Product Line 2.2. Improved donors and genes/QTLs conferring valuable traits


Rice varieties in all environments require similar basic traits, especially good grain quality and resistance to diseases, nematodes, and insect pests. Breeding for resistance requires knowledge on resistance mechanisms, genetics, and epidemiology, to deploy efficient resistances that reduce crop losses (in yield and quality). There is an urgent need to broaden the gene pool of rice varieties through the transfer of genes from diverse sources. Advances in tissue culture, molecular markers, and genomics offer new potential to broaden the gene pool of rice by tapping the genetic variability hidden in the wild species and to further enhance the efficiency of alien gene introgression. Insect damage reduces yields in rice and causes farmers to use insecticides that are harmful to the environment and human health. For quantitative traits such as yield, many genes and many environmental factors collectively determine trait performance. Favorable alleles are likely to be spread across more than two lines, therefore requiring the assembly of alleles from different sources in a single inbred line in order to achieve significant improvement. In recurrent selection (RS), multiple genotypes are crossed and the resulting plants intercrossed to increase the chance of creating novel allelic combinations.

 Products and activities

2.2.1. Novel gene sources for breeding
New genes will be introduced from Oryza species through hybridization and backcrossing in elite parents. The favorable genes or alleles will be tagged with molecular markers for marker-assisted selection. African (O. glaberrima) strains will be used to developed stress-tolerant cultivars and develop new interspecific varieties containing greater and more targeted parts of the African rice genome, following on the successful NERICA varieties in Africa. Wild species of the AA genome will be used to introduce yield-enhancing genes into elite cultivars. Specialized genetic stocks will be developed.

2.2.2. Disease-resistant rice
The focus will be on blast, bacterial blight, rice yellow mottle virus (RYMV), tungro virus, brown spot, and sheath blight diseases. New universal genomics-based tools will be developed to characterize and understand the pathogen population structure of blast and bacterial blight. Disease-resistance loci will be identified for tungro virus. Epidemiology of brown spot resistance will be studied and resistance components will be quantified. Phenotyping methods for sheath blight resistance will be developed, resistance mechanisms clarified, and QTLs identified. Strengthening of partnerships and capacity development will be high priorities. New global research networks for addressing key rice diseases will be established as an important strategy for achieving stable disease resistance in rice.

2.2.3. Insect-resistant rice
A number of resistance genes/QTLs have been identified for resistance against planthoppers and leafhoppers. Varieties with resistance to and tolerance of stem borers in Asia have been identified. Sources of durable resistance against major Asian rice pests are available. Resistance screening (phenotyping) will need to be improved, but could also be expanded to determine broad-spectrum resistances (i.e., lepidopteran and diopsid stem borers). New knowledge-based screening methods will help devise better deployment strategies and develop pyramided product lines and seed mixes. IRRI’s experience and expertise in breeding for resistance can support initiatives in Latin America and Africa. Key products would include resistant and tolerant varieties tested against a broad range of insect pests and with associated knowledge-based deployment strategies. NILs and MAS can be used to strategically deploy genes with different modes of action in a multiline approach for mega-varieties and commercial hybrids.

2.2.4. Population improvement
About 100 lines will be identified as potential parents by group discussion (expert view), and genome-wide SSR profiles will be generated. Parental lines will be selected for the development of 10-parent recurrent selection (RS) populations (high yielding, wide adaptation, physiological trait-oriented, drought-prone lowland, and upland). The recessive male-sterile gene contained in the IR36 mutant and the dominant male-sterile gene contained in PXDMS will each be transferred into five parental lines. This is to increase the genetic potential of and genetic diversity among the male-sterile lines to be used in future recurrent selection (RS). Computer simulation experiments will be designed to investigate the effects of key factors on RS efficiencies such as heritability, crossing schemes including male-sterility-facilitated and manual crossing, selection intensity, etc. The results of these simulations will then be used to design more efficient RS schemes.

 Uptake and impact pathway

The next users for prebreeding products and genetic characterization are rice breeders working in GRiSP, the private sector, and NARES. Intermediate users are seed producers and marketers. Final users are farmers, who may also be next users when generated materials are released directly as varieties. There is an assumption that NARES scientists will have sufficient capacity and available resources to use new donors, breeding populations, and screening methods for new traits or resistance genes. Germplasm sources and information, as well as phenotyping methods, should be available from theme 1, and in some cases there will be linkage with management practices and epidemiology in theme 3.

 Financing strategy

Currently, this research is largely funded from unrestricted sources and various restricted grants of different length, including the Japan Rice Breeding project, BMGF-CSISA, ADB-Planthoppers, and Pioneer-SKEP. Additional annual funding of $1 million is needed over 5 years to support epidemiology and crop health research (personnel and equipment, partnerships).