High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

Abstract

Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

Fig. 1

Hexaploid-based PCoA analysis depicting the relative distances between hexaploids and other Avena accessions used in this study on the first two axes. Each point represents a sample derived from a single seed from an accession. The number of accessions for each species is shown in Table 1. Some accessions are represented by multiple samples (see Online Resource 1) (colour figure online)

Fig. 2

PCoA analysis including all extant hexaploids and theoretical in silico hexaploid species generated by combining tag counts from diploid-plus-tetraploid combinations. The symbols and colours represent in silico combinations that clustered together, as labelled. The blue “+” symbols represent all extant hexaploid species analysed in this study (colour figure online)

Fig. 3

PCoA analysis including all extant AC (DC) tetraploids and theoretical in silico tetraploid species generated by combining tag counts from A-genome diploid plus C-genome diploid combinations. The symbols and colours represent in silico combinations that clustered together, as labelled. The green triangles represent all extant AC (DC) tetraploid species analysed in this study (colour figure online)

Fig. 4

E-painting of chromosome representations in the hexaploid oat consensus map. The 21 chromosome representations with Mrg identification numbers described by Chaffin et al. (2016) are shown as elements of the circle, scaled by cM distance, and ordered by inferred genome origin. Four concentric rings of different colours indicate which chromosomes within the map contain a relatively high frequency of matches to the ancestral group represented by the respective ring: blue (innermost ring) represents A-genome diploids; red (second ring) represents the A_c/d-variant genome of the group containing A. canariensis, A. damascena and A. lusitanica; orange (third ring) represents C-genome diploids; and green (outermost ring) represents AC (DC)-genome tetraploids. The three outermost arcs are an interpretation of the genome contributions to the majority of chromosomes within each arc, based on hybridization pattern to the ancestral genomes (colour figure online)