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. 2019 Jan 24:9:1993.
doi: 10.3389/fpls.2018.01993. eCollection 2018.

Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum)

Alexandra M Przewieslik-Allen  1 , Amanda J Burridge  1 , Paul A Wilkinson  1 , Mark O Winfield  1 , Daniel S Shaw  1 , Lorna McAusland  2 , Julie King  2 , Ian P King  2 , Keith J Edwards  1 , Gary L A Barker  1
Affiliations

Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum)

Alexandra M Przewieslik-Allen et al. Front Plant Sci. .

Abstract

The genus Aegilops contains a diverse collection of wild species exhibiting variation in geographical distribution, ecological adaptation, ploidy and genome organization. Aegilops is the most closely related genus to Triticum which includes cultivated wheat, a globally important crop that has a limited gene pool for modern breeding. Aegilops species are a potential future resource for wheat breeding for traits, such as adaptation to different ecological conditions and pest and disease resistance. This study describes the development and application of the first high-throughput genotyping platform specifically designed for screening wheat relative species. The platform was used to screen multiple accessions representing all species in the genus Aegilops. Firstly, the data was demonstrated to be useful for screening diversity and examining relationships within and between Aegilops species. Secondly, markers able to characterize and track introgressions from Aegilops species in hexaploid wheat were identified and validated using two different approaches.

Keywords: Aegilops; genotyping array; introgression; single nucleotide polymorphism (SNP); wheat; wheat relative.

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Figures

Figure 1
Figure 1
Relationships between species in the genus Aegilops. The genome classification of each species is indicated within circles representing the species and arrows designate hybridisations between species. The color of the outline of each circle represents the section the species is allocated to.
Figure 2
Figure 2
Principal coordinate analysis (PCoA) plots colored by species. (A) Coordinate 1 is plotted along the y-axis, coordinate 2 is plotted along the x-axis. (B) Detail of clusters with negative PC1 and PC2 values. Pie charts indicate the numbers of each species belonging to designated clusters.
Figure 3
Figure 3
Phylogeny of Aegilops accessions used in the study based upon a maximum likelihood tree generated using all genotype data. Bootstrap support values are given at branch points and are based upon 10,000 replicates. Clades are colored according to genome designations given in the inner circles in Figure 1.
Figure 4
Figure 4
Chromosome locations of SNPs on the HD array, the wheat relative array and SNPs that are polymorphic between members of the genus Aegilops and Triticum aestivum from the wheat relative array.
Figure 5
Figure 5
Distribution of SNPs from the Axiom® Wheat-Relative Genotyping Array in the wheat genome. The x-axis represents the physical distance along each chromosome, split into 10 Mbp windows.
Figure 6
Figure 6
Identification of Aegilops sharonensis introgression segments in 41 recombinant wheat lines resistant to African Puccinia graminis f. sp. Tritici. Genotype calls from the array were compared to Ae. sharonensis over a 10 SNP window and a score of over 40% is considered indicative of introgressed material and is highlighted in red.
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References

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