Molecular Phylogeography of Domesticated Barley Traces Expansion of Agriculture in the Old World

Abstract

Barley (Hordeum vulgare ssp. vulgare) was first cultivated 10,500 years ago in the Fertile Crescent and is one of the founder crops of Eurasian agriculture. Phylogeographic analysis of five nuclear loci and morphological assessment of two traits in >250 domesticated barley accessions reveal that landraces found in South and East Asia are genetically distinct from those in Europe and North Africa. A Bayesian population structure assessment method indicates that barley accessions are subdivided into six clusters and that barley landraces from 10 different geographical regions of Eurasia and North Africa show distinct patterns of distribution across these clusters. Using haplotype frequency data, it appears that the Europe/North Africa landraces are most similar to the Near East population (FST = 0.15) as well as to wild barley (FST = 0.11) and are strongly differentiated from all other Asian populations (FST = 0.34–0.74). A neighbor-joining analysis using these FST estimates also supports a division between European, North African, and Near East barley types from more easterly Asian accessions. There is also differentiation in the presence of a naked caryopsis and spikelet row number between eastern and western barley accessions. The data support the differential migration of barley from two domestication events that led to the origin of barley—one in the Fertile Crescent and another farther east, possibly at the eastern edge of the Iranian Plateau—with European and North African barley largely originating from the former and much of Asian barley arising from the latter. This suggests that cultural diffusion or independent innovation is responsible for the expansion of agriculture to areas of South and East Asia during the Neolithic revolution.

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

“…The spatial genetic structure of extant barley has been described earlier both on a worldwide scale (Malysheva-Otto et al, 2006;Saisho and Purugganan, 2007) and across Europe (Jones et al, 2011 using microsatellite markers. With only 14 microsatellite markers genotyped in landrace barley from historical seed collections, Leino and Hagenblad (2010) were able to show geographic structuring in barley on a much finer scale-within Sweden.…”

“…Phylogeographic studies of landrace crops have often been restricted to single individuals (for example, Saisho and Purugganan, 2007;Isaac et al, 2010;Van Heerwaarden et al, 2011) or aggregate samples from accessions, using pooling schemes (for example, Hunt et al, 2011;Jones et al, 2011;Oliveira et al, 2012). This allows a much higher number of accessions to be studied, but comes at the cost of ignoring within-accession genetic diversity.…”

“…Geographic patterns in the distribution of genetic diversity can give information about the geographic origin of lineages or the effects of migration routes (Avise, 2009) and have, among other species, been applied to crop plants (for example, Olsson and Schaal, 1999;Londo et al, 2006;Saisho and Purugganan, 2007). Insights into the genetic structure of crop species provide not only a better understanding of their evolutionary history but can also increase the knowledge about cultural exchange in agrarian communities (Van Heerwaarden et al, 2011;Oliveira et al, 2012;Roullier et al, 2013).…”

“…vulgare) was domesticated about 10 000 years ago (Badr et al, 2000), most likely from multiple domestication centers (Morrell and Clegg, 2007;Saisho and Purugganan, 2007;Fuller et al, 2011;Ren et al, 2013). An adaptable species, barley has been of great importance also in regions where climate or soil is sub-optimal for agriculture.…”

Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway

“…11, based on molecular variation of a marker tightly linked to the nud locus, suggested the monophyletic origin of naked barley, but the issue remains unsolved yet. Recent comprehensive molecular evolutionary studies on the barley crop as a whole favor the interpretation of multiple domestication events at different locations (12,13).…”