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μCT Trait Analysis Reveals Morphometric Differences Between Domesticated Temperate Small Grain Cereals and Their Wild Relatives

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μCT Trait Analysis Reveals Morphometric Differences Between Domesticated Temperate Small Grain Cereals and Their Wild Relatives

Nathan Hughes et al. Plant J.

Abstract

Wheat and barley are two of the founder crops domesticated in the Fertile Crescent, and currently represent crops of major economic importance in temperate regions. Due to impacts on yield, quality and end-use, grain morphometric traits remain an important goal for modern breeding programmes and are believed to have been selected for by human populations. To directly and accurately assess the three-dimensional (3D) characteristics of grains, we combine X-ray microcomputed tomography (μCT) imaging techniques with bespoke image analysis tools and mathematical modelling to investigate how grain size and shape vary across wild and domesticated wheat and barley. We find that grain depth and, to a lesser extent, width are major drivers of shape change and that these traits are still relatively plastic in modern bread wheat varieties. Significant changes in grain depth are also observed to be associated with differences in ploidy. Finally, we present a model that can accurately predict the wild or domesticated status of a grain from a given taxa based on the relationship between three morphometric parameters (length, width and depth) and suggest its general applicability to both archaeological identification studies and breeding programmes.

Keywords: X-ray microcomputed tomography; barley; domestication; grain traits; phenomics; wheat; μCT.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
3D visualization of reconstructed μCT images, whole spike (left panels) and representative isolated grains (right panels). (a) wild einkorn, (b) einkorn, (c) wild emmer and (d) emmer. See Movies [Link], [Link], [Link], [Link] for animated gifs of reconstructed spikes.
Figure 2
Figure 2
Relationship between domestication status and morphometric trait variation of wild (red boxes, 237 grains) and domesticated (blue boxes, 513 grains) einkorn wheat. Horizontal lines in boxplots represent median, boxes indicate the upper and lower interquartile range, whiskers indicate the largest and smallest values within 1.5 times the interquartile range and points indicate outliers outside this range for grain volume (a), length (b), width (c), depth (d), surface area (e) and surface area to volume ratio (f). Asterisks indicate that the values are significantly different at P < 0.01, ns, not significant.
Figure 3
Figure 3
Principal component analysis of grain traits obtained by 3D μCT analysis for wild (red circles, n = 237) and domesticated (blue circles, n = 513) einkorn wheat, with two times standard deviation outlined. The first two principal components are shown.
Figure 4
Figure 4
Grain trait analysis of wild (red boxes, 34 grains) and domesticated (blue boxes, 122 grains) emmer wheat. Horizontal lines in boxplots represent the median, boxes indicate the upper and lower interquartile range, whiskers indicate the largest and smallest values within 1.5 times the interquartile range and points indicate outliers outside this range for grain volume (a), length (b), width (c), depth (d), surface area (e) and surface area to volume ratio (f). Asterisks indicate that the values are significantly different at P < 0.01, ns, not significant.
Figure 5
Figure 5
Morphometric changes in wheat grain traits across ploidy and domestication status (wild – red boxes, domesticated – blue boxes). Horizontal lines in boxplots represent median, boxes indicate the upper and lower interquartile range, whiskers indicate the largest and smallest values within 1.5 times the interquartile range and points indicate outliers outside this range for grain volume (a), length (b), width (c), depth (d), surface area (e) and surface area to volume ratio (f). Letters above the boxes indicate significance groups at P < 0.01.
Figure 6
Figure 6
Analysis of grain trait changes associated with barley domestication. (a) 3D reconstruction of representative wild (left) and domesticated (right) barley grains. Grain traits measured were volume (b), length (c), width (d), depth (e) and surface area to volume ratio (f). Horizontal lines in boxplots represent median, boxes indicate the upper and lower interquartile range, whiskers indicate the largest and smallest values within 1.5 times the interquartile range and points indicate outliers outside of this range (red boxes − wild, 49 grains; blue boxes − domesticated, 141 grains). Asterisks indicate that the values are significantly different for P < 0.01.
Figure 7
Figure 7
Modelling the domestication status of einkorn wheat grains. Multiple regression model shows the predicted (y axis) and actual (wild − red circles and domesticated − blue circles) domestication status of einkorn with an R 2 value of 0.95 for 750 individual grains analysed.

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