Molecular Basis of Evolutionary Events That Shaped theHardnessLocus in Diploid and Polyploid Wheat Species (Triticum and Aegilops)

Abstract

The Hardness (Ha) locus controls grain hardness in hexaploid wheat (Triticum aestivum) and its relatives (Triticum and Aegilops species) and represents a classical example of a trait whose variation arose from gene loss after polyploidization. In this study, we investigated the molecular basis of the evolutionary events observed at this locus by comparing corresponding sequences of diploid, tertraploid, and hexaploid wheat species (Triticum and Aegilops). Genomic rearrangements, such as transposable element insertions, genomic deletions, duplications, and inversions, were shown to constitute the major differences when the same genomes (i.e., the A, B, or D genomes) were compared between species of different ploidy levels. The comparative analysis allowed us to determine the extent and sequences of the rearranged regions as well as rearrangement breakpoints and sequence motifs at their boundaries, which suggest rearrangement by illegitimate recombination. Among these genomic rearrangements, the previously reported Pina and Pinb genes loss from the Ha locus of polyploid wheat species was caused by a large genomic deletion that probably occurred independently in the A and B genomes. Moreover, the Ha locus in the D genome of hexaploid wheat (T. aestivum) is 29 kb smaller than in the D genome of its diploid progenitor Ae. tauschii, principally because of transposable element insertions and two large deletions caused by illegitimate recombination. Our data suggest that illegitimate DNA recombination, leading to various genomic rearrangements, constitutes one of the major evolutionary mechanisms in wheat species.

Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae)

“…Therefore, smaller-scale changes, not detected with GISH, must have taken place to explain the genetic losses uncovered here. Smaller-scale genetic changes may be the result of gene-conversion events (Salmon et al, 2010;Flagel et al, 2012) or deletions (Chantret et al, 2005;Lukens et al, 2006). The PCR assay employed here could only have revealed homeolog loss if all copies of a gene from one parent were missing.…”

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

“…However, available data in wheat synthetic amphidiploids do not support the movement of transposable elements. (68) Instead, illegitimate recombination (between homoeologous sequences) may induce sequence rearrangements in specific loci controlling grain hardiness (Ha) (72) and leaf rust resistance (Lr10) (73) in hexaploid wheat (Triticum aestivum) and its diploid and tetraploid relatives (Triticum and Aegilops species). Therefore, recombination between homoeologous chromosomes with or without transposon involvement may be a general mechanism for observed inter-chromosomal exchanges in allopolyploids.…”

Sequence diversity and copy number variation of Mutator-like transposases in wheat

“…Partial sequences of MULE transposases were isolated by PCR from several grass species including common wheat (Lisch et al 2001). Genome sequencing analysis led to the identification of a few MULEs in einkorn wheat (Yan et al 2002), durum wheat (Wicker et al 2003) and common wheat (Chantret et al 2005), as well as in Aegilops tauschii (synonymous to Ae. squarrosa), a wild D genome donor species to common wheat (Li et al 2004;Chantret et al 2005).…”