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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

2012 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:
Trait data was collected on O. barthii and O. glaberrima wild species accessions, and these will be genotyped as part of an association mapping study. Four backcross inbred line populations are being developed from crosses between O. barthii with M-202 (O. sativa) and CG14 (O. glaberrima). In addition, four chromosome segment substitution line (CSSL) populations involving O. rufipogon and O. nivara are under development. One of these four will be planted in FY13 to study yield potential. A Lemont/O. meridionalis population was tested for reaction to sheath blight for the second year, and it will be genotyped for a QTL analysis. Studies were conducted to assess factors associated with weed-suppressive activity in rice and their response to different cultural practices. A 3-year study was completed comparing weed control of weed-suppressive rice cultivars when grown under furrow irrigation and conventional flood systems. Using a set of CSSLs that differed in tillering, weed competitive traits (like rice root) and leaf areas, tillering, and plant height were evaluated in a weed infested field. We studied field methods to test the feasibility of conducting a large-scale evaluation of weed suppression potential of allelopathic mapping populations that are being developed. Weed suppression will be very important in reduced herbicide or organic management systems. We initiated a field test to evaluate using conditioned (imbibed) seed in a drill-seeded system as a means of enhancing weed competition under reduced inputs. Tillering ability impacts both weed suppression and yield potential. We completed evaluation of tiller initiation in a greenhouse study using KBNT-lpa/Zhe733 RILs. The population has been genotyped, and QTL analysis will be completed this year. Results will be compared with other QTL studies to identify the most robust tillering QTLs that can be subsequently fine mapped and incorporated into improved germplasm. Five CSSLs containing specific tillering QTLs were evaluated to study the effect of plant spacing on tiller production and yield. Those with the most robust QTLs will be released as improved germplasm. A methodology was developed for screening a mapping population for tolerance to cold temperature (12C) at germination. Some 275 RILs were screened at 26C to determine baseline germination rate. Due to labor shortages and equipment repairs, the evaluation of the RILs at 12C will be completed at the end of CY12. These data will be used to associate genomic insertions with cold tolerance. Methane and nitrous oxide were determined in a field study to assess greenhouse gas emissions (GHGE) in response to different rice cultivars and fertilizer rates. Methane emissions from cultivars differed by a factor of 4; however, cultivars did not vary much for nitrous oxide emissions. In contrast, as fertilizer rates increased, nitrous oxide emissions increased, but there was little change in methane. These results suggest that choice of cultivar and fertilizer management may help reduce GHGE from rice fields.

4. Accomplishments
1. Developing a U.S. rice cultivar with allelopathic/weed-suppressive traits. Improving the weed suppression potential of rice cultivars may allow farmers to reduce herbicide use and fight herbicide-resistant weeds. However, achieving this goal has been difficult due to the complexity of incorporating weed suppressive traits into high yielding rice lines that also retain commercially acceptable quality. ARS and University of Arkansas scientists in Stuttgart, Arkansas, collaborated to develop and field-test the first U.S. weed-suppressive rice cultivar (STG06L-35-061) derived from allelopathic (naturally weed-suppressive) parents. This cultivar has exhibited greater barnyardgrass suppression than U.S. cultivars while maintaining commercially acceptable yields, high milling and cooking quality, and resistance to rice blast disease. Genomic analysis showed that DNA segments from the allelopathic parents were found on two chromosomes of STG06L-35-061, indicating these regions may be a possible source of weed suppressive traits. STG06L-35-061 is potentially suitable for organic rice production systems or conventional systems in which growers are attempting to reduce input costs associated with herbicides.

2. Discovery of sheath blight and blast resistance in the rice ancestral species Oryza nivara. New sources of sheath blight disease resistance are needed to decrease the use of fungicides. Accessions of Oryza nivara, the species that cultivated rice was derived from, often contain novel resistance genes lost during domestication that can be used to improve new rice cultivars. ARS researchers at Stuttgart, Arkansas, identified four possible sheath blight resistance genes and two possible blast resistance genes attributed to an accession of O. nivara that was used in a cross. Efforts are currently underway to incorporate these sheath blight and blast resistance genes into the background of cultivated rice.

3. Using wild species of rice to improve grain yield. Most cultivated rice comes from the Oryza sativa species. However there are several other wild relatives of rice that have been shown to have pest resistance traits. ARS scientists at Stuttgart, Arkansas, collaborated with Cornell University on a project funded by the National Science Foundation to determine if these wild species may also have yield-enhancing genes. A genetic population was developed using a US rice cultivar, Jefferson, crossed with the wild species Oryza rufipogon. Genetic insertions from the wild species on chromosomes two and six in the Jefferson background were found to give a 25% yield increase. These results demonstrated that wild ancestral species that possess no obvious agronomic merit are an important genetic resource for improving the yield potential of cultivated rice.

4. Increased atmospheric CO2 may allow transfer of herbicide resistance in rice to weeds. Red rice, a common weed found in rice production fields, is genetically similar to cultivated rice. Projected increases in atmospheric CO2 levels are expected to adversely affect some crop-weed interactions, but the potential effects of this phenomenon on the movement of genes from herbicide-resistant rice cultivars into weedy red rice is not known. In controlled-environment experiments under current and elevated atmospheric CO2 levels, ARS scientists in Stuttgart, Arkansas, and Beltsville, Maryland, showed that increasing CO2 concentrations from early 20th century levels (300 parts per million) to projected, mid-21st century levels (600 parts per million), more than tripled the flow of the herbicide resistance gene between weedy red rice and a rice cultivar with resistance to the herbicide imidazolinone, which could potentially lead to herbicide-resistant weedy red rice populations. This increase was associated with differential increases in plant size in the weed and greater synchrony in flowering times between the two at the highest CO2 level. These results suggest that rising atmospheric CO2 could result in unintended adverse weed-rice interactions in production fields.

5. Rice disease management under organic production. There is an increasing demand for organically produced rice; however, because typical fungicides cannot be used in an organic system, information is needed to manage diseases and optimize yields. ARS scientists at Stuttgart, Arkansas, and Texas A&M University scientists evaluated the yield potential and disease susceptibility of rice grown under organic management. Six organic-based fertilizer products were tested at four rates. Higher rates of the fertilizer products resulted in increased yields and decreased incidence of seedling disease, narrow brown leaf spot, and brown spot. In addition, a study looking at cultivation practices and green manure crops found that there was greater incidence of straighthead disease when rice was planted following no-till cultivation as compared to conventional tillage followed by drill or water seeding. These studies demonstrated that disease pressures, pest management methods, and cultivation practices that will be successful in organic rice production may be different from what has been found for production of other organic crops and in production of rice under conventional management.

6. Confirming genomic regions associated with resistance to rice sheath blight disease. Sheath blight disease causes significant crop losses worldwide; however, because the trait is complexly inherited, progress from breeding for disease resistance has been limited. ARS researchers in Stuttgart, Arkansas, collaborated with researchers at University of Arkansas-Fayetteville, Louisiana State University, and University of Arkansas Rice Research and Extension Center on a multi-institution project supported by USDA-NIFA named RiceCAP to develop reliable genetic markers for resistance to rice sheath blight disease. The initial location of the quantitative resistance genes were identified in a genetic mapping population that was evaluated using genetic markers and a greenhouse disease screening assay. The linked genetic markers were verified using the same mapping population evaluated in inoculated field experiments conducted in Arkansas, Texas, and Louisiana over a two-year period. The data indicate that the previously identified quantitative resistance genes and DNA markers linked to these genes are robust and can be used in marker-assisted breeding efforts to improve sheath blight disease resistance in rice.

7. A “Rice Diversity Panel” for discovering new marker-trait associations. A diverse collection of rice cultivars from around the world that is well characterized both genetically and agronomically can be used to discover the location of DNA markers and their association with traits of economic interest. ARS researchers at Stuttgart, Arkansas, purified seed of some 400 accessions, collected data on 32 traits of each accession, and increased the seed for distribution. In collaboration with researchers at Cornell University, all the accessions were characterized with 44,100 SNP genetic markers. The genetic data and seed of the accessions are publicly available for use by researchers to identify additional marker-trait associations. Once these are identified, the markers can be used to efficiently incorporate the desired trait into cultivated rice through breeding.

8. Suppressiing genetic recombination on rice chromosome 12. Genetic analysis of rice cultivars and breeding populations has revealed that there are sections of chromosomes that are inherited as large blocks of DNA due to suppression of genetic recombination. One such linkage block exists near the centromere of rice chromosome 12, where the rice blast resistance gene Pi-ta resides. ARS researchers in Stuttgart, Arkansas, collaborated with a researcher at Jiliang University in China and investigated how much recombination suppression was due to incompatibility between the indica and japonica rice subspecies. Five populations derived from indica and japonica and indica and indica parents were studied. Large linkage blocks ranging from 4.1 megabases to 10 megabases were identified. However, significantly smaller blocks ranging from less than 800 kb to 2.1 megabases were identified in indica by indica crosses as compared to indica by japonica crosses. This suggests that large linkage blocks at the centromere of rice chromosome 12 could be due to genetic incompatibility between subspecies. Thus making crosses within the same subspecies gene pool may result in greater recombination and genetic variability within linkage block regions and offer more potential for breeding.

9. Rice cultivars suppress root growth of grass weed species. Sprangletop and barnyardgrass are two of the most troublesome weed species in rice in the southern US, because of their large root mass that competes with establishment of rice roots. ARS and University of Arkansas scientists in Stuttgart, Arkansas, used an ARS-developed stable carbon isotope (C-13) analysis method to show that weed-suppressive indica rice cultivars reduced root growth of both sprangletop and barnyardgrass more than traditional commercial cultivars did. Rice tended to reduce growth of barnyardgrass roots less than sprangletop, which helps explain the overall greater competitiveness by barnyardgrass. Greater knowledge of the rice-weed interactions at the root level will aid in the development and optimization of weed-suppressive rice cultivars that will provide farmers with additional tools for cost-effective control of these damaging pests in rice.

10. Disarming the pathogen - improving blast disease resistance in rice. Rice blast disease is one of the most destructive diseases worldwide. ARS researchers in Stuttgart, Arkansas, collaborated with researchers at the University of Arkansas, Fayetteville, to determine resistance stability of rice blast disease in a project funded by the Arkansas Rice Research and Promotion Board. The AVR-Pita1 gene in the rice blast fungus determines the effectiveness of resistance of the Pi-ta resistance gene that is found in 11 US rice cultivars. Four field isolates of the fungus were obtained that were able to cause disease on rice cultivars that possess the Pi-ta gene. In this study, we introduced the AVR-Pita1 gene into these fungal isolates and found that it knocked out their ability to infect rice cultivars possessing Pi-ta. Understanding the molecular basis for the pathogen-plant interaction that induces defense mechanisms and results in a resistance reaction by the plant will lead to novel strategies to prevent rice blast disease.

11. Rice cultivars differ in foliar Vitamin C content. Ascorbic acid, also known as Vitamin C, is a key antioxidant for both plants and animals. In plants, it is involved with key biochemical processes and has been associated with the plant's ability to respond to physiological stress. ARS scientists at Stuttgart, Arkansas, in collaboration with researchers at Arkansas State University in Jonesboro, Arkansas, evaluated ascorbic acid levels in rice during plant growth and development. Whereas in model plant species like Arabidopsis, Vitamin C levels decline with age, in rice we observed peaks in foliar content at an early vegetative stage and during reproduction. In addition, wide differences in total foliar content of Vitamin C were determined in 24 rice accessions from around the world. These results lead the way to explore if genetic differences and timing of production of Vitamin C in rice can be associated with increase tolerance to such physiological stresses as extremes in temperature, drought, and saline water.

Review Publications
Gealy, D.R., Gealy, G.S. 2011. 13Carbon isotope discrimination in roots and shoots of major weed species of southern U.S. rice fields and its potential use for analysis of rice-weed root interactions. Weed Science. 59(4):587-600.

RoyChowdhury, M., Jia, Y., Jackson, A.K., Jia, M.H., Fjellstrom, R.G., Cartwright, R. 2012. Analysis of rice blast resistance gene Pi-z in rice germplasm using pathogenicity assays and DNA markers. Euphytica. 184:35-46.

Gealy, D.R., Moldenhauer, K. 2012. Use of 13C isotope discrimination analysis to quantify distribution of barnyardgrass and rice roots in a four-year study of weed-suppressive rice. Weed Science. 60:133–142.

Thomson, M.J., Zhao, K., Wright, M.H., McNally, K.L., Rey, J., Tung, C., Reynolds, A., Scheffler, B.E., Eizenga, G.C., McClung, A.M., Hyunjung, K., Ismail, A.M., De Ocampo, M., Mojica, C., Reveche, M., Dilla, C.J., Mauleon, R., Leung, H., Bustamante, C.D., McCouch, S.R. 2011. High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 29:875–886.

Roychowdhury, M., Jia, Y., Cartwright, R.D. 2012. Structure, function, interaction, co-evolution of rice blast resistance genes. Acta Agronomica Sinica. 38: 381-393.

Lee, S., Jia, Y., Jia, M.H., Gealy, D.R., Olsen, K.M., Caicedo, A.L. 2011. Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA. PLoS One. 6(10):e26260. doi:10.1371/journal.pone.0026260.

Shivrain, V.K., Burgos, N.R., Agrama, H.A., Lawton-Rauh, A., Lu, B., Sales, M.A., Boyett, V.A., Gealy, D.R., Moldenhauer, K.K. 2010. Genetic diversity of weedy red rice (Oryza sativa) in Arkansas, USA. Weed Research. 50:289-302. DOI: 10.1111/j.1365-3180.2010.00780.x.

Thurber, C.S., Reagon, M., Gross, B.L., Olsen, K.M., Jia, Y., Caicedo, A.L. 2010. Molecular evolution of the sh4 shattering locus in U.S. weedy rice. Molecular Ecology. 19:3271-3284.

Nelson, J., Oard, J.H., Groth, D., Utomo, H., Jia, Y., Liu, G., Moldenhauer, K.K., Correa-Victoria, F.J., Fjellstrom, R.G., Scheffler, B.E., Prado, G.A. 2012. Sheath-blight resistance QTLs and in japonica rice germplasm. Euphytica. 184:23-24. 10.1007/s10681-011-0475-1.

Jia, Y. 2011. Gene discovery of crop disease in the postgenome era. In: Gu, W., Wang, Y., editors. Gene Discovery for Disease Models, 1st edition. John Wiley & Sons, Inc. p. 425-441.

Jia, Y., Liu, G., Correa-Victoria, F.J., Mcclung, A.M., Oard, J.H., Bryant, R.J., Jia, M.H., Corell, J.C. 2012. Registration of four rice germplasm lines with improved resistance to sheath blight and blast diseases. Journal of Plant Registrations. 6(1):95-100.

Zhao, G., Yan, Z., Jia, Y., Deren, C.W., Dai, L. 2012. Analysis of rice blast resistance in rice breeding parents from USA using molecular markers and pathogenicity assays. Molecular Plant Breeding of China. 10:207-213.

RoyChowdhury, M., Jia, Y., Jia, M.H., Fjellstrom, R.G., Cartwright, R. 2012. Identification of the rice blast resistance gene Pi-b in the national small grains collection. Phytopathology 102(7):700-706.

Jia, Y., Jia, M.H., Wang, Z., Liu, G. 2012. Indica and Japonica crosses resulting in linkage block and recombination suppression on rice chromosome 12. PLoS One. 7(8):Article e43066.

Brooks, S.A., Anders, M.A., Yeater, K.M. 2009. Effect of cultural management practices on the severity of false smut and kernel smut of rice. Plant Disease. 93:1202-1208.

Dai, Y., Jia, Y., Correll, J.C., Wang, X., Wang, Y. 2010. Diversification and evolution of the avirulence gene AVR-Pita1 in field isolates of Magnaporthe oryzae. Fungal Genetics and Biology. 47:973-980.

Miller, H.B. 2011. Non-nutritive mineral effects on rice. Plant Stress. 5:82-91.

Jia, Y. 2009. A user friendly method to isolate and single spore the fungi Magnaporthe oryzae and Magnaporthe grisea obtained from diseased field samples. Plant Health Progress. Available: doi:10.1094/PHP-2009-1215-01-BR.

Goss, B.L., Reagon, M., Hsu, S., Caicedo, A.L., Jia, Y., Olsen, K.M. 2010. Seeing red: The origin of grain pigmentation in US weedy rice. Molecular Ecology. 19:3380-3393.

Lee, F.N., Cartwright, R.D., Jia, Y., Correll, J.C. 2009. Field resistance expressed when the PI-TA gene is compromised by Magnaporthe oryzae. In: Wang, G.-L., Valen, B., editors. Advances in Genetics, Genomics and Control of Rice Blast Disease. Springer Science and Media. p. 281-290.

Reagon, M., Thurber, C.S., Olsen, K.M., Jia, Y., Caicedo, A.L. 2011. The short and the long of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Molecular Ecology. 20:3743-3756.

Rioux, R., Manmathan, H., Singh, P., De Los Reyes, B., Jia, Y., Tavantzis, S. 2011. Comparative analysis of putative pathogenesis-related gene expression in two Rhizoctonia solani pathosystems. Current Genetics. 57:391-408.

Last Modified: 04/28/2017
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