Molecular Diversity and Landscape Genomics of the Crop Wild Relative Triticum urartu Across the Fertile Crescent

Modern plant breeding can benefit from the allelic variation existing in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next-generation sequencing was used to generate 1.3 million genome-wide SNPs on ex situ collections of Triticum urartu L., the wild donor of the Ausub-genome of modern wheat. A set of 75,511 high quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from West to East. The incorporation of geographic information of sampling points showed that genetic diversity did correlate to geographic distance (R2= 0.19), separating samples from Jordan and Lebanon, to samples from Syria and Southern Turkey, to samples from Eastern Turkey, Iran, and Iraq. The wild emmer genome was used to derive SNPs physical positions on the 7 chromosomes of the Ausub-genome, allowing to describe a relatively slow linkage disequilibrium decay in the collection. Outlier loci were described on the basis of geographical distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and put in relation to allelic variation with a genome-wide association approach, identifying several marker-environment associations (MEAs). Fifty-seven MEAs were associated with altitude and temperature measures, while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential, some already reported in wheat, including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials to be incorporated in modern crop breeding. This article is protected by copyright. All rights reserved.