Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2018
Publication Date: 11/15/2018
Citation: Huggins, T.D., Chen, M., Fjellstrom, R.G., Jackson, A.K., McClung, A.M., Edwards, J. 2018. Association analysis of three diverse rice (Oryza sativa L.) germplasm collections for loci regulating grain quality traits. The Plant Genome. https://doi:10.3835/plantgenome2017.09.0085.
Interpretive Summary: The value of rice (Oryza sativa L.) for producers and consumers is dependent on grain quality. In rice, a broad range of traits determine grain quality including grain shape, translucency, milling yield, cooking characteristics, sensory traits, and nutritional aspects. US rice germplasm collections contain a diversity of rice with a tremendous range in grain quality traits. To better understand the genetics of rice grain quality, globally diverse rice varieties were evaluated for molecular markers and grain quality traits. The analysis identified genes and new sources of variation for improving sensory traits, cooking quality, and translucency. The results will be used to develop molecular markers to accelerate breeding efforts to create new rice varieties with superior grain quality. This will contribute to increasing the economic value of US rice.
Technical Abstract: In rice (Oryza sativa L.), end-use/cooking quality is vital for producers and millions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality, will provide vital information to enhance desirable traits while reducing the impact of unfavorable environmental conditions through improved breeding strategies. Genome-wide association (GWA) analysis of three rice diversity panels, USDA rice core subset (1,364 accessions), mini-core (203 accessions) and HDRA-mini-core (383 accessions), using simple sequence repeats and/or single nucleotide polymorphic markers revealed large and small effect loci associated with known genes and previously uncharacterized regions. Clustering of significant regions from GWA results suggests that multiple grain quality traits are influenced together. The 11 novel candidate loci for grain starch traits and 7 candidates for grain chalk identified are involved in the starch biosynthesis pathway. This study highlights the intricate pleiotropic relationships that exist in complex genotypic-phenotypic associations.