SignificanceRice architecture is an important agronomic trait for determining yield; however, the complexity of this trait makes it difficult to elucidate the molecular mechanisms. This study applied a strategy of using principal components (PCs) as dependent variables for a genome-wide association study (GWAS). SPINDLY was identified to regulate rice architecture by suppressing gibberellin (GA) signaling. Further study using GA-signaling mutants confirmed that levels of GA responsiveness regulate rice architecture, suggesting that the utilization of a favorable SPINDLY allele will improve crop productivity. The strategy presented in this study of performing GWAS using PC scores will provide valuable information for plant genetics and will improve our understanding of complex traits at the molecular level.
Inefficient use of phosphorus (P) in agriculture adds to production costs, increases the risk of eutrophication of waterways, and contributes to the rapid depletion of the world's non-renewable rock phosphate supplies. The removal of large quantities of P from fields in harvested grains is a major driver in the global P cycle, but opportunities exist to reduce the amount of P in harvested grains through plant breeding. Using rice (Oryza sativa L.) as a model crop, we examine our current understanding of the process of P loading into grain and its regulation by genetic and environmental factors. We expose a dearth of knowledge on the physiological processes involved in loading P into grains, poor resolution of the genes and networks involved in P mobilization from vegetative tissues to grains, and limited understanding of genetic versus environmental contributions to variation in grain P concentrations observed among genotypes. We discuss potential breeding strategies and highlight key research gaps that should be addressed to facilitate these breeding approaches. Given the strong economic and environmental incentives for a low grain P trait, we suggest that some of the investment and resources currently directed to determining the molecular regulation of P starvation responses in model plant species should be diverted to resolving the physiology, genetics, and molecular regulation of P loading into cereal grains.
Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome-wide association study using an indica-predominant diversity panel, we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS-11, was associated with a 32.4% increase in lateral root number. The locus was validated in independent backgrounds, and a predicted glycosyl hydrolase, TIPS-11-9, was identified as the causal gene for observed phenotypic differences. TIPS-11-9 was differentially expressed in emerging lateral roots of contrasting qTIPS-11 haplotypes, which was likely due to differences in cis-regulatory elements and auxin responsiveness. Abolishment of Tips-11-9 function through T-DNA insertion in a qTIPS-11-positive background resulted in a reduction of lateral root number, which negatively affected biomass accumulation, particularly under phosphorous-limiting conditions. Marker-assisted introgression of qTIPS-11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia.
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