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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Unraveling the rich phenotypic and genetic diversity in rice for varietal improvement

item Eizenga, Georgia
item McClung, Anna
item McClung, Anna
item Mccouch, Susan -
item Ali, Liakat -
item Imai, Ize -
item Kim, Hyunjun -
item Prasad, Bishwajit -
item Ahn, Sang-Nag -

Submitted to: Proceedings 8th SABRAO Congress
Publication Type: Proceedings
Publication Acceptance Date: December 20, 2011
Publication Date: December 12, 2012
Citation: Eizenga, G.C., Mcclung, A.M., Mccouch, S., Ali, L.M., Imai, I., Kim, H., Prasad, B., Ahn, S. 2012. Proceedings of the 12th SABRAO Congress on Plant Breeding towards 2025: Challenges in a Rapidly Changing World. 23-24.

Technical Abstract: Asian cultivated rice (Oryza sativa L.) has two distinct varietal groups identified as the indica and japonica subspecies. With the advent of molecular markers the indica subspecies was divided into the indica and aus subpopulation groups and the japonica subspecies into the aromatic, tropical japonica and temperate japonica subpopulation groups. The wild species progenitor of O. sativa is O. rufipogon Griff. (O. nivara Sharma et Shastry). A multitude of traits important in agronomic improvement have been identified in accessions of O. rufipogon, O. nivara and other closely related species. To explore the genetic potential of the rich diversity found in rice we assembled a Rice Diversity Panel consisting of 413 O. sativa accessions. Using this panel, an association mapping study was conducted based on 44,100 SNP (single nucleotide polymorphism) markers and 34 agro-morphological and grain quality traits. Several marker-trait associations unique to particular subpopulations were identified, and SNPs associated with QTL and functional genes affecting agronomically important traits. The usefulness of O. rufipogon (O. nivara) for improving sheath blight resistance and enhancing yield in cultivated rice was demonstrated utilizing advanced backcross (ABC) mapping populations. QTL mapping in two different Bengal x O. nivara ABC populations where the O. nivara accessions were sheath blight resistant, revealed seven significant sheath blight QTL on chromosomes (chr.) 1, 3, 5, 6, 9 and 10. The QTL on chr. 6 was the most significant and located in the same region as a QTL for days to heading, suggesting the longer period of time to maturity may be confounding the sheath blight ratings by making the plants appear more resistant to disease. A major QTL for plant height was noted on chr. 1 in the region of sd-1 and for plant type on chr. 9 in the region of a gene for tiller angle (TAC1). Sixty-two introgression lines (ILs) selected from the Jefferson x O. rufipogon ABC population and four commercial check cultivars were grown in replicated yield trials across two years in four locations in the southern USA. These ILs contained target introgressions from O. rufipogon at yield-related QTL on chr.1, 2, 3, 6, 8, and 9. The highest yielding families carried introgressions on chr. 2 and chr. 6. These ILs out-yielded the Jefferson parent by >20%. To further explore the transgressive variation observed, inter-specific chromosome segment substitution lines (CSSL) libraries are being developed using three genetically diverse O. rufipogon (O. nivara) accessions as donor parents. These donors were crossed to both parents: the indica cultivar, IR64, developed by IRRI, and the U.S. tropical japonica cultivar, Cybonnet. Once developed, these CSSLs will be used to explore the value of diverse O. rufipogon alleles in elite O. sativa backgrounds, dissect complex quantitative trait variation, and explore the genetic basis of transgressive variation.

Last Modified: 12/21/2014