Abstract
Although the plant lipidome show an enormous level of structural and functional diversity, our knowledge about its genetic control and its connection to whole-plant phenotypes is very limited. Here, we profiled 563 lipid species with UPLC-FT-MS in 289 field-grown inbred lines genotyped with 56,110 SNPs. Genome-wide association study identified 174 associations for 76 lipids explaining up to 31.4% of the genetic variance (P-value 8.4 × 10−18). Candidate genes were found for lipid synthesis, breakdown, transfer, and protection against peroxidation. The detected SNP-lipid associations could be grouped into associations with 1) individual lipids, 2) lipids from one biochemical class, and 3) lipids from several classes, suggesting a multilevel genetic control architecture. We further found a strong connection between the lipidome and agronomic traits in field-evaluated hybrid progeny. A cross-validated prediction model yielded correlations of up to 0.78 suggesting that the lipidome accurately predicts agronomic traits relevant in hybrid maize breeding.
Highlights
The plant lipidome show an enormous level of structural and functional diversity, our knowledge about its genetic control and its connection to whole-plant phenotypes is very limited
In Arabidopsis thaliana, most of the biochemical steps involved in lipid biosynthesis are known and the key genes have been identified, the regulation of the processes that results in the final lipid composition is only weakly understood
Quantitative genetic approaches have been followed more recently in Arabidopsis thaliana[10] and maize[11] to identify loci involved in storage oil formation; this analysis was limited to one class of lipids, i.e. triacylglycerides
Summary
The plant lipidome show an enormous level of structural and functional diversity, our knowledge about its genetic control and its connection to whole-plant phenotypes is very limited. We profiled 563 lipid species with UPLC-FT-MS in 289 field-grown inbred lines genotyped with 56,110 SNPs. Genome-wide association study identified 174 associations for 76 lipids explaining up to 31.4% of the genetic variance (P-value 8.4 3 10218). Quantitative genetic approaches have been followed more recently in Arabidopsis thaliana[10] and maize[11] to identify loci involved in storage oil formation; this analysis was limited to one class of lipids, i.e. triacylglycerides. Using UPLC-FT-MS, we measured 563 distinct leaf lipids in 289 diverse maize inbred lines genotyped with 56,110 SNPs. In addition we asked the question whether or not lipid profiles can be used for predicting general combining ability (GCA) of the parent lines reflecting the average performance of their hybrid progeny as previously successfully shown for primary metabolites[13]. GCA was estimated for four traits by crossing 285 lines from the Dent heterotic pool with two single-cross testers from the Flint heterotic pool and evaluating their testcross progeny in three locations over two years
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