Project Number: 6203-21220-001-00
Project Type: Appropriated

Start Date: Jun 23, 2008
End Date: Jun 22, 2013

Objective:
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 US 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.

Approach:
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 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 (11 degC) 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 be 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.