loci in two different O. satival/O. nivara advanced backcross populations. Molecular Breeding. 31(4):889-907. doi: 10.1007/s11032-013-9843-y.

Last Modified: 10/17/2017
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