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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

2010 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
Recombinant inbred lines carrying the major sheath blight resistance gene (qSB9-2) are being crossed with the recurrent parent to generate 1000 backcross progeny.Near isogenic lines will be evaluated for resistance, and with additional markers to finely map the region responsible for the resistance. A high-resolution mapping study of a sheath blight phytotoxin sensitivity gene was completed. The gene was mapped to a 35kb interval on the long arm of chromosome 7, in the same position as a region known for sheath blight resistance. Future work is to map-base clone the gene, which will be the first sheath blight resistance gene identified. Fifteen breeding lines were identified with defects in the Ptr(t) blast resistance locus, and these will be used to establish marker and trait association. The Ptr(t) locus was mapped within 8 kb region on chromosome 12. Sequence analysis of the corresponding regions in the cultivar Katy [Ptr(t)Pi-ta] a source of the gene, and two mutants are nearly completed. The yeast two-hybrid system is being used to examine potential candidate proteins within the region. In cooperation with Penn State University, a resistant protein that can recognize the avirulence gene in the pathogen (AVR-Pita) was identified and mapped to the Pi-ta2 resistance gene in the plant. Sequence diversity of Pi-ta2 gene will be used to develop better marker for breeding for resistance. The set of 400 O. sativa and 100 O. rufipogon accessions was genotyped with 44,000 SNP markers, and association mapping studies are underway. Field studies were performed to evaluate differential weed suppression of various sources of indica-based rice germplasm in early and late planting environments and in flooded and upland irrigation systems. Greenhouse and growth chamber hydroponic bioassays were designed to detect differential root exudation for eventual identification of allelopathic chemicals by weed-suppressive with and without exposure to ultraviolet radiation stress. In cooperation with Texas A&M University, field tests were conducted to evaluate water weevil suppression in roots using indica cultivars that are also weed-suppressive. A fast and simple procedure was developed to rapidly estimate root and shoot areas from digitized photos of field-grown plants. With ARS cooperators at Beltsville, MD, we showed that gene flow from herbicide-resistant rice to red rice in growth chambers was as much or more under elevated CO2 levels than under normal levels. In cooperation with University of Arkansas, we initiated multi-year evaluation of seed longevity and dormancy of red rice biotypes in flooded and non-flooded soil overwintering conditions. Conducted field growouts, phenotyping, leaf sampling, and marker analysis of several hundred progeny of putative indica rice X red rice outcrosses. Completed marker analysis of a red rice biotype genotyping study.

4. Accomplishments
1. Five rice breeding lines with resistance to sheath blight disease released. One way to develop long-lasting disease resistance in crop cultivars is to incorporate multiple resistance genes, making it more difficult for the pathogen to overcome the resistance. ARS researchers in Stuttgart, Arkansas, in cooperation with scientists from the University of Arkansas, developed five rice breeding lines designated as RIL103, RIL158, RIL186, RIL220, and RIL221. These contain major and minor genes linked with sheath blight resistance that were derived from two cultivars that have been grown commercially in the USA, and thus also have good grain quality traits, early maturity, and glabrous leaves and hulls. These genetic materials are expected to be useful for breeding for improved sheath blight resistance in US rice cultivars.

2. Genetic Markers Developed for the Pi-km Blast Resistance Gene in Rice. Blast disease is a major yield limitation for rice production worldwide. There are a number of major genes for blast resistance that have been deployed by breeders in rice cultivars. Little is known about the mechanisms of plant defense in response to rice blast. One of the resistance genes used by breeders is Pi-k which is a complex gene. ARS researchers in Stuttgart, Arkansas studied one form of the gene, Pi-km, in 15 rice cultivars. Alignment of the DNA sequences of these cultivars revealed a section of the Pi-km gene that is consistent across cultivars and another section that is highly variable. These sequence variations were found to be associated with resistance to different races of the blast pathogen. DNA markers were developed that can be used by breeders to stack resistance genes in new cultivars. This will result in cultivars that require less fungicide to be protected from rice blast disease.

3. Rice Genotyped with SNP Markers to Understand Population Substructure: Crosses between the two major rice varietal groups, Indica and Japonica have resulted in high yielding varieties and incorporated desirable traits across varietal groups but there is little understanding of what occurred on the genotypic level. ARS researchers in Stuttgart, Arkansas, collaborated with researchers at Cornell University on a project funded by the National Science Foundation to genotype a diverse collection of 400 rice accessions with a new type of DNA marker called single nucleotide polymorphism (SNP) markers. The 1,536 SNP markers validated the population substructure by dividing the Indica varietal group into indica and aus, and the Japonica varietal group into temperate japonica, tropical japonica and aromatic. Also, SNP markers for plant height, seed length, starch (amylose) content and a blast resistance gene were identified. Understanding the rice population substructure will enable breeders to select parents for developing high yielding hybrids and pyramiding desirable traits found in accessions belonging to different subpopulation groups.

4. Modeling susceptibility to smut diseases of rice in response to fertilizer. False and kernel smut in rice are common diseases that reduce yield and grain quality. They are difficult to control because few sources of genetic resistance are known and the use of fungicides is generally not practical. ARS and university scientists in Stuttgart, Arkansas, determined that cultivars vary in susceptibility to grain smuts depending on the amount of fertilizer nitrogen applied. Some cultivars have high incidence of disease at high levels of nitrogen, whereas other cultivars maintain low levels of disease regardless of fertilizer input. These results indicate that optimum fertilizer rates can be determined that maximize grain yield and maintain miminum levels of smut disease.

5. Identification of a major gene for resistance to sheath blight disease in rice. Sheath blight disease is a major constraint for rice production worldwide. ARS scientists in Stuttgart, Arkansas, in collaboration with university scientists in Louisiana, Kansas, and Arkansas, and researchers in Colombia identified chromosomal regions that are linked with sheath blight resistance in a mapping population that was evaluated under both field and greenhouse conditions and genotyped with 111 genetic markers. Four chromosomal regions were identified that together accounted for 47% of the resistance observed in the field. That on chromosome 9 has been previously identified in other studies, indicating that it is a robust resistance gene. In addition, two other regions were identified that explained resistance to sheath blight isolates from either the Colombia location or from the southern US. Genetic markers that are linked to the sheath blight resistance region on chromosome 9 will be useful to breeders for developing improved cultivars that will require less fungicides to maintain yield.

6. Mapping Resistance Genes to Common Races of the Rice Blast Pathogen. Quantitative trait loci (QTLs) are chromosomal regions that possess genes that control the expression of traits. Finding genetic markers linked to QTL that control important traits in rice helps breeders develop improved cultivars. An ARS researcher in Stuttgart, Arkansas identified QTLs that condition resistance to six out of twelve common races of the blast pathogen found in the USA (IB1, IB45, IB49, IB54, IC17, and ID1). A genetic mapping population was used that was developed from the US cultivar Lemont, that is moderately- susceptible, crossed with the moderately-resistant indica cultivar, Jasmine 85. Eight QTLs on chromosomes 3, 8, 9, 11, and 12 were identified, each providing resistance to different blast races with the degree of resistance ranging from 5.2 to 26.5%. This study demonstrates the usefulness of tagging individual blast QTLs using different races of the pathogen. The information will be used by breeders to develop new cultivars that possess resistance to multiple races of this major disease causing pathogen.

7. Cropping Systems that Help Control the Incidence of Rice Grain Smuts. False and kernel smut in rice are common diseases that reduce yield and grain quality. They are difficult to control because few sources of genetic resistance are known and the use of fungicides is generally not practical. ARS and university scientists in Stuttgart, Arkansas, explored how crop management strategies could be used to control grain smut diseases on susceptible rice varieties. They determined that various cropping systems like three-phase crop rotations with rice once every third year and no-till soil conservation methods successfully controlled rice grain smuts. The discovery will reduce economic losses where smuts are significant disease problems, fungicides are ineffective, and resistant rice varieties are unavailable.

8. New method for studying weed competition in rice. Evaluating rice/weed root interactions is difficult due to the intertwining growth of roots in the field. A 13C stable isotope method that quantifies these interactions between roots of weed-suppressive rice cultivars and weeds under flooded field conditions was developed previously for barnyardgrass. In this research, ARS scientists in Stuttgart, Arkansas, expanded the proven method to additional weed species of rice, including broadleaf signalgrass, fall panicum, bearded sprangletop, Amazon sprangletop, crabgrass, and yellow nutsedge. The method proved reliable and predictive over several environments, and shoot 13C values closely mirrored the root 13C values in all species. Having a method that can evaluate interactions between rice and weed roots under field conditions will help in the development and understanding of weed-suppressive rice cultivars, which will ultimately provide farmers with additional tools to control weeds.

9. Rice cultivars identified that differ in susceptibility to stackburn. Stackburn is a phenomenon that causes the rice grain to become discolored under poor storage conditions where the grain is subjected to moisture, heat, and fungal growth. Grain from 20 diverse rice varieties were tested for their tendency to yellow when subjected to heat and moisture. Nipponbare and Chiyonishiki are two varieties from Japan that showed low discoloration. In contrast, Mars and Somewake cultivars were susceptible. Finding cultivars that differ in their susceptibility to stackburn is the first step in understanding the genetic control of this trait. Identification of rice cultivars that do not discolor under variable storage conditions will provide farmers with an additional tool to improve their economic returns.

10. Evolution of the gene that controls grain shattering in eedy red rice. Red rice is a common weed found in rice production fields that is difficult to control, in part, because the grain easily shatters, falling off the plant to become a problem in subsequent years. ARS scientists in Stuttgart, Arkansas, with cooperators at University of Massachusetts and Washington University investigated the shattering trait in a collection of U.S. weedy rice accessions, as well as in rice cultivars and other wild relatives of rice. It was found that all U.S. weedy rice accessions shatter seeds easily, in contrast to a lower shattering ability seen in cultivated rice. Analysis of the shattering gene, sh4, showed that both cultivated and weedy rice share similar DNA sequences at this gene that are associated with decreased seed shattering. This suggests that weedy red rice evolved from cultivated rice and that it has acquired the shattering trait through alternative genetic mechanisms. These new findings should be helpful for designing strategies to prevent shattering in rice cultivars and in controlling weedy species of rice that shatter.

Review Publications
Jia, Y. 2009. Artificial introgression of a large fragment around the Pi-ta rice blast resistance gene in backcross progenies and several elite rice cultivars. Heredity. 103(4):333-339.

Shivrain, V.K., Burgos, N.R., Gealy, D.R., Sales, M.A., Smith, K.L. 2009. Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids. Pest Management Science. 65:1124-1129. DOI 10.1002/ps.1802.

Gealy, D.R., Agrama, H.A., Eizenga, G.C. 2009. Exploring genetic and spatial structure of U.S. weedy red rice (Oryza sativa) in relation to rice relatives worldwide. Weed Science. 57:627-643. DOI: 10.1614/WS-09-018.1.

Lee, S., Costanzo, S., Jia, Y., Olsen, K.M., Caicedo, A.L. 2009. Evolutionary dynamics of the genomic region around the blast resistance gene Pi-ta in AA genome Oryza species. Genetics. 183:1315-1325.

Brooks, S.A., Anders, M.M., Yeater, K.M. 2010. Effect of furrow irrigation on the severity of false smut in susceptible rice varieties. Plant Disease. 94(5):570-574.

Costanzo, S., Jia, Y. 2010. Sequence variation at the rice blast resistance gene Pi-km locus: Implications for the development of allele specific markers. Plant Science. 178-523-530.

Jia, Y., Moldenhauer, K.A. 2010. Development of morogenic and digenic rice lines for blast resistance genes of Pi-ta, Pi-kh/Pi-ks. Journal of Plant Registrations. 4:163-166.

Han, Z., Wu, F., Deng, G., Qian, G., Yu, M., Jia, Y. 2009. Structural and expressional analysis of the B-hordein genes in Tibetan hull-less barley. Genetica. 138-227-239.

Reagon, M., Thurber, C.S., Gross, B.L., Olsen, K.M., Jia, Y., Caicedo, A.L. 2010. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evolutionary Biology. 10(180):1-16.

Gealy, D.R., Fischer, A.J. 2010. 13C discrimination: A stable isotope method to quantify root interactions between C3 rice (Oryza sativa) and C4 barnyardgrass (Echinochloa crus-galli) in flooded fields. Weed Science. 58(3):359-368.

Last Modified: 2/23/2016
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