The Wheat Genetics Resource Center at Kansas State University has genotyped a collection of 600 Ae. tauschii accessions and selected a set of 40 lines that are the most genetically diverse and capturing more than 95% of the allelic diversity. This mini-core includes 28 accessions from Lineage 1 [strangulata type] and 12 from Lineage 2 [eusquarrosa type]. The mini-core represents 13 countries spanning the distribution of Ae. tauschii; three accession are of unknown origin; 27.5% are from Iran and 17.5% are from Afghanistan, countries with the largest density of this species.

Single nucleotide polymorphism (SNP) discovery and genotyping was performed in single step with Tassel 5 GBSv2 pipeline using the Ae. tauschii genome assembly (Aet v4.0; NCBI BioProject PRJNA341983) as the reference. Tassel was run with bowtie2 aligner for tags mapping in Linux HPC environment via shell script. Population level SNP filtering was performed and SNPs with a minor allele frequency (MAF) less than 0.01 and missing data more than 20% were removed. SNPs with heterozygosity greater than 5% were removed because Ae. tauschii accessions are highly inbred. Individual samples with more than 80% missing SNP calls and more than 5% heterozygosity were also removed.

All SNPs were used to select a representative core-set from the Ae. tauschii collection. The core-set was selected in two steps. First, the software package PowerCore was used with default settings, which selects the lines to retain most diverse alleles by implementing advanced M (maximization) strategy. Then the number of selected accessions was further reduced with a phenotypically guided selection using the available phenotypic data for a leaf rust composite culture, stem rust race TTKSK, and Hessian fly biotype D resistance. The diversity captured by the MiniCore was assessed by the percent segregating SNPs present in the selected accessions relative to the whole collection.

Reference:
Genomic analysis confirms population structure and identifies inter-lineage hybrids in Aegilops tauschii. 2019. Singh N, Wu S, Tiwari V, Sehgal S, Raupp J, Wilson D, Abbasov M, Gill B, and Poland J. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.00009