Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

Abstract

Modern plant breeding can benefit from the allelic variation that exists 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 single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the A subgenome 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 geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the A subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using 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 for incorporation into modern crop breeding.

Time‐specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus

“…Overlap between associated signals and selective signatures may suggest that the selected genes and alleles may be involved in the biological adaptation of juvenile stem growth. Similar ‘landscape genomics’ research areas have been reported in the annual plant Medicago truncatula (Guerrero et al ., ), Triticum urartu (Brunazzi et al ., ) and undomesticated woody species, which can provide further insight into the potential genes and mechanisms of adaptation to the environment.…”

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation

“…The interest of the wild reservoir as source of readily available adaptations to climate change for crops is now largely acknowledged (Warschefsky et al, 2014; Dempewolf et al, 2017). As a result, a considerable number of studies look at adaptive genes in crop wild relatives (Berthouly-Salazar et al, 2016; Fustier et al, 2017; Brunazzi et al, 2018; von Wettberg et al, 2018) with the aim of identifying genes that could be introduced in crops by artificial breeding schemes (Hajjar and Hodgkin, 2007). However, another mechanism allowing to rapidly acquire new variants that is largely overlooked in crop research for breeding is spontaneous gene flow.…”

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

“…The AB genomes of durum wheat can be hybridized with wild species such as Aegilops tauschii , the donor of the D genome, to create synthetic hybrids targeting adaptive traits (Reynolds et al ., , ). Alleles coming from Triticum urartu , the wild donor of the A wheat genome that still grows in highly differentiated natural populations (Brunazzi et al ., ), have also been successfully introgressed in durum wheat amphiploids and lines (Alvarez et al ., ). The closely related wild emmer ( Triticum dicoccoides , genome AB, 2 n = 4 x = 28) may also be used to accelerate the introduction of novel diversity into wheat breeding through durum wheat (Valkoun, ).…”