The Wheat Genetics Resource Center at Kansas State University has genotyped a collection of 888 tetraploid Triticum accessions and selected a set of 92 lines that are the most genetically diverse and capture more than 95% of the allelic diversity. This mini-core includes 37 Triticum timopheevii accessions and 55 Triticum turgidum accessions.

TASSEL-GBS V5.0 pipeline was used for SNP discovery. The pipeline was modified for SNP discovery without reference genome. More than 199 k SNPs were discovered that were used for further analysis. Population level SNP filtering was performed and SNPs with minor allele frequency less than 0.01 and missing data of more than 20% were removed. Further, SNPs with heterozygosity greater than 5% were removed because all the used tetraploid wheat accessions were highly inbred. Fisher’s exact test at alpha 0.001 with Bonferroni correction was performed to determine if the putative SNPs were from allelic tags as described. Individual samples with more than 80% missing SNP calls and more than 5 % heterozygosity were also removed. Retained markers and samples were used for further analyses. After all the filtering steps, 65,535 tags were eventually used for the diversity study.

The core sets of tetraploid wheat accessions were identified in two steps using the integration of genotypic and phenotypic datasets. In the first step, identified SNPs were first used with the software package PowerCore to identify core set using default settings, selecting the lines to retain the most diverse alleles by implementing advanced M (maximization) strategy. One of the limitations of this software was its inability to use more than 15,000 SNPs so we included only SNPs with less than 10-15 % missing data. In the second step, the number of selected accessions was further reduced by phenotypically guided selection using the available phenotypic data for growth patterns, leaf rust composite, stem rust (race TTKSK) and Hessian fly biotype D resistance. The entire genetic diversity captured by the Mini-Core was assessed by the percent segregating SNPs present in the selected accessions relative to the whole collection.

Source: Yadav IS, Singh N, Wu S, Raupp J, Wilson DL, Rawat N, Gill BS, Poland J, and Tiwari VK. 2022. Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii. Journal of Advanced Research https://doi.org/10.1016/j.jare.2022.08.020