Abstract
The origin and domestication of cultivated barley have long been under debate. A population-based resequencing and phylogenetic analysis of the single copy of RPB2 gene was used to address barley domestication, to explore genetic differentiation of barley populations on the worldwide scale, and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation. Our results revealed significant genetic differentiation among three geographically distinct wild barley populations. Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau, supporting polyphyletic origin of cultivated barley. The results of haplotype frequencies supported multiple domestications coupled with widespread introgression events that generated genetic admixture between divergent barley gene pools. Our results not only provide important insight into the domestication and evolution of cultivated barley, but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations, thus further facilitating the effective use of the wild barley germplasm.
Highlights
Barley is one of the oldest, most widely distributed, extensively cultivated, and economically important crops
A total of 21 haplotypes were identified in the 88 wild barley accessions, of which 18 haplotypes were identified in the Southwest Asian, 5 in the Central Asian and 4 in the Tibetan wild barley populations
Distributional, archaeological, cytogenetic, and isozyme studies have demonstrated that Tibetan wild barley was different from the Fertile Crescent samples[33], which was supported by the genome-wide Diversity array technology (DArT) data[32], transcriptome profiling[34], and population-based genetic diversity analysis[35]
Summary
Barley is one of the oldest, most widely distributed, extensively cultivated, and economically important crops. Diversity array technology (DArT) data and population-based phylogenetic analyses indicated that the Tibetan Plateau and its vicinity is one of the domestication centers of cultivated barley[32,33]. Recent transcriptome profiling and population-based genetic diversity analysis provided strong evidence that barley domestication may have occurred independently in geographically distinct regions[34,35]. Additional evidence is still needed to shed further light on cultivated barley domestication, in particular, the position of Qinghai-Tibet Plateau wild barley in origin and domestication events. Recent advances in the phylogenetic and domestication history analysis with specific resequencing on multiple loci have been widely available in many crops[25,36,44,45,46]. A high level of polymorphisms present in this gene indicated that RPB2 is an excellent tool in investigating molecular evolution and phylogenetic relationships[54,55,56]
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