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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Research Project #434318

Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

2018 Annual Report

1. Conserve, regenerate, characterize and expand rice germplasm and blast fungal collections to provide new genetic resources for rice research. 1A. Conserve and characterize the current NSGC rice collection through phenotypic and genotypic analysis to provide true to type and viable genetic resources for distribution to the research community. 1B. Determine the allelic value of Tropical japonica germplasm for improving US rice cultivars. 1C. Identify new sources of germplasm and associated alleles that result in increased grain yield under AWD management system and growing conditions of the southern U.S. 1D. Characterization of agronomic and physiological performance of weedy (red) rice germplasm biotypes in AWD management systems. 1E. Expand the NSGC collection with the development and characterization of an O. glaberrima/barthii and an O. rufipogon rice wild relative diversity panels and evaluate for agronomic and biotic stress tolerance traits. 1F. Characterize the rice blast fungus M. oryzae (Mo) collection for AVR genes and their response to changing climate and production practices. 2. Discover genomic regions and candidate genes/alleles associated with high yield, reduced environmental impacts, resistance to biotic and abiotic stresses, beneficial microbial interactions, and novel/superior grain qualities that are expressed across environments and management systems (GxExM) by developing and utilizing bioinformatics tools, high throughput phenotyping, and omics-driven analyses. 2A. Map QTLs for root architecture at the seedling stage… 2B. Identify QTL associated with quality production under AWD management… 2C. Evaluate three Chromosome Segment Substitution Line (CSSL) libraries… 2D. Fine map yield enhancing loci derived from O. rufipogon introgressions… 2E. Identify genomic regions associated with increased quality production in response to extremes in temperature. 2F. Identify genomic regions associated with increased quality production in response to biotic stress derived from O. sativa and its wild relatives. 2G. Fine-map and conduct candidate gene analyses for kernel fissure resistance (FR)… 2H. Identify genomic regions… 3. Identify optimum gene combinations using modeling of interactions between agronomic traits, reduced environmental impacts, biotic and abiotic stress tolerance, the plant-microbiome, and rice grain quality parameters that are expressed across environments and management systems (GxExM). 3A. Determine impact of reduced input systems on weed suppression. 3B. Identification and validation of effective QTLs for disease resistance… 3C. Determine the impact of AWD irrigation management… 3D. Determine the impact of abiotic stress… 4. Develop and deploy improved rice germplasm for production under existing and new management systems and for new market opportunities. 4A. Develop improved cultivars and germplasm for production in the southern U.S… 4B. Deploy yield enhancing loci derived from O. rufipogon introgressions… 4C. Determine if yield penalty is associated with disease resistance… 4D. Facilitate the development of new rice cultivars… Please see Project Plan for all listed Sub-objectives.

Rice is one of the most important cereal grains and it is important to sustain USA rice production for both domestic and global food security. A major challenge in rice production is diminishing irrigation resources. One approach being adopted uses alternate wetting and drying (AWD) irrigation that reduces water use by 20%. Yet there are many questions as to how to optimize quality production under this management system. In addition, record high temperatures during grainfill have resulted in yield and quality losses. This project will use genetic resources, genomic sequence data, and high throughput phenotyping to understand the genes and physiological processes that impact rice yield and quality under changing cultural practices and climates. The approach includes 1) exploring diverse genetic resources for novel traits and genes for developing improved rice cultivars that are resilient to changing climates and production practices, 2) identifying genes through mapping of quantitative trait loci (QTL), 3) identifying combinations of genes that result in increased yield and grain quality, and 4) developing and deploying unique combinations of genes in germplasm that will benefit the US rice industry. Central to the program is curation of the USDA’s world rice collection of over 19,000 cultivars. Subsets of this collection are used to create diversity panels that explore specific gene pools (e.g. O. glaberrima, O. rufipogon, Aus, etc.) for response to biotic and abiotic stresses. In addition, a collection of US rice blast (Magnaporthea oryzea) pathotypes will be evaluated for their ability to causes disease in response to different rice genotypes, management systems, and climatic environments (G x M x E). Segregating mapping populations developed from bi-parental matings and chromosome segment substitution lines (CSSLs) developed using wild species will be used to map QTL for response AWD and heat stress, yield production, disease resistance, kernel fissure resistance, and grain nutritional quality. Recombinant inbred lines (RILs) and CSSLs that possess QTLs for these traits will be used to determine which combinations of genes/QTLs provide the most robust response to production under systems using reduced inputs and having high disease and weed pressure as well as abiotic stresses such as drought and high temperatures. Although most of our previous research has focused on above ground traits, this project will include evaluation of root architecture traits and plant-soil-soil microbiome interactions that may be driving above ground phenotypes and responses. Outcomes from this research will include identification of unique germplasm, location of important QTLs, new methods for accurate and efficient phenotyping, and genetic markers linked to QTLs that can be used in marker assisted breeding. Our goal is to deploy improved germplasm that can be used directly as cultivars or as parental stocks in breeding programs that possess unique combinations of genes that provide high yield, superior milling and processing quality, are resilient to pest pressures and abiotic stress, and have unique nutritional quality that will result in high crop value.

Progress Report
This new project, initiated on March 25, 2018, has had modest progress made during the first four months. This project continues research from project 6028-21000-010-00D. Please see the report for project 6028-21000-010-00D for more information. Due to the Geneticist position being vacant, rejuvenation of National Small Grains Collection (NSGC) accessions was not attempted during the 2018 growing season. Exploring Tropical Japonica (TRJ) germplasm will identify new genes that will benefit U.S. rice breeding. Genotyping of 650 TRJ accessions was completed and bioinformatic analysis to identify an informative subset of 200 accessions for a TRJ diversity panel to mine alleles is underway. To identify genomic regions in U.S., germplasm that may be either beneficial or a genetic bottleneck, a set of 170 U.S. accessions, including founders, historic breeding lines, and modern varieties, were re-sequenced at greater than 30x coverage. Identity by descent (IBD) analysis is now underway. Double crosses between four TRJ varieties were used to develop a Multi-parent Advanced Generation InterCross (MAGIC) population composed of 800 DCF4 lines to develop new combinations of valuable alleles. To explore underutilized germplasm and identify genetic materials that can be a source of new genes for drought tolerance in rice, over 160 Aus varieties originating from drought prone areas were phenotyped in the greenhouse. Sixty of these accessions are being grown in a replicated field trial under water stressed conditions to determine germplasm and plant traits for further research. In addition, 28 weedy red rice lines and five rice cultivars are being compared in a field trial managed using alternate wetting and drying (AWD) and conventional flood. Weedy red rice may be more difficult to control if water saving rice production practices are used. However, they may also possess wild, undomesticated stress tolerance traits that would be beneficial in breeding. Recombinant inbred lines (192 RILs) from a Cybonnet/Saber mapping population are being grown under AWD to identify traits and genomic regions associated with water stress tolerance. Because this is a field study subjected to unpredictable levels of rain, two levels of AWD were implemented to assure a water stress treatment rather than one treatment being a conventional flood. Selected RILs from this year’s experiment will be tested next year under one level of AWD along with a flood treatment to validate drought tolerance/irrigation responsive RILs. A strong root system is key to rice productivity, competition with weeds, and efficient utilization of production inputs. Three mapping populations are being explored for differences in root traits. Phenotyping of root and shoot biomass was completed on 7 week old plants in a Francis/Rondo RIL population, root imaging completed on 80 PI312777/Katy RILs, and pure seed of the TeQing-into-Lemont (TIL) population is being produced for future evaluation. From the PI312777/Katy population, RILs are being evaluated for weed suppressiveness and associated physiological traits under AWD and flood irrigation and in a flood with weed-free or weedy conditions. Our research has shown root biomass is key to methane emissions in flooded rice fields. To better understand the relationships driving methane emissions, soil rhizospheric samples from 10 Francis/Rondo RILs segregating for methane and root biomass, were collected at four plant stages. Soil microbial DNA libraries were constructed and genome assembly and annotation are being performed. In addition to searching for genetic resources for abiotic stress tolerance, a diversity panel of the weedy rice ancestral species, O. rufipogon (O. nivara) and O. glaberrima, along with African cultivars, will be evaluated for novel blast and sheath blight disease resistance genes following seed increase in the winter greenhouse. In addition, an Advanced Backcrossing (ABC) population developed from TRJ/O. nivara is evaluated for sheath blight disease resistance in the field. To be able to develop rice varieties that are resistant to blast disease under changing environmental conditions and production methods, blast isolates from the southern U.S. in 2018 will be compared with isolates collected over the last 3 years to determine if the pathogen is changing. A panel of blast isolates representing the genetic diversity in the U.S. since 1960 was assembled and six isolates were selected to test a new method for high throughput phenotyping for resistance. Massive amounts of mycelia with spores will be used to infect rice lines with different combinations of blast resistance genes. To identify new blast resistance genes, a mapping population of 360 RILs from the cross of Minghui 63 (R) with M202 (S) was evaluated with six isolates and DNA will be extracted for genetic mapping. To identify effective blast resistance genes and germplasm under reduced water use, a panel of 150 rice germplasm lines with different combinations of resistance genes are being grown in field trials under different water management systems, in Puerto Rico, Louisiana and in Arkansas. Seed is being produced on 200 BC6F2s (Katy//M202) to determine if a yield penalty is associated with disease resistance. Three Cybonnet/Saber (C/S) RILS with Ptr but without Pita blast resistance genes are being evaluated for yield components with parental controls. To identify novel genes controlling yield, three mapping populations derived from crosses with three diverse O. rufipogon accessions are being evaluated. Yield component data was completed on two of the populations with the third evaluated this growing season. Previous research using a Jefferson/O. rufipogon backcross population identified large quantitative trait loci (QTL) associated with yield increases. Backcrossing is underway with three RILs, each having a different introgression, with plans to obtain segregating progeny that will be used for fine mapping of these regions. In addition, pairwise crosses using these same introgression lines were initiated to produce progeny with combined yield QTL. Some 70 potential parental lines developed at Dale Bumpers National Rice Research Center (DBNRRC) are being evaluated for yield, agronomic traits and above ground biomass in a field trial. These will later be evaluated for cold and salt tolerance along with markers associated with blast resistance and grain quality. The best parental lines for use in deployment of new genes/alleles identified in this project will be identified. Advanced selections (200) obtained from southern U.S. breeders and are being prepared for genetic marker analysis for grain quality, agronomic and disease resistance traits along with phenotypic physicochemical traits. In addition to improving the productivity of rice, research is being conducted to incorporate improved or novel qualities that will increase market value. Near infrared spectroscopic imaging is being tested as a high throughput phenotyping method for grain quality by scanning 1,600 mutant lines of cv. Katy. Grain samples are being prepared to obtain a far-infrared spectrum of the grain physicochemical profile. Imaging results will be compared with conventional physicochemical analyses as predictors of grain cooking and nutritional quality. Milling quality is a major determinant of rice crop value. To fine map QTLs associated with grain fissuring resistance (FR), approximately 10,000 informative SNPs surrounding five FR QTLs were identified. Kompetitive Allele Specific PCR (KASP) markers will be developed to detect additional recombination in the QTLs regions using 500 F5/6 RILs. Developing cultivars possessing grain quality traits that are resilient to climate fluctuations will help to ensure crop value. A study was initiated using growth chambers with two CO2 (400 and 600 ppm) levels and temperatures (27/22 and 33/28°C during grainfill stage) to assess seven RILs that possess a combination of four major genes resulting in differences in grain chalk. Physiological and agronomic traits will be evaluated to understand the temporal and spatial relationship of sink and source as it impacts grain quality. Soil nutrients impact grain nutritional value. F2 progeny from three mapping populations segregating for arsenic (As) and calcium (Ca) were used to identify offspring having very high versus low grain-As or grain-Ca. These progenies are being advanced to the F3 in the field to verify their phenotypic differences before using them for future mapping studies. In addition to traditional quality traits, the project aims to develop varieties that possess novel nutritional qualities. Using single seed descent (SSD), 800 F3 RILs were produced from a cross, IR36M4 x ‘242’, that is segregating for phytonutrients in pigmented bran and resistant starch in the endosperm. F4 seeds possessing colored bran were selected for breeding advancement and to combine these traits. This same cross is being used to study the genetic control of resistant starch. Using genetic markers linked to two genes involved in starch synthesis, four genotypic classes, beIIbWxa, BEIIbWxa, beIIbWxop, and BEIIbWxop were selected among the progeny and resistant starch concentrations determined. Currently, resistant starch also was measured in the F3 generation grains in two of these classes with the remaining two classes to be completed soon. Analysis of KatyM x IR36M4 progeny, where both parents have enhanced levels of resistant starch, identified two different resistant starch mutations exist in the parents, with the IR36M4 mutation mapping to a known starch branching gene (beIIb), and the KatyM mutation still being sought. The same four genotypic classes were identified in the F2 and F3 progeny and are currently planted in field plots to a) map the KatyM gene, and b) investigate the effect of variable amylose starch concentrations (controlled by the Wx locus) on resistant starch concentrations.