Targeted resequencing reveals genomic signatures of barley domestication

Abstract

Summary Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear.To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci.We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts.These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.

Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley

“…Notably, no significant cytonuclear interactions between the cytoplasm and the nuclear loci were identified. Nevertheless, the QTL found for period and amplitude plasticity do not fully fall on candidate genes in the barley gene pool, which were proposed as potential regulators of this trait under domestication (Pankin, Altmüller, Becker, & von Korff, ). frp2.2 , for example, which we already validated in this study as having a significant and reproducible effect on clock shortening under heat (Figure ) does not overlap with candidate genes.…”

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

“…New evidence suggests that domesticated barley is actually descended from a number of wild barley populations, leading to a mosaic genome (Poets et al ; Pankin et al ). To explain the putative domestication of barley outside the core center of southeast Turkey, Özkan et al () proposed that the practice of cultivating wild plants was an idea imported to the Israel‐Jordan Valley from southeast Turkey.…”

“…Recent work suggests that, like emmer wheat, barley possesses contributions from multiple wild populations (Poets et al ; Pankin et al ). In addition to the evidence suggesting multiple wild populations contributed to the genomes of modern wheat and barley, it has been proposed that domestication was not a rapid process (Allaby et al ) and that the rate of domestication was likely not constant (Allaby et al ).…”

The Impact of Genetic Changes during Crop Domestication

“…Number of Species Asteraceae (daisies) 32,581 Orchidaceae (orchids) 28,237 Fabaceae (legumes) 20,856 Rubiaceae (coffees) 13,686 Poaceae (grasses) 11,430 The largest families of gymnosperms (12 families,~1110 species, conifers, cycads) are the Zamiaceae (a group of cycads containing 232 species) and Pinaceae (pines, containing 231 species).…”

“…Chickpea is thought to have a monophyletic origin, given the narrow distribution of its wild progenitor [26] and the limited genetic diversity of the cultigen [7,27]. Domesticated barley (Hordeum vulgare) [28,29] and emmer wheat (Triticum turgidum L.) [23] have more polyphyletic tendencies. Both show traces of mosaic eastern and western ancestral origins from opposite ends of the Near Eastern Fertile Crescent.…”