Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes

Abstract

The Glu-1 locus, encoding the high-molecular-weight glutenin protein subunits, controls bread-making quality in hexaploid wheat (Triticum aestivum) and represents a recently evolved region unique to Triticeae genomes. To understand the molecular evolution of this locus region, three orthologous Glu-1 regions from the three subgenomes of a single hexaploid wheat species were sequenced, totaling 729 kb of sequence. Comparing each Glu-1 region with its corresponding homologous region from the D genome of diploid wheat, Aegilops tauschii, and the A and B genomes of tetraploid wheat, Triticum turgidum, revealed that, in addition to the conservation of microsynteny in the genic regions, sequences in the intergenic regions, composed of blocks of nested retroelements, are also generally conserved, although a few nonshared retroelements that differentiate the homologous Glu-1 regions were detected in each pair of the A and D genomes. Analysis of the indel frequency and the rate of nucleotide substitution, which represent the most frequent types of sequence changes in the Glu-1 regions, demonstrated that the two A genomes are significantly more divergent than the two B genomes, further supporting the hypothesis that hexaploid wheat may have more than one tetraploid ancestor.

Figure 1.—

Gene organization and comparison of orthologous and homologous Glu-1 regions from ancestral wheat and hexaploid wheat genomes. Genes are represented by numbered pentagons, with their corresponding names listed below. The letters “a” and “b” denote distinct copies of the duplicated genes. The arrows of the pentagons indicate the direction of the potential transcription of these genes. Solid pentagons represent inactive genes or pseudogenes caused by sequence rearrangements identified in the analysis. Positions and addresses of BAC clones selected for complete sequencing of the regions are indicated. Regions involved in sequence duplications resulting in two copies of receptor protein kinase (D1, D1′) and two copies of HMW glutenin (D2, D2′) are labeled only in the A genome. A 30-kb segment is provided as a scale reference.

Figure 2.—

Pairwise comparisons of the Glu-1 regions between the two homologous genomes. The dot plot was performed using the DOTTER program (Sonnhammer and Durbin 1995) with default parameters between two A-genome sequences from T. turgidum and T. aestivum (A), two B-genome sequences from T. turgidum and T. aestivum (B), and two D-genome sequences from Ae. tauschii and T. aestivum (C). Each distinct gap in the dot plot is assigned a number, and sequence rearrangements causing the gaps are described in the text.

Figure 3.—

Insertion and deletion of retrotransposons that differentiate two homologous D genomes. Retrotransposons that are colinear between the hexaploid D and diploid D genomes are boxed in gray. Retrotransposons that have inserted or rearranged by deletion in only one of the genomes are represented by hatched boxes. Genes are represented by pentagons. Dy and Dx are short for the y-type and x-type HMW-glutenin genes from the D genome. The letters “s” and “p” following the names of the retroelements indicate solo or partial, respectively.

Figure 4.—

A. Number of shared vs. nonshared retroelements between the two homologous wheat genomes. Shared and non-shared retroelements between the homologous genomes are represented by the black and gray bars, respectively. B. Indel frequency and size distribution in three wheat genomes. Indels identified in each pair of homologous genomes were categorized into four groups. The indel frequency for each group was normalized to the number of indels per 10 kb in the graph. C. Percentage of total indel length contributed by indels of different sizes. Indel length represented by different indel sizes were calculated and then divided by the total indel length for each of the A, B and D genomes. The total indel lengths are 10,738, 11,382, and 13,612 bp for the A, B, and D genomes, respectively.