Genomic Analysis Confirms Population Structure and Identifies Inter-Lineage Hybrids in Aegilops tauschii.

Narinder Singh,Duane Wilson,Jesse Poland,John Raupp,Vijay Tiwari,Bikram Gill,Mehraj Abbasov,Sunish Sehgal,Shuangye Wu

doi:10.3389/fpls.2019.00009

Abstract

Aegilops tauschii, the D-genome donor of bread wheat, Triticum aestivum, is a storehouse of genetic diversity, and an important resource for future wheat improvement. Genomic and population analysis of 549 Ae. tauschii and 103 wheat accessions was performed by using 13,135 high quality SNPs. Population structure, principal component, and cluster analysis confirmed the differentiation of Ae. tauschii into two lineages; lineage 1 (L1) and lineage 2 (L2), the latter being the wheat D-genome donor. Lineage L1 contributes only 2.7% of the total introgression from Ae. tauschii for a set of United States winter wheat lines, confirming the great amount of untapped genetic diversity in L1. Lineage L2 accessions had overall greater allelic diversity and wheat accessions had the least allelic diversity. Both lineages also showed intra-lineage differentiation with L1 being driven by longitudinal gradient and L2 differentiated by altitude. There has previously been little reported on natural hybridization between L1 and L2. We found nine putative inter-lineage hybrids in the population structure analysis, each containing numerous lineage-specific private alleles from both lineages. One hybrid was confirmed as a recombinant inbred between the two lineages, likely artificially post collection. Of the remaining eight putative hybrids, a group of seven from Georgia carry 713 SNPs with private alleles, which points to the possibility of a novel L1–L2 hybrid lineage. To facilitate the use of Ae. tauschii in wheat improvement, a MiniCore consisting of 29 L1 and 11 L2 accessions, has been developed based on genotypic, phenotypic and geographical data. MiniCore reduces the collection size by over 10-fold and captures 84% of the total allelic diversity in the whole collection.

Highlights

World population is projected to reach 9.7 billion by 2050, increasing pressure on the food system and challenging food security (Fao et al, 2014)
lineage 1 (L1) is spread across the entire Ae. tauschii geographical range, whereas lineage 2 (L2) is only present in Transcaucasia and around the Caspian Sea region (Figure 1)
We developed a small set of Ae. tauschii (MiniCore) consisting of 29 L1 and 11 L2 accessions to facilitate wheat improvement

Summary

Introduction

World population is projected to reach 9.7 billion by 2050, increasing pressure on the food system and challenging food security (Fao et al, 2014). Among other major food crops, is currently at an estimated genetic gain of 1% per year This must more than double to achieve the estimated 2.4% per year to meet the projected production levels needed to provide enough calories and Genomic Analysis of Ae. tauschii protein to the billions around the world in the coming decades (Ray et al, 2013). Limited genetic diversity present in the elite wheat cultivars pose a serious threat to this goal (Akhunov et al, 2010). To mitigate this genetic diversity problem, use of crop wild relatives and progenitors, such as goat grass (Ae. tauschii Coss.), presents a promising solution and the best resource. Much greater genetic diversity is present in this wild donor of the D-genome (Naghavi et al, 2009)

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