Abstract
Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.
Highlights
It will be important to assess the ability of these loci to control Carbon/Nitrogen partitioning at both the whole plant and field level to test if they can be utilized in agronomic settings. Expanding these results will require the development of additional populations that are larger and include reciprocal crosses
The plants were watered twice a week with nutrient water prepared by UC Davis Research Greenhouses throughout the following study
Expanding these results will require the development of additional populations that are larger and include reciprocal crosses
Summary
Growth of the Lemont × Teqing Rice RIL population.Seeds of the 280 lines of the Lemont ×TeqingRice recombinant inbred population together with parent lines were obtained[25]. The LT-RILs and the parental genotypes were grown in two separate experiments in the fall of 2011 within a greenhouse at the University of California, Davis. Two plants per LT-RIL line and two plants per each parental genotype were grown with one plant per each of two randomized complete blocks. This provides four independent replicates for most of LT-RIL lines, and each of the parental genotypes. We placed approximately 3–5 seeds from each line in the center of a pot and thinned the plants to leave one seedling per pot one week after sowing. No boron was added to the irrigation water as there is sufficient boron in the potting soil and water in the facility (http://greenhouse.ucdavis.edu/research/ materials/mediafert.html)
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