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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Research Project #425080

Research Project: Using Genetic Approaches to Reduce Crop Losses in Rice Due to Biotic and Abiotic Stress

Location: Dale Bumpers National Rice Research Center

2014 Annual Report

The long-term objective of this project is to seek a better understanding of the genetic and molecular bases of rice response to biotic and abiotic stresses in an effort to maintain high yields, improve crop resilience to changes in climate and cultural management practices, and to reduce reliance on pesticides for crop protection. Obj. 1: Evaluate novel sources of disease resistance to develop closely linked genetic markers for breeding, and elucidate plant-pathogen interactions. 1A: Develop new genetic markers associated with genes that control resistance response to rice blast disease 1B: Explore new genetic resources that possess novel alleles for major and minor genes that convey resistance to the sheath blight pathogen Obj. 2: Identify and genetically map traits associated with weed suppression in indica rice germplasm. 2A: Develop methods to quantify alleleopathy chemicals and other weed suppressive traits using greenhouse, laboratory, and field assays 2B: Characterize relative contribution of agronomic traits and allelopathy to weed suppression effective under reduced-irrigation systems or reduced-pesticide/organic systems 2C: Validate and fine-map QTLs associated with early tiller production for development of genetic markers suitable for breeding for weed suppression in US genetic backgrounds 2D: Identify QTLs associated with weed suppression using RIL mapping population derived from an allelopathic weed suppressive/non-suppressive tropical japonica cross Obj. 3: Explore rice genetic resources for use in adapting to climate change and mitigating greenhouse gas emissions. 3A: Identify genetic resources that can be used in breeding to adapt to extremes in temperature at the seedling and flowering stage 3B: Identify genetic resources that can be used to mitigate methane emissions in rice production Obj. 4: Investigate the use of genetic resources for production under irrigation systems that use less water. 4A: Discover chromosomal regions linked to yield potential under reduced water use systems 4B: Develop genetic resources that can be used in saline soils where water is limited

Wild rice accessions will be evaluated for blast disease resistance and sources with novel genes will be used in a backcrossing program to both map the novel QTL and develop germplasm with improved resistance. A major gene that provides resistance to a blast race that is virulent on all sources of resistance commonly used in the USA will be finely mapped. Closely linked DNA markers will be used for its introgression using marker assisted selection into improved germplasm for use by breeders. The interaction and evolutionary dynamics of genes involved in blast resistance in both rice and the pathogen will be examined. The genetic identity of contemporary and historical field isolates will be determined using genomic techniques and international differentials. Small differences in resistance response to sheath blight disease will be evaluated and used to identify the location of quantitative resistance QTL. Newly introduced wild accessions of rice and diverse global cultivars will be evaluated for novel sheath blight resistance alleles which will be incorporated to US germplasm for use by breeders. A major sheath blight resistant QTL will be finely mapped so that DNA markers and improved germplasm can be developed. Rice root imaging, plant growth patterns, early tillering, and allelopathic activity associated with weed suppression will be determined and used in mapping studies. Weed suppression traits effective under reduced-irrigation systems or reduced-pesticide/organic systems will be characterized. Cold temperature tolerance at the seedling stage and high temperature stress at the flowering stage will be assessed using diversity panels and mapping populations. A greenhouse study will be conducted using rice cultivars demonstrated to differ in methane emissions under field conditions to determine plant traits that may explain these differences. Best nitrogen fertilizer management practices for minimizing greenhouse gas emissions will be identified using intermittent flood and genetic resources previously shown to differ in methane emissions. The key components including best cultural management techniques and agronomic and phenological traits associated with greenhouse gas reduction relevant to southern US germplasm will be identified. Genetic markers that are linked to key phenotypic traits associated with productivity under intermittent flood will be identified for ultimately developing cultivars that can be grown under reduced water use. Genetic resources and markers that demonstrate genetic differences for salinity tolerance at the seedling stage will be identified to develop improved germplasm and cultivars for US rice production. The outcome of this research will result in genetic markers linked to traits that can be incorporated into new cultivars that are resilient to disease, weed pressure, salinity, extremes in temperatue, and can be grown under production practices that use less water and have reduced greenhouse gas emissions.

Progress Report
Although progress was made on many objectives, several were delayed or put on hold as a result of on-going critical vacancies (2), the filling of one vacancy late in FY14, and the loss of two other scientists early in FY14. Projects delayed or put on hold include fine mapping of the Pi-Shu blast resistance gene, mapping of novel sheath blight resistance genes, association analysis of cold tolerance, screening of mapping population parents for salt tolerance and heat tolerance, characterization of cultivars for methane emissions, and studying the interaction of methane emissions with water management. Progress on other objectives and grant-funded projects are as follows. A controlled inoculation method was improved for evaluating sheath blight disease. A total of 600 recombinant inbred lines from Lemont x Jasmine 85 cross was evaluated using this method. Subsequently, 100 lines exhibiting contrasting phenotypic responses were selected for further evaluation. The phenotypic data from repeated experiments were used to correlate with single nucleotide polymorphic markers identified from an ABC transporter gene sequenced from Lemont and Jasmine 85. Research is being pursued with scientists at the Noble Foundation to see if this ABC transporter is also responsive to rice blast fungus. Rice leaves inoculated at different time points with a blast isolate were evaluated for gene expression using qRT-PCR. Preliminary results suggest that this ABC transporter is only responsive for sheath blight infection, and not blast infection. Linkage analysis of previously collected data on tillering rates among a population of KBNTlpa/Zhe733 RILs identified putative tillering loci on chromosomes 1, 2, 3, 5, 6, and 12. Cross-progeny (F2 and BC1) were created from a Presidio x Zhe733 cross to support validation of these putative QTLs. In a USDA-NIFA collaborative project, avirulence genes in field isolates of the blast fungus were used to identify corresponding resistance genes in rice plants. Thus far, the presence or absence of AVR-Pi9, AVR-Pita, AVR-Pizt, AVR-Pik, and ACE genes in 380 field isolates of blast were determined by PCR using gene specific primers. Initial screening revealed 74%, 65%, 82%, 20%, and 76% of the tested isolates carried AVR-Pi9, AVR-Pita1, AVR-Pizt, AVR-Pik, and ACE, respectively, and results were presented at a scientific meeting. Selected isolates based on AVR gene contents are being tested with monogenic lines from IRRI that carry the corresponding resistance genes. Collection and purification of blast isolates are being continued in 2014. The sheath blight field isolates RR0102 and RR0134 have been used as pathogen tools for genetic studies and breeding in the southern US. These two isolates were selected for genome sequence analysis in order to identify critical pathogenicity factors that may help identify host resistance genes and chemical control targets. The genome of the sheath blight fungus is known to be heterogenic with multiple nuclei that will hinder the genome assembly effort. As a practical alternative, a newly developed tipping technique was used to purify the fungus for 5 generations and DNA is being extracted for next-gen sequencing in a project funded by National Science Foundation. A hydroponic salt tolerance evaluation method has been developed and validated using a known panel of cultivars that differ in salt tolerance. The method has been successfully used to evaluate a mapping population as part of a collaborative National Science Foundation project. The chromosome segment substitution lines (TILs) were evaluated for response to heat stress and to water stress in two separate field studies. Preliminary results from the latter study were summarized and presented at a scientific meeting. We developed rapid methods to accurately measure the physiological stresses induced by 'intermittent' irrigation in crop and weed canopies. These responses can be used as indicators to identify water-stress-tolerant rice cultivars and to determine optimum time periods for irrigating rice so as to minimize physiological stress. The two parental lines from an allelopathic rice x non-allelopathic rice mapping population have been extensively characterized for root architecture traits and productivity responses to reduced irrigation water and other environmental parameters. We have also analyzed more than 1000 seed samples from two indica rice x weedy red rice mapping populations to ascertain genetic keys to weedy red rice traits such as germination and dormancy. The Rice Diversity Panel 1, consisting of 421 global rice accessions, was evaluated for seedling cold tolerance. Subsequently, genome wide association analyses (GWAS) were conducted, and preliminary results revealed 15 a priori candidate genes affecting cold tolerance. Four of these were in previously identified QTL regions. Currently, a bi-parental population is being evaluated for possible use in validating the results of the GWAS analysis. A second year of research funded through Southern SARE project with Texas AgriLife to evaluate the impact of cover crops, cultivars, and organic fertilizer amendments on organically produced rice was completed. Results indicated that choice of cultivar is much more important than cultural management practices in optimizing yield under organic systems.

1. Weeds in rice fields becoming more difficult to control. Rice cultivars with herbicide resistance (HR) have been used to control weedy, red rice for more than a decade, and now comprise more than half of all rice in the southern USA. However, the HR gene can be inadvertently transferred from these cultivars into weedy, red rice through outcrossing. Researchers with ARS in Stuttgart, Arkansas, in collaboration with University of Massachusetts and University of Arkansas assessed new populations of HR red rice collected from farm fields to determine the potential involvement of outcrossing from commonly grown HR rice. They found DNA segments in these new populations of HR red rice that are known to come from HR rice cultivars, and showed that they contain the specific HR gene that confers resistance that is present in the HR rice cultivars. This research confirmed that there are recently formed populations of red rice that have strong resistance to some current herbicides and will require other measures like crop rotation and new herbicide chemistries to control.

2. Quick DNA preparation method developed to identify genes in rice blast fungus. The fungus Magnaporthe oryzae is the causal agent of a worldwide destructive disease of rice: rice blast disease. Having a means to characterize the disease-causing genes in the pathogen will help breeders develop new cultivars with improved resistance. ARS scientists in Stuttgart, Arkansas, and researchers at University of Arkansas and the International Rice Research Institute, the Philippines, developed a simplified method to isolate and amplify DNA from the fungus. The new method saves time and labor, and reduces the use of chemicals for analysis. This is a rapid, reliable, and low-cost alternative to the existing DNA extraction protocols used in research and clinical laboratories and will help study many other fungal cultures as well.

3. Sheath blight disease resistance identified in Oryza meridionalis, a related species of rice. Sheath blight is one of the most prevalent fungal diseases of cultivated rice and causes significant economic damage to rice production worldwide. No source of complete resistance to sheath blight disease has been identified in cultivated rice, Oryza sativa, but wild relatives of cultivated rice are a potential source of resistance. ARS scientists at Stuttgart, Arkansas, identified sheath blight resistance in the O. meridionalis accession (IRGC105608) to be located in the long arm of chromosome 9 by evaluating the progeny of a cross between the Southern U.S. variety, Lemont and O. meridionalis. Efforts are underway to continue incorporating this novel sheath blight resistance into Lemont and to make adapted progeny lines available to rice breeders to develop superior sheath blight resistant varieties for the U.S. rice industry.

4. Quick DNA preparation method developed to identify genes in rice blast fungus. The fungus Magnaporthe oryzae is the causal agent of a destructive disease of rice, rice blast disease. Having a means to characterize the disease-causing genes in the fungus will help breeders develop new cultivars with improved resistance. ARS scientists in Stuttgart, Arkansas, and researchers at University of Arkansas and the International Rice Research Institute, the Philippines, developed a new method to detect genes in the fungus using a piece of filter paper containing the fungus that is directly transferred for DNA isolation and amplification. The new method saves time and labor, and reduces the use of chemicals for analysis. This will help in the study of many other fungal cultures and is a rapid, reliable, and low-cost alternative to the existing DNA extraction protocols used in research and clinical laboratories.

5. Identification of candidate genes associated with positive and negative heterosis in rice. Hybrid rice is grown around the world and produces superior rice yields due to heterosis. Heterosis causes increased plant vigor, growth, and yield as a result of the combination of different genes from the parent cultivars that are the basis for the hybrid, yet the molecular and genetic bases of rice heterosis are poorly understood. ARS scientists in Stuttgart, Arkansas, and researchers at University of Arkansas, Ohio State University, and University of Delaware identified several thousand commonly and specifically expressed genes in the rice cultivars Nipponbare and 93-11, and their F1 hybrid. The differentially expressed genes in the F1 hybrid were mapped to yield-related quantitative trait loci (QTL) regions. Many highly expressed genes, including those that may be involved in heterosis, were located in these yield QTL regions. The study identified the starting genomic materials to further investigate the molecular bases of yield-related traits and heterosis in rice.

6. Effectiveness and durability of the rice Pi-ta gene in China. Development of diseases in plants is a result of the interaction of genes in the plant with genes in the pathogen. The AVR-Pita1 gene in the fungus Magnaporthe oryzae, which causes rice blast disease, determines how effective the resistance gene (Pi-ta) is in the rice plant. ARS scientists in Stuttgart, Arkansas, and researchers at Yunnan Academy of Agricultural Sciences, China, determined the feasibility of the Pi-ta gene for preventing blast disease and to understand the genetic basis of disease susceptibility. Field isolates of the pathogen from several rice production regions in Yunnan province, China, were evaluated using molecular markers and pathogenicity assays. Approximately 50% of the blast fungal isolates contained AVR-Pita1 and were found to be non-infectious to rice plants with Pi-ta. The study demonstrated that Pi-ta has been useful in managing blast disease in the rice production areas where blast fungi was isolated. However, changes in the DNA sequence of the protein coding region of AVR-Pita1 in disease-causing isolates demonstrated that genetic changes in the blast fungus are the major causes of instability in rice blast disease resistance.

7. Heading date and plant height tagged with molecular markers in rice. Heading date (days to flowering) and plant height are two agronomic traits important for rice production that are conditioned by quantitative trait loci (QTLs). The US adapted variety Kaybonnet low phytic acid (lpa1-1) and Zhe733, from China, have been used for improving rice quality and yield in the US and worldwide, respectively, yet genetic loci for these two agronomic traits have been unavailable. ARS scientists in Stuttgart, Arkansas, and researchers at University of Arkansas identified five QTLs (chromosomal regions) responsible for plant height, and three QTLs responsible for heading date, using a genetic mapping population developed from Kaybonnet low phytic acid (lpa1-1) and Zhe733. A major gene for heading date was found on chromosome 3 that contributed 20% of the phenotypic variation, and one for plant height contributed to 42% of phenotypic variation. QTL identified in our study coincided closely with positions reported previously in other rice populations worldwide, suggesting that these QTL have coevolved and have become domesticated. The tightly linked markers that flank these QTL regions will be useful for facilitating the incorporation of these traits into advanced breeding lines using marker assisted selection.

8. Cultivars can help reduce greenhouse gas emissions from flooded rice fields. Rice is generally produced in flooded fields, which results in oxygen-depleted soils and growth of methane-producing soil bacteria. Agricultural activities are associated with significant production of greenhouse gases like methane. ARS and University of Arkansas researchers in Stuttgart, Arkansas, in collaboration with researchers at University of California, Davis, demonstrated that methane accounts for over 90% of the greenhouse gas emissions from rice fields, whereas there is little nitrous oxide released. In addition, wide variation in methane emissions among cultivars grown in different environments was observed. The results indicate that choice of cultivar can play a significant role in reducing methane emissions from rice fields without sacrificing production of grain yield.

Review Publications
Dai, Y., Winston, E., Correll, J.C., Jia, Y. 2014. Induction of avirulence by AVR-Pita1 in virulent U.S. field isolates of Magnaporthe oryzae. The Crop Journal. 2(1):1-9.
Lee, S., Jia, M.H., Jia, Y., Liu, G. 2014. Tagging quantitative trait loci for heading date and plant height in important breeding parents of rice (Oryza sativa). Euphytica. 197(2):191-200. DOI 10.1007/s10681-013-1051-7.
Gealy, D.R., Anders, M., Watkins, B., Duke, S.E. 2014. Crop performance and weed suppression by weed-suppressive rice cultivars in furrow- and flood-irrigated systems under reduced herbicide inputs. Weed Science. 62(2):303-320.
Ren, J., Yu, Y., Gao, F., Zeng, L., Lu, X., Wu, X., Yan, W., Ren, G. 2013. Application of resistance gene analog markers to analysis of genetic structure and diversity in rice. Genome. 56(7):377-387.
Wang, X., Lee, S., Wang, J., Ma, J., Bianco, T.A., Jia, Y. 2014. Current advances on genetic resistance to rice blast disease. Book Chapter. pgs. 195-217. DOI: 10.5772/56824. Publisher: In Tech Editor: Wengui Yan.
Li, J., Sun, Y., Liu, H., Wang, Y., Jia, Y., Xu, M. 2013. Genetic variation and evolution of the Pit blast resistance locus in rice. Genetic Resources and Crop Evolution. 61:473-489. DOI 10.1007/s10722-013-0051-8.
Li, J., Lu, L., Jia, Y., Li, C. 2014. Effectiveness and durability of the rice Pi-ta gene in Yunnan province of China. Phytopathology. 104(7):762-768.
Venu, R.C., Ma, J., Jia, Y., Liu, G., Jia, M.H., Nobuta, K., Sreerekha, M.V., Moldenhauer, K., McClung, A.M., Meyers, B.C., Wang, G. 2014. Identification of candidate genes associated with positive and negative heterosis in rice. PLoS One. 9(4):e95178.
Ma, J., Jia, M.H., Jia, Y. 2014. Characterization of rice blast resistance gene Pi61(t) in rice germplasm. Plant Disease. 98(9):1200-1204.
Jia, Y., Wamishe, Y.A., Zhou, B. 2014. An expedited method to isolate DNA for PCR from Magnaporthe oryzae stored on filter paper. The Crop Journal. 2(5):267-271.
Wang, Z., Jia, Y. 2014. Development and characterization of rice mutants for functional genomic studies and breeding. In: Tomlekova, N.B., Kozgar, M.I., Wani, M.R., editors. Mutagenesis: Exploring Novel Genes and Pathways. Wageningen Academic Publishers. p. 307-322.
Lu, W., Pan, L., Zhao, H., Jia, Y., Wang, Y., Yu, X., Wang, X. 2014. Molecular detection of Xanthomonas oryzae pv. oryzae, Xanthomonas oryzae pv. oryzicola, and Burkholderia glumae in infected rice seeds and leaves. The Crop Journal. 2:398-406. doi: 10.1016/j.cj.2014.06.005.
Ziska, L.H., Tomecek, M.B., Gealy, D.R. 2014. Assessment of cultivated and wild, weedy rice lines to concurrent changes in CO2 concentration and air temperature: Determining traits for enhanced seed yield with increasing atmospheric CO2. Functional Plant Biology. 41:236-243.
Adviento-Borbe, M.A., Pittelkow, C.M., Anders, M., Van Kessel, C., Hill, J.E., McClung, A.M., Six, J., Linquist, B.A. 2013. Optimal fertilizer N rates and yield-scaled global warming potential in drill seeded rice. Journal of Environmental Quality. 42(6):1623-1634.