Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights

Abstract

Plants produce a variety of metabolites that have a critical role in growth and development. Here we present a comprehensive study of maize metabolism, combining genetic, metabolite and expression profiling methodologies to dissect the genetic basis of metabolic diversity in maize kernels. We quantify 983 metabolite features in 702 maize genotypes planted at multiple locations. We identify 1,459 significant locus–trait associations (P≤1.8 × 10−6) across three environments through metabolite-based genome-wide association mapping. Most (58.5%) of the identified loci are supported by expression QTLs, and some (14.7%) are validated through linkage mapping. Re-sequencing and candidate gene association analysis identifies potential causal variants for five candidate genes involved in metabolic traits. Two of these genes were further validated by mutant and transgenic analysis. Metabolite features associated with kernel weight could be used as biomarkers to facilitate genetic improvement of maize.

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

“…Moreover, 788 novel genes (33.46%) were associated (P < 4.25E-4, 1/n) with 487 metabolic traits measured in maize kernels (Table S9, Wen et al 2014), which implied that those novel genes could play more complex roles within cellular metabolism processes; thus, this study provides fresh resources for the genetic study of maize kernel quality and production. Metabolic processes are commonly controlled by transcription regulation.…”

Evolutionarily Distinct BAHD N-acyltransferases are Responsible for Natural Variation of Aromatic Amine Conjugates in Rice

“…Spermidine hydroxycinnamoyl transferases responsible for the production of hydroxycinnamoyl spermidines have been identified in Arabidopsis, Nicotiana attenuata, and rice (Grienenberger et al, 2009;Luo et al, 2009;Onkokesung et al, 2012;Dong et al, 2015). More recently, PHTs (putrescine hydroxycinnamoyl transferases) have been identified in both dicots (Nicotiana) and monocots such as maize and rice (Onkokesung et al, 2012;Wen et al, 2014;Chen et al, 2014). Interestingly, the BAHD enzymes HCBT from Dianthus caryophyllus and HHT (hydroxycinnamoyl-CoA:hydroxyanthranilate N-hydroxycinnamoyltransferase) from oat (Avena sativa), have also been reported to catalyze the acylation of arylmonoamines, anthranilate and 5-hydroxyanthranilate, respectively (Yang et al, 1997;Ishihara et al, 1998).…”

“…As an initial step to understand the genetic determinants of PAs, we focused on the possible role of acylation, the final and key step in PA biosynthesis, by looking for BAHD acyltransferases within the confidence intervals of the identified loci (Grienenberger et al, 2009;Luo et al, 2009;Onkokesung et al, 2012;Wen et al, 2014). Eleven candidate genes that were made up of five tandem pairs were assigned to the loci identified, with two of them having been partially characterized in a previous study (Figures 3 and 4B;Chen et al, 2014).…”

“…To this end, Os04g56900 for agmatine acyltransferase, Os09g37180 for putrescine acyltransferase, and Os-TBT1 (wide substrate specificity) and Os-TBT2 (narrow substrate specificity) for tryptamine/serotonin acyltransferase were selected. Considering the redundancy and close linkage between the two members of each tandem pair, we adopted the gain-of-function strategy to establish their in vivo functions, by overexpressing each of them individually in ZH11, which has been widely used as a host in rice transformation and in previous work on PAs in rice Wen et al, 2014;Dong et al, 2015), under the control of the maize ubiquitin promoter. PA-targeted profiling was performed by LC-MS to determine the differences in the quantity and profiles of PAs between the wild type and the transgenic lines for each individual construct.…”

“…Eleven rice phenolamides in this study refer to different combinations of CoA-thioesters and amine moieties. combined metabolite-based linkage and association studies have provided powerful forward-genetic strategies for dissecting the genetic and biochemical bases of metabolism in plants (Riedelsheimer et al, 2012;Gong et al, 2013;Chen et al, 2014;Wen et al, 2014Wen et al, , 2015Alseekh et al, 2015;Matsuda et al, 2015). As for the BAHD family of enzymes in rice, OsAT1 has been reported to be involved in responses to rice blight and blast (Mori et al, 2007).…”