title: An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci.
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.
authors.affiliation: Department of Plant Sciences, University of California, Davis, One Shield Avenue CA 95616, USA.
authors.forename: Baohua
authors.initials: B
authors.lastname: Li
authors.affiliation: Department of Plant Sciences, University of California, Davis, One Shield Avenue CA 95616, USA.|Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.|National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
authors.forename: Seyed Abolghasem
authors.initials: SA
authors.lastname: Mohammadi
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.|National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Dongxin
authors.initials: D
authors.lastname: Huai
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yongming
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Plant Sciences, University of California, Davis, One Shield Avenue CA 95616, USA.|DynaMo Center of Excellence, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Kliebenstein
mesh_terms: D002244:Carbon / Q000378:metabolism*; D017343:Genes, Plant; D055432:Metabolomics; D009584:Nitrogen / Q000378:metabolism*; D012275:Oryza / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D040641:Quantitative Trait Loci; D013269:Stochastic Processes
chemical_list: D002244:Carbon; D009584:Nitrogen