Project Number: 6028-21220-005-00-D
Project Type: In-House Appropriated

Start Date: Jul 10, 2013
End Date: Mar 25, 2018

Objective:
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

Approach:
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.