Identifying the Genetic Basis of Local Adaptation in Wild Emmer Wheat

As a rich source of genomic variation, the wild relatives of wheat have been broadly used in breeding. To identify the accessions of wild relatives carrying alleles conferring adaption to extreme climatic conditions, the analysis of the eco-geographic patterns of genomic variation was performed in wild emmer wheat, the tetraploid ancestor (AABB genome) of the wheat genome. We have associated the patterns of genomic variation in wild emmer (AABB genome) with climate data from the accessions’ collection sites. We genotyped a population of 475 georeferenced wild emmer accessions from Israel using 90K iSelect SNP array and sequence-based genotyping. The data was mapped to a recently assembled wild emmer genome and missing SNPs predicted by imputation. Out of 341,228 SNPs from sequence data and 26,697 genotype calls from 90K SNP array, we retained 26,628 and 11,355 SNPs, respectively. The analysis of population stratification revealed three genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Correlation among bioclimatic variables associated with the distribution of wild emmer identified seven distinct climatic groups. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. Environmental association scans have been performed to identify adaptive SNPs correlating with local climates. To further dissect the alleles favored during climatic adaptation and to assess the value of detected adaptive variation for wheat breeding, we are performing phenotypic evaluation of wild emmer-derived wheat lines in the field conditions.