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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
1. Molecular basis of the instability of rice blast resistance identified. The major resistance gene Pi-ta is known to be effective in preventing infections by races of the fungal pathogen Magnaporthe oryzae that carry the corresponding avirulence gene AVR-Pita1. However, plant resistance can be overcome by genetic variability in the pathogen. ARS scientists in Stuttgart, Arkansas, and researchers at the University of Arkansas; Central South University, China; and Hunan Hybrid Rice Research and Development Center, China, studied the genetic identity and pathogenicity of 169 isolates of M. oryzae from rice cultivars, with and without the Pi-ta blast resistance gene. The altered AVR-Pita1 and diverse genetic fingerprinting pattern of isolates virulent on rice cultivars that carry Pi-ta were determined. This research demonstrated that genetic changes in the blast fungus are the major causes of instability in rice blast resistance.

2. Methane is the main target for reducing greenhouse gas emissions in rice fields. Development of rice production practices that minimize the release of greenhouse gases while maintaining high yields is a major concern. ARS and University of Arkansas researchers at Stuttgart, Arkansas, along with scientists at University of California, Davis ,examined methane and nitrous oxide emissions in US rice fields. The research showed that methane emissions during the growing season had a major impact on global warming potential, whereas, even when above optimum rates of nitrogen fertilizer were applied, nitrous oxide had less impact. This demonstrates that in drill seeded flooded rice paddies, practices which reduce methane emissions during the growing season will likely have the biggest impact on reducing global warming potential in rice production systems.

3. Genetic markers developed for quantitative blast resistance in rice. Mapping of new blast resistance genes is important for developing resistant rice cultivars using marker-assisted selection (MAS). ARS scientists in Stuttgart, Arkansas, and researchers at the University of Arkansas, Ohio State University, Hunan Hybrid Rice Research and Development Center, Hunan Agricultural University, Chinese Academy of Agricultural Sciences, and China Agricultural University have developed a high density genetic map using a mapping population derived from the cross of sequenced reference genomes of Nipponbare and 93-11. Four major quantitative resistant genes for resistance to rice blast disease were mapped with closely linked molecular markers. These new resistance genes can be used to develop new varieties with blast resistance via MAS and to seek a deeper understanding of the molecular basis of rice blast resistance.

4. New method developed to identify blast resistance (R) genes. Rice blast disease, caused by a fungal pathogen, is able to overcome individual resistance genes deployed in new varieties within a few years after release. ARS scientists in Stuttgart, Arkansas and researchers at Jilin Academy of Agricultural Sciences, China examined disease reaction using a set of rice lines developed by the International Rice Research Institute with each carrying one of 24 major R genes in a universal susceptible genetic background. Evaluation against more than 40 blast races demonstrated the spectrum of resistance that each gene conveys. This study will help breeders stack R genes into new cultivars to provide durable resistance to this devastating disease.

5. Weedy red rices adapt independently to agricultural environments. Understanding the evolutionary mechanisms of invasive species can benefit crop improvement and weed management. ARS scientists in Stuttgart, Arkansas and researchers at the University of Massachusetts examined quantitative trait loci (QTL) underlying invasive traits of weedy red rice. These QTLs were found to differ in two distinct US populations of weedy rice. This demonstrated that weedy rice groups have adapted to the same agricultural environment through different genetic paths. These genes may prove useful in developing improved varieties of rice that have greater resilience to climate change.

6. Weedy red rice takes advantage of increased CO2 and temperature levels. Understanding and managing rice-weed interactions are important for sustainable crop production, but the unintended consequences of simultaneous increases in atmospheric CO2 levels and temperature on these interactions is not known. ARS researchers in Beltsville, Maryland, and Stuttgart, Arkansas, measured the growth and grain yields of three rice cultivars and a weedy red rice line at a range of CO2 and temperature levels. Only the weedy red rice line exhibited a significant increase in biomass and grain yield with increasing CO2 at all temperatures. The increase in yield due to CO2 and air temperature was positively associated with the number of stems, and the ratio of stem production at standard and high levels of CO2 30 days after planting was predictive of the yield response to increasing CO2. These findings are useful because they indicate that wild or weedy rice lines could be a promising source of genes that could help rice breeders capitalize on the increasing global temperature and CO2 levels, and that differences in early stem formation may help identify rice lines that respond positively to high CO2 levels.

7. Oryza nivara, a rice wild relative, has the potential to improve seedling vigor and yield. Improved seedling vigor would increase the weed competitiveness of rice after planting. Other reports have shown, O. nivara (O. rufipogon), the wild species progenitor of cultivated rice, has the potential to improve the yield of cultivated rice, O. sativa. ARS scientists in Stuttgart, Arkansas, in collaboration with scientists at Davis, California, identified quantitative trait loci for seedling vigor, as measured by increased coleoptile and shoot length and increased panicle length and grain length that are attributed to the wild rice species, O. nivara. Four lines had grain yields greater than the cultivated parent, M-202. Incorporating improved seedling vigor from O. nivara into adapted rice would increase competitiveness with weeds. Knowing the genes that affect yield component traits like panicle length and grain size will impact selection for improved rice yield.

8. Rice production and weed control with reduced irrigation and herbicide inputs. Weeds are becoming increasingly troublesome to rice farmers because some are developing resistance to the herbicides meant to kill them, and production is further at risk because irrigation water necessary for a healthy crop and weed control is becoming less accessible and more expensive. In cooperation with University of Arkansas scientists, ARS researchers in Stuttgart are attempting to counter these trends by identifying rice varieties that produce high yields with less water, and also suppress weeds naturally. In field experiments comparing rice yields and natural weed suppression under traditional flood irrigation (high water consumption) and an alternative furrow irrigation system (less consumption), and conventional and reduced rates of herbicide, a variety that releases weed-fighting chemicals (allelochemicals) and a hybrid rice cultivar produced the highest rice yields and the best weed control. Although furrow-irrigated fields were less productive than traditionally-flooded fields, the weed-suppressive varieties controlled weeds using reduced rates of herbicide. This work demonstrated that some rice varieties can tolerate higher levels of stress from weeds in different irrigation environments, and may be useful for management of rice fields with limited inputs.

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: 05/27/2017
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