Introduction

A key factor in the transition from hunting−gathering to settled food production was the cultivation and subsequent domestication of cereals, including wheat and barley (Zeder, 2008; Shewry, 2009). The earliest domesticated forms of wheat were the diploid einkorn, Triticum monococcum subsp. monococcum (genome AA) and the tetraploid emmer, T. turgidum subsp. dicoccum (genome AABB), derived from the wild relatives T. monococcum subsp. aegilopoides, and T. turgidum subsp. dicoccoides, respectively. Furthermore, domestication of tetraploid wheat eventually gave rise to the modern tetraploid crop, T. turgidum durum (pasta wheat) and, through hybridisation with Aegilops tauschii (genome DD), to the hexaploid wheats T. aestivum aestivum (bread wheat) and T. aestivum spelta (spelt). Barley, Hordeum vulgare, was also domesticated in the Fertile Crescent from the wild progenitor H. spontaneum and, together with wheat, represent the key founder crops on which western agriculture was built (Brown et al., 2009; Pankin and von Korff, 2017).

The group of traits that emerged during domestication by human selection, and can distinguish a crop from their wild progenitors, is known as the ‘domestication syndrome’. The term, coined by Hammer (1984), can include morphological, biochemical, developmental and physiological traits (Abbo et al., 2014). Some domestication traits are specific to particular ‘domesticated crop‐wild progenitor’ pairs, for example transformation from short and coarse fibres to long and fine ones during cotton domestication (Butterworth et al., 2009), or the increased seed capsule size found in domesticated poppies (Zohary et al., 2012). Other domestication traits are common across entire groups, such as reduced ear shattering in grasses or indehiscent pods in legumes (Zohary et al., 2012). Domestication syndrome traits are often disadvantageous in the wild, and individuals that possess these may succeed only under human management. For example, disarticulation of ears (‘shattering’) in wild grasses increases the area where spikelets might fall and germinate, but non‐shattering variants have arisen in numerous grain crops, presumably because they are easier for farmers to harvest (Doust et al., 2014).

Archaeobotanists often infer that the domestication status of cereal remains by establishing indehiscence of the ear or the rachis fragments (Brown et al., 2009; Tanno and Willcox, 2012). However, grains are much more frequently found in the archaeological record, especially from the period when agriculture emerged in the Fertile Crescent. In the absence of diagnostic rachis samples, the possibility of distinguishing wild and domesticated cereals based on grain size and shape is a contentious issue that affects discussions on the place(s) and pace of domestication (Zohary et al., 2012). From the analysis of archaeological grains, some authors agree that domestication led to an increase in wheat and barley grain size, independently from the evolution of rachis toughness (Nesbitt and Samuel, 1998; Fuller, 2007; Brown et al., 2009). Other authors have suggested that the overlap in sizes between archaeological and present‐day wild and domesticated cereal grains indicates that these traits diversified after domestication and a secure diagnosis cannot be made (Abbo et al., 2014). Identifying the morphological and genetic basis of domestication syndrome traits is a rich field of research, but it remains an open question whether there are traits that distinguish crops from their wild progenitors that have not yet been described (Stetter et al., 2017; Roucou et al., 2018).

Other important domestication syndrome traits in cereals include an increase in yield, reduction in seed dormancy, synchronous tillering and more compact growth (Fuller, 2007; Brown et al., 2009). Yield itself is a complex trait that can be decomposed into various components, such as seed size and seed number per plant. Increased seed number is mostly achieved by changing seed packing within the inflorescence and by increasing the number of fertile flowers (Preece et al., 2017, 2018). Increased seed size is thought to be a major contributor to the increased yield observed in domesticated cereals compared with their wild progenitors, often expressed as a ‘thousand grain weight’ measure (TGW) (Preece et al., 2017, 2018). An increase in the duration of growth, resource allocation to reproductive tissues and seed dimensions all contribute to grain size increase. Cultivation methods, such as tillage, are also thought to have contributed to grain size increases as bigger seeds could tolerate sowing at increased depths and therefore be selected for indirectly (Zohary et al., 2012). In addition, food processing methods may have led to selection for grains with bigger endosperm as they would be easier and more profitable to mill (Fuh et al., 2014). Alternatively, larger grains could have arisen via pleiotropic effects or genetic linkage and driven by selection that favoured larger organs and plants (Kluyver et al., 2017). Recently, the effect of grain size on harvestable yield has been noted in water‐limited environments (Rebetzke et al., 2016). Grain shape is associated with grain quality, endosperm characteristics and the ability to pack more grains per spikelet (Evers and Millar, 2002). However, in wheat, only a few previous studies have considered changes in grain shape as part of the domestication syndrome (Gegas et al., 2010). Consumer preference is also believed to have driven divergent selection in cereal species such as rice (Oryza sativa) in which long grain shape is preferred in India, while most Chinese varieties have smaller and rounder grains and recent research has suggested that this might also be true for wheat (Calingacion et al., 2014; Liu et al., 2016).

Phenotypic variation in wheat grain shape is surprisingly understudied, perhaps due to the difficulty in quantifying this trait using traditional imaging methods. Previous morphometric studies suggest that grain shape does indeed differ between wild and domesticated wheat and barley but they used destructive and laborious methods often focusing on single mapping populations (Giura and Saulescu, 1996; Campbell et al., 1999; Dholakia et al., 2003; Breseghello and Sorrells, 2007; Sun et al., 2009; Gegas et al., 2010; Williams and Sorrells, 2014; Bonhomme et al., 2016, 2017).

Originally developed as a medical diagnostic tool, X‐ray microcomputed tomography (μCT) is a non‐invasive imaging technique based on differential X‐ray attenuation due to material composition and density. The ability to provide an accurate three‐dimensional (3D) representation and quantification of internal structures in a non‐invasive and non‐destructive way, combined with partial or full automation, means that μCT is a useful tool for studying complex plant morphology. High‐resolution μCT has been successfully used to analyse various plant traits as well as environmental responses (reviewed in Dhondt et al., 2010). We have recently shown that using μCT scanning of ripe wheat spikes, combined with an image analysis pipeline, we can accurately extract and measure grain and spike parameters (Strange et al., 2015; Hughes et al., 2017). In addition to length and width, which can be acquired from photography and flat‐bed scanning, μCT acquires depth, volume and other information that, combined, can provide a more complete description of grain size and shape variation.

In this study, we use μCT analysis to measure differences in cereal grain size and shape between different wild and domesticated cereals. We describe that grain shape changed between domesticated and wild taxa and that the major change was an increase in grain depth. Grain width also increased, but to a lesser extent, while minimal changes in grain length were detected. Grain shape, therefore, seems to be an important component of grain shape changes during domestication. We developed a model able to, for a given species, classify the domestication status of grain samples of a certain taxa. Finally, examination of a panel of 14 diverse European bread wheat varieties, which represent the founders of a diverse multiparent advanced generation intercross mapping population (Cockram and Mackay, 2018), indicates that grain depth remains a variable and plastic trait even in modern cultivars.