Resequencing Data Indicate a Modest Effect of Domestication on Diversity in Barley: A Cultigen With Multiple Origins

Abstract

The levels of diversity and extent of linkage disequilibrium in cultivated species are largely determined by diversity in their wild progenitors. We report a comparison of nucleotide sequence diversity in wild and cultivated barley (Hordeum vulgare ssp. spontaneum and ssp. vulgare) at 7 nuclear loci totaling 9296bp, using sequence from Hordeum bulbosum to infer the ancestral state of mutations. The sample includes 36 accessions of cultivated barley, including 23 landraces (cultivated forms not subject to modern breeding) and 13 cultivated lines and genetic stocks compared to either 25 or 45 accessions of wild barley for the same loci. Estimates of nucleotide sequence diversity indicate that landraces retain >80% of the diversity in wild barley. The primary population structure in wild barley, which divides the species into eastern and western populations, is reflected in significant differentiation at all loci in wild accessions and at 3 of 7 loci in landraces. "Oriental" landraces have slightly higher diversity than "Occidental" landraces. Genetic assignment suggests more admixture from Occidental landraces into Oriental landraces than the converse, which may explain this difference. Based on θπ for silent sites, modern western cultivars have ~73% of the diversity found in landraces and ~71% of the diversity in wild barley.

Molecular evidence of RNA polymerase II gene reveals the origin of worldwide cultivated barley

“…1). As we observed, previous studies also reported that a significant proportion of Western genetic composition appeared in Indian and East Asian barleys, and the Eastern alleles were also found in Occidental landraces253265. It was suggested that Central Asia is the sole route for wild barley migration between the Near East and the Tibetan Plateau32, as inferred in our haplotypes analysis; Hap1, Hap10 and Hap12 were shared among three wild barley populations and are most frequent in the Tibetan or Southwest Asian wild barleys, while rare in Central Asian wild barley population (Table 1; Fig.…”

“…Distinct genetic loci determining traits-brittle rachis were found in Eastern and Western barleys1821. The concept of polyphyletic domestication of cultivated barley was also bolstered by numerous genetic studies22232425. Recent resequencing data from multiple loci, for instance, proposed that barley has been domesticated at least twice in two locations, within the Fertile Crescent and at location 1,500–3,000 km farther East22.…”

“…Recent advances in the phylogenetic and domestication history analysis with specific resequencing on multiple loci have been widely available in many crops2536444546. However, not all genes reflect the history of a crop accurately.…”

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

“…spontaneum), the progenitor of cultivated barley, is a rich source of genetic diversity. Resequencing-based estimates indicate that barley landraces retain 80% and modern cultivars retain 71% of the diversity found in the wild (Saisho and Purugganan 2007;Morrell et al 2014). Despite low levels of outcrossing in both wild and cultivated barleys (0-2%) (Abdel-Ghani et al 2004), wild barley populations exhibit much lower LD than typical breeding populations (Morrell et al 2005;Caldwell et al 2006;Hamblin et al 2010).…”

A peacock’s tale: runaway agricultural evolution and the development of pre-pottery Neolithic communities in the southern Levant

“…Floral biology and degree of geographical overlap will affect frequencies of outcrossing. Barley's widespread distribution from northern Africa to the Himalayan foothills (see Zohary et al 2012:58) and favourable floral characteristics appear to have provided ample opportunities for introgression, with around 80% of wild barley genetic diversity retained in barley cultivars and landraces (Morrell et al 2014). Abbo et al (2009:44) argued that introgression between wild and domestic emmer wheat occurred on a more moderate scale, reflecting the more confined geographic distribution of wild emmer from Israel to the Iranian Zagros mountains, along the Fertile Crescent (see Özkan et al 2011:12-14;Zohary et al 2012:42).…”