Metabolome dynamics during wheat domestication

Abstract

One of the most important crops worldwide is wheat. Wheat domestication took place about 10,000 years ago. Not only that its wild progenitors have been discovered and phenotypically characterized, but their genomes were also sequenced and compared to modern wheat. While comparative genomics is essential to track genes that contribute to improvement in crop yield, comparative analyses of functional biological end-products, such as metabolites, are still lacking. With the advent of rigorous mass-spectrometry technologies, it is now possible to address that problem on a big-data scale. In attempt to reveal classes of metabolites, which are associated with wheat domestication, we analyzed the metabolomes of wheat kernel samples from various wheat lines. These wheat lines represented subspecies of tetraploid wheat along primary and secondary domestications, including wild emmer, domesticated emmer, landraces durum, and modern durum. We detected that the groups of plant metabolites such as plant-defense metabolites, antioxidants and plant hormones underwent significant changes during wheat domestication. Our data suggest that these metabolites may have contributed to the improvement in the agricultural fitness of wheat. Closer evaluation of specific metabolic pathways may result in the future in genetically-engineered high-yield crops.

Figure 1

Three-dimensional models of principal component analyses (PCA). Each ball represents a quantile-normalized metabolome of one wheat line replica sample. (A) Embryo metabolomes—two perspectives. (B) Endosperm metabolomes—two perspectives. The dashed circles surround distinct groups of wheat metabolomes. WEW—wild emmer; WED (PE)—primitive emmer; LD—landraces durum; MD—modern durum. (C). Evolutionary history of allotetraploid and allohexaploid wheat: Diploid wheats (2n = 2 ×  = 14), from the Tritcum-Aegilops group have diverged ~ 4Mya from a diploid progenitor whose genome is indicated here as PP. Intergeneric hybridization between the diploid T. urartu (genome AA) as male and the donor of BB genome as female, (an unknown species similar to Ae. speltoides), followed by chromosome doubling, gave rise (~ 0.5Mya) to the wild allotetraploid wheat, Triticum turgidum, ssp. dicoccoides (genome BBAA, 2n = 4 ×  = 28), the direct progenitor of durum and bread wheat. Domestication of allotetraploid wheat took place ~ 10,500 years ago and was followed by a second round of intergeneric hybridization chromosome doubling between domesticated allotetraploid wheat and the donor of the D genome, Ae. Tauschii (2n = 2 ×  = 14, genome DD), giving rise, ~ 9000 years ago, to bread wheat, an allohexaploid (2n = 6 ×  = 42, genome AABBDD).

Figure 2

Comparative metabolomics. Identified metabolites that underwent significant changes in association with wheat domestication. Each metabolome is a result of group-averaged metabolite values from all the replicas and wheat lines that belong to that group. A statistical comparison is made between each pair of groups from a total of 4 groups: WEW—wild emmer; WED (PE)—primitive emmer; LD—landraces durum; MD—modern durum. (A,C) Comparison of embryo metabolomes. (B,D) Comparison of endosperm metabolomes. (A-B) Small pie charts—comparisons between the WE group and the LD/MD groups. Metabolites that underwent a significant increase or decrease in two comparisons (WE to LD and WE to MD). Variable metabolites either did not undergo statistically significant changes or did not increase or decrease in both comparisons. Large pie charts—comparisons between the WE, PE group and the LD/MD groups. Metabolites that underwent a significant increase or decrease in three comparisons (WE to PE, PE to LD and PE to MD) were considered to be steadily changed metabolites. Conserved metabolites did not undergo any statistical changes in any comparison. Variable metabolites did not undergo a steady increase or a steady decrease in all three comparisons. (C-D) Venn diagrams depict the numbers of statistically changed metabolites in the following comparisons: WE to PE, PE to both LD and MD, and WE to both LD and MD, and steadily changed metabolites. Increased metabolites on the left and decreased metabolites on the right.

Figure 3

Categories of biological function. Embryo metabolomes. Identified metabolites that underwent a significant increase in association with wheat domestication (WE to LD and MD) were classified according to chemical structure and biological function. (A) Metabolites that are involved in plant defense mechanisms. (B) Metabolites that are known to be antioxidants. (C) Plant hormones and their intermediates. (D) Proteinogenic amino acids.

Figure 4

Volcano plots were generated based on comparative metabolomics between the average embryo metabolomes of each group (only identified metabolites, see also Fig. 3). WEW—wild emmer; DEW—primitive emmer; LD—landraces durum; MD—modern durum. All the metabolites that are above the horizontal line of p < 0.05 were considered significant. Red rectangles insets—the most significantly changed metabolites are shown in Tables S1 and S2.