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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

2015 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
ARS in-house and grant supported research has progressed despite 2 scientific positions that have been vacant since the inception of the project, and 3 new scientific vacancies that occurred during 2014/15 along with several support vacancies. To fine map the qSHB9-2 genomic region responsible for sheath blight disease resistance, a total of 200 BC2F2 progeny have been genotyped and phenotyped and recombinants at this locus are being identified. As part of a National Science Foundation (NSF) funded project, two-field isolates of the sheath blight fungus, RR0102 and RR0134, displaying different speeds of fungal growth were used for DNA and Ribonucleic acid (RNA) extractions for genome sequencing and RNAseq. Genome sequencing and expression data were obtained and further genome assembly and functional analysis of Rhizoctonia (R.) solani genes are in progress. Plans to evaluate the Pan Ju/Lemont population for novel sheath blight resistance quantitative trait loci (QTLs) were abandoned because the population was confounded by extreme differences in plant maturity. With the resignation of one scientist associated with this project, the research has been stopped. Likewise efforts to finish the work to map the Pi-Shu blast resistance gene have been delayed due to the loss of two of the scientists that were on this project. As part of a USDA-NIFA funded project with Kansas State University a total of 360 field isolates of blast from 2014 were purified. Race identity of forty isolates in 2013 and 2014 collections were examined. Rep-polymerase chain reaction (PCR) method was developed and used to select 24 isolates for pathogenicity assays. Twenty-four isolates were inoculated onto respective monogenic lines and differential blast races for respective resistance genes are being identified. Initial sequence analysis of 200 isolates was completed and isolates that contain different haplotypes are being sequenced. Sequence analysis of 200 isolates of the avirulence gene AVR-Pi9 was completed and polymorphic isolates were identified for verification and pathogenicity assays. Initial PCR analysis showed that 90% of (100) field blast isolates carried AVR-Pib that is consistent with the fact that resistance gene Pi-b has been effective in U.S. PCR primers for both mating types were tested on archived blast isolates and will be used to check selected isolates collected from 2012-2015. Forty field blast isolates from 2012-2014 were selected for further testing. Results will be verified by the end of December. Fifty isolates from 2015 fields were purified. Progress was made on developing efficient methods to assess morphological and physiological traits in rice that are associated weed suppression. This included crop and weed photosynthesis and growth under field and greenhouse conditions and seedling digital imaging using fluorescence, near infrared, and visible detectors. Microtubes were placed in field plots for solid-phase root zone extraction of rice root allelochemical exudates. Studies were conducted to assess factors associated with different allelopathic/weed-suppressive indica germplasm under reduced irrigation practices and using chemically pre-treated seeds at planting. The latter approach did not appear to be promising. A total of 330 lines of a population segregating for allelopathic/weed-suppressive traits was tested in replicated field trials for growth rate, tillering (number and angle), chlorophyll content, photosynthesis, and light interception pattern. The population is now genotyped and ready for QTL mapping. In an effort to fine-map early tiller production which is important for weed suppression as well as yield, phenotypic and molecular analysis of field-grown F2 and greenhouse grown BC1F1 plants confirmed the existence of loci affecting early tiller production on chromosome 2, 3, 5 and 8, and showed that these genes were effective in enhancing tiller production in drill-seeded field-grown plants as well as potted greenhouse-grown plants. Some progress was made on research related to stress factors associated with climate change even though two vacancies are associated with these objectives. The second year of a field study to look at yield components in response to reduced irrigation practices using an indica/tropical japonica mapping population was conducted. However, the second year of the field study looking at the same population for heat tolerance was not performed. The Rice Diversity Panel 1 (RPD1) consisting of 421 global rice accessions that has been extensively genotyped with 700k single nucleotide polymorphism (SNP) markers was evaluated for cold tolerance at germination and a subset of 185 japonica accessions was evaluated for cold tolerance at the reproductive stage. Genome-wide association studies identified five to seven chromosomal regions associated with seedling cold tolerance depending on the subpopulation evaluated. Some of these regions also were discovered by QTL analysis of bi-parental populations and 27 candidate genes were found to reside in the associated regions. Some of the candidate genes identified were previously reported to be related to cold stress. Cold tolerance at the reproductive stage was measured as seed weight per panicle with accessions having more tolerance producing more seed. Four regions were associated with seed weight per panicle with four candidate genes located in these regions. Although planned greenhouse and field studies to look at mitigation of methane emissions in rice production were not conducted due to the vacancies, field tests were conducted in cooperation with ARS scientists in Beltsville, MD, to test hypothesis that yields of historical U.S. rice varieties will increase under present-day ‘elevated’ CO2 levels (~400 parts per million (ppm)) compared with the same varieties grown at the lower levels of CO2 (350 ppm) present in the 1960s. Although a mapping population has been screened for salt tolerance as part of a NSF funded grant with UC Riverside that is linked with the other project plan at Dale Bumpers National Rice Research Center (DBNRRC), the objective to screen Oryza species and parents of mapping populations for seedling salt tolerance was not completed. It is expected by the end of the project plan significant accomplishments will be made in the objectives 1 and 2. Achieving the objectives 3 and 4 will depend on the filling of critical vacancies.

1. A new genetic resource for finding genes linked with disease resistance and agronomic traits in rice. Sheath blight is one of the most damaging diseases of rice in the southern U.S. and worldwide and it is managed primarily through the use of fungicides. ARS scientists at Stuttgart, Arkansas, released a population of over 500 breeding lines that were developed from the sheath blight resistant cultivar ‘Jasmine 85’, from the Philippines, crossed with the susceptible U.S. cultivar ‘Lemont’. This population has been used to identify sheath blight resistance genes and, because it is segregating for other agronomic traits, will be useful for developing new cultivars with improved disease resistance and agronomic traits.

2. Stacking resistance genes to protect rice plants from disease. Resistance genes in rice protect the plant from disease caused by the rice blast fungus. ARS scientists at Stuttgart, Arkansas, evaluated rice cultivars from the USDA National Small Grains Collection and found cultivars that possess two major blast resistance genes. When these genes are stacked together in one cultivar they provide resistance to a broad spectrum of isolates of the blast pathogen. Eight rice cultivars were identified that carry more than two blast resistance genes and will serve as useful breeding resources to improve blast resistance in rice cultivars in the U.S. and worldwide.

3. A new disease resistance gene is found that will protect rice production fields. Dee Geo Woo Gen (DGWG), a rice variety from Taiwan, carries one of the major sources of the semi dwarf gene which has been used to reduce the stature of rice and has played a critical role in the “green revolution”. ARS scientists at Stuttgart, Arkansas, identified a resistance gene to prevent the fungus that causes blast disease in DGWG and located this gene on rice chromosome 11. Further analysis revealed that this is a new source of disease resistance for breeders to use. In addition, genetic markers were found that are linked to the gene which will facilitate its use in marker assisted breeding. This will result in new cultivars that are less dependent on fungicide applications to have stable rice yields.

4. More than one way to evolve a weed. Weedy rice is biotype of cultivated rice that can infest production fields and reduce crop value. Understanding how weedy rice may respond to changing climate will benefit future weed control efforts. In collaboration with scientists at the University of Massachusetts and Washington University, ARS scientists at Stuttgart, Arkansas, identified genes for some weediness traits that were controlled either by single or multiple genes. These findings demonstrated that weedy rice possesses many gene combinations that facilitates its ability to adapt and suggests that weedy rice will continue to be a difficult problem to control even under a changing climate.

5. Novel blast resistance genes discovered in weedy red rice. Weedy red rice is a persistent weed in rice production fields and can reduce crop value. However, ARS scientists at Stuttgart, Arkansas, found that U.S. weedy rice can also be a source of new genes for controlling rice blast disease, which is a worldwide threat. Using DNA evaluation methods, 28 chromosomal regions were found that were linked with blast resistance from two sources U.S. weedy rice. Compared against other known resistance genes, it was found that some of these genes are novel and suggests that U.S. weedy will be useful for breeding new disease resistant rice cultivars for the U.S.

6. Disease resistance gene found in wild species of rice. In collaboration with scientists at Yunnan Agricultural University, China, ARS scientists at Stuttgart, Arkansas, examined the origins of disease resistance genes by taking a closer look at one major rice blast resistance gene, Pi-d2. DNA sequence variation of this gene was found in 35 cultivated rice, Oryza (O.) sativa, varieties and 6 wild species of rice. Pi-d2 was found in accessions of O. rufipogon, a putative progenitor of cultivated rice, suggesting that Pi-d2 originated in wild species of rice before the evolution and selection of cultivated rice. This study validated the theory that wild rice is a source of novel resistance genes to blast disease. These findings will help us discover critical DNA sequences of resistance genes and that can be used to develop novel rice cultivars that are naturally resistant to blast disease.

7. Evolution of a rice disease resistance gene. The Pi-ta gene has been effectively used to control rice blast disease in the southern U.S. and worldwide. In collaboration with scientists from the University of Nevada and the Noble Foundation, ARS scientists at Stuttgart, Arkansas, used a newly developed evolutionary statistical analysis method to understand selection and divergence of Pi-ta during crop domestication. Results suggest that Pi-ta may have recently appeared in U.S. cultivated rice and its weedy red rice variant either through evolution or human selection. Two regions of the Pi-ta gene that are critical for the disease resistance response were found among the domesticated cultivars but not in the wild species of rice. This information is critical for developing new disease resistance cultivars using the Pi-ta gene.

8. A wide range in weedy red rice flowering time may allow capture of genes from cultivated rice. Weedy red rice is a persistent weed in rice production fields due to seed shattering and dormancy, and because it is so genetically similar to cultivated rice, it has been impossible to control with herbicides. However, over the last decade herbicide resistant varieties of rice have been developed that allow excellent control of most weeds in production field. ARS researchers at Stuttgart, Arkansas, in collaboration with scientists at the University of Massachusetts and Washington University, examined the extent to which flowering time overlapped between cultivated rice and weedy red rice which could allow transfer of genes between the two. Flowering time was found to differ between two distinct weedy rice groups, such that straw-hulled (SH) weeds flower earlier and black-hulled awned (BHA) weeds flower later than cultivated rice. Comparing flowering differences between weedy rice groups and wild progenitor species of rice suggests that this trait evolved rapidly. From a weed management standpoint, there is potential for overlap in flowering of SH and BHA weeds and U.S. rice cultivars. This could potentially permit gene flow between herbicide resistant rice and weedy rice making weed control more difficult.

9. A more efficient means of breeding for increased grain yield in rice. A high yielding rice plant has a proper balance between the number of stems (tillers) produced and the number of seeds produced per tiller. Too few tillers will produce too few seed heads while too many tillers may divert energy and nutrients away from the developing grain. ARS researchers in Stuttgart, Arkansas, identified five chromosomal regions affecting tiller number (TN) at various plant growth stages in a genetic mapping population. Of these five, three also increased the number of seed heads per plant, and thus are the regions of most interest by rice breeders for producing cultivars with high grain yields. It was further determined that these three regions were associated with very rapid plant growth and very early initiation of tillering, both detectable in the first 2 weeks of plant growth. Breeders can use this information to indirectly select very early in the life cycle those plants most likely to develop increased seed heads and grain yield. Genetic markers linked to the desirable TN chromosomal regions can also be used for marker assisted selection by breeders developing new rice varieties.

10. Release of three high-tillering breeding lines for increasing rice yields. ARS researchers in Stuttgart, Arkansas, developed three germplasm lines useful for introducing a total of seven novel genes for improved tiller (the number of plant stems) production into U.S. breeding materials. These three germplasm lines each contain 3 to 5 genes responsible for the enhanced tillering found in a high-yielding rice cultivar from China. These genes are now combined with the long grain shape, improved milling quality, and the desired cooking quality required in U.S. rice cultivars. In addition to increased tillering, the three high-tillering germplasm lines also exhibit increased panicle number and grain yield and are in genetic background that is well adapted to U.S. production.

11. Controlling weedy red rice, an increasing constraint to global rice production. To meet increasing global demand for rice, production must increase under conditions of diminished natural resources and rising production costs. Key constraints such as limited availability of irrigation water and labor are a driving force for the transition from water/ transplanting to dry/direct seeding (DSR) planting systems, particularly in Asia. DSR can result in an increase in weed competition, particularly from red rice (or weedy rice), an aggressive weedy version of cultivated rice. ARS researchers in Beltsville, Maryland, and Stuttgart, Arkansas, collaborated with rice experts from four U.S. universities, and international institutions in Brazil and six other foreign countries to examine and review the key biological bases to the competitiveness of weedy red rice, including evolutionary, ecological, physiological, and genetic factors, and proposed a number of regional and global management strategies and research areas to improve weedy red rice detection and control.

12. U.S. weedy red rice can easily cross with cultivated rice making it more difficult to control. Red rice is a major weed problem in rice in the southern U.S. and can outcross with commercial cultivars forming new hybrid plants that are difficult to control in rice fields. Indica rice, a type of rice grown in tropical regions of Asia, has begun to be used in the U.S. in breeding programs and on organic rice farms, but little is known about its potential to outcross with weedy red rice biotypes in U.S. agroecosystems. Scientists with ARS in Stuttgart, Arkansas, and Fort Collins, Colorado, and with the University of Arkansas used DNA marker analysis to show that weedy red rice outcrossed to indica varieties at a rate only about one quarter that for the U.S. commercial variety, Kaybonnet. The difference was primarily due to differences in flowering synchronization between the weedy red rice and the cultivated rice, with Kaybonnet flowering synchronously with the red rice, and indica varieties flowering many days later. Seed production of the red rice was higher when grown next to the Kaybonnet than to the indica varieties, demonstrating that indicas were better competitors against red rice. These experiments showed for the first time that U.S. weedy red rice plants can be a pollen source for outcrossing to indica rice varieties as well as common commercial varieties and may result in the formation of potentially damaging red rice hybrid crosses in U.S. agroecosystems.

13. High yields under organic rice production practices – it’s all in the genes. There is an increasing demand for organic rice which is produced without the use of agricultural chemicals. However, organic rice yields tend to be much lower than rice produced using conventional practices. ARS researchers at Stuttgart, Arkansas, in collaboration with scientists at Texas A&M Agrilife, Beaumont, Texas, conducted studies to determine the impact of winter cover crops and applications of different rates of organic fertilizer products on grain yield and disease incidence. Over the three years of the study, no significant impact was observed on improving yields with these cultural practices. However, a reduction in disease incidence was observed with higher fertility rates. Selecting a cultivar that has high yield potential under organic production was far more important in assuring high yields than cultural management practices.

Review Publications
Li, J., Sun, Y., Liu, H., Wang, Y., Jia, Y., Xu, M. 2015. Natural variation of rice blast resistance gene Pi-d2. Genetics and Molecular Research. 14(1):1235-1249.
Jia, Y., Liu, G., Jia, M.H., McClung, A.M. 2014. Registration of a rice gene mapping population of Lemont X Jasmine 85 recombinant inbred lines. Journal of Plant Registrations. 9:128-132.
Amei, A., Lee, S., Mysore, K.S., Jia, Y. 2014. Statistical inference of selection and divergence of rice blast resistance gene Pi-ta. Genes, Genomes, Genetics. 4:2425-2432.
Thurber, C.S., Reagon, M., Olsen, K.M., Jia, Y., Caicedo, A.L. 2014. The evolution of flowering strategies in US weedy rice. American Journal of Botany. 101(10):1737-1747. doi:10.3732/ajb.1400154.
Liu, Y., Qi, X., Young, N.D., Olsen, K.M., Caicedo, A.L., Jia, Y. 2015. Characterization of resistance genes to rice blast fungus magnaporthe oryzae in a “Green Revolution” rice variety. Molecular Breeding. 35:52. DOI 10.1007/s11032-015-0256-y.
Simmonds, M.B., Anders, M., Adviento-Borbe, M.A., Van Kessel, C., Mcclung, A.M., Linquist, B.A. 2015. Seasonal methane and nitrous oxide emissions of several rice cultivars in direct-seeded systems. Journal of Environmental Quality. 44:103-114.
Wang, J., Correll, J.C., Jia, Y. 2015. Characterization of rice blast resistance genes in rice germplasm with monogenic lines and pathogenicity assays. Crop Protection. 72:132-138.
Liu, Y., Qi, X., Gealy, D.R., Olsen, K.M., Caicedo, A.L., Jia, Y. 2015. QTLs analysis for resistance to blast disease in US weedy rice. Molecular Plant-Microbe Interactions. p. 1-36.
Burgos, N.R., Singh, V., Tseng, T., Black, H.L., Young, N.D., Huang, Z., Hyma, K.E., Gealy, D.R., Caicedo, A.L. 2014. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice. Plant Physiology. 166:1208-1220.
Gealy, D.R., Burgos, N.R., Yeater, K.M., Jackson, A.K. 2015. Outcrossing Potential between U.S. Blackhull Red Rice and Indica Rice Cultivars. Weed Science. 63:647-657. DOI: 10.1614/WS-D-14-00150.1.
Ziska, L.H., Gealy, D.R., Caicedo, A.L., Gressel, J., Vidotto, F., Lawton-Raugh, A.L., Theisen, G., Norsworthy, J., Ferrero, A., Vidotto, F., Johnson, D., Ferreira, F.G., Marchesan, E., Menezes, V., Cohn, M.A., Burgos, N., Linscombe, S., Carmona, L., Tang, R., Merotto, Jr., A. 2015. Weedy (red) rice: An emerging constraint to global rice production. Advances in Agronomy. 129:181-228.
Qi, X., Liu, Y., Vigueira, C., Young, N., Caicedo, A.L., Jia, Y., Gealy, D.R., Olsen, K.M. 2015. More than one way to evolve a weed: parallel evolution of U.S. weedy rice through independent genetic mechanisms. Molecular Ecology. 24:3329–3344. DOI: 10.1111/mec.13256.
Eizenga, G.C., Jia, M.H., Pinson, S.R., Gasore, E.R., Prasad, B. 2015. Exploring sheath blight quantitative trait loci in a Lemont/O. meridionalis advanced backcross population. Molecular Breeding. 35(6):140. doi:10.1007/s11032-015-0332-3.