Genome organisation and retrotransposon driven molecular evolution of the endosperm Hardness (Ha) locus in Triticum aestivum cv Glenlea

A review of the occurrence of Grain softness protein-1 genes in wheat (Triticum aestivum L.)

Grain softness protein-1 (Gsp-1) is a small, 495-bp intronless gene found throughout the Triticeae tribe at the distal end of group 5 chromosomes. With the Puroindolines, it constitutes a key component of the Hardness locus. Gsp-1 likely plays little role in grain hardness, but has direct interest due to its utility in phylogeny and its role in arabinogalactan peptides. Further role(s) remain to be identified. In the polyploid wheats, Triticum aestivum and T. turgidum, the gene is present in a homoeologous series. Since its discovery, there have been conflicting reports and data as to the number of Gsp-1 genes and the level of sequence polymorphism. Little is known about allelic variation within a species. In the simplest model, a single Gsp-1 gene is present in each wheat and Aegilops tauschii genome. The present review critically re-examines the published and some unpublished data (sequence available in the NCBI nucleotide and MIPS Wheat Genome Databases). A number of testable hypotheses are identified, and include the level of polymorphism that may represent (and define) different Gsp-1 alleles, the existence of a fourth Gsp-1 gene, and the apparent, at times, high level of naturally-occurring or artifactual gene chimeras. In summary, the present data provide firm evidence for at most, three Gsp-1 genes in wheat, although there are numerous data that suggest a more complex model.

The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome

BACKGROUND AND AIMS

Peanut (Arachis hypogaea) is an allotetraploid (AABB-type genome) of recent origin, with a genome of about 2·8 Gb and a high repetitive content. This study reports an analysis of the repetitive component of the peanut A genome using bacterial artificial chromosome (BAC) clones from A. duranensis, the most probable A genome donor, and the probable consequences of the activity of these elements since the divergence of the peanut A and B genomes.

METHODS

The repetitive content of the A genome was analysed by using A. duranensis BAC clones as probes for fluorescence in situ hybridization (BAC-FISH), and by sequencing and characterization of 12 genomic regions. For the analysis of the evolutionary dynamics, two A genome regions are compared with their B genome homeologues.

KEY RESULTS

BAC-FISH using 27 A. duranensis BAC clones as probes gave dispersed and repetitive DNA characteristic signals, predominantly in interstitial regions of the peanut A chromosomes. The sequences of 14 BAC clones showed complete and truncated copies of ten abundant long terminal repeat (LTR) retrotransposons, characterized here. Almost all dateable transposition events occurred <3·5 million years ago, the estimated date of the divergence of A and B genomes. The most abundant retrotransposon is Feral, apparently parasitic on the retrotransposon FIDEL, followed by Pipa, also non-autonomous and probably parasitic on a retrotransposon we named Pipoka. The comparison of the A and B genome homeologous regions showed conserved segments of high sequence identity, punctuated by predominantly indel regions without significant similarity.

CONCLUSIONS

A substantial proportion of the highly repetitive component of the peanut A genome appears to be accounted for by relatively few LTR retrotransposons and their truncated copies or solo LTRs. The most abundant of the retrotransposons are non-autonomous. The activity of these retrotransposons has been a very significant driver of genome evolution since the evolutionary divergence of the A and B genomes.

Wheat (Triticum aestivum L. and T. turgidum L. ssp. durum) Kernel Hardness: I. Current View on the Role of Puroindolines and Polar Lipids

Wheat hardness has major consequences for the entire wheat supply chain from breeders and millers over manufacturers to, finally, consumers of wheat-based products. Indeed, differences in hardness among Triticum aestivum L. or between T. aestivum L. and T. turgidum L. ssp. durum wheat cultivars determine not only their milling properties, but also the properties of flour or semolina endosperm particles, their preferential use in cereal-based applications, and the quality of the latter. Although the mechanism causing differences in wheat hardness has been subject of research more than once, it is still not completely understood. It is widely accepted that differences in wheat hardness originate from differences in the interaction between the starch granules and the endosperm protein matrix in the kernel. This interaction seems impacted by the presence of either puroindoline a and/or b, polar lipids on the starch granule surface, or by a combination of both. We focus here on wheat hardness and its relation to the presence of puroindolines and polar lipids. More in particular, the structure, properties, and genetics of puroindolines and their interactions with polar lipids are critically discussed as is their possible role in wheat hardness. We also address future research needs as well as the presence of puroindoline-type proteins in other cereals.

Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat

The introgression of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties beginning in the 1960s led to improved lodging resistance and yield, providing a major contribution to the 'green revolution'. Although wheat Rht-1 and surrounding sequence is available, the genetic composition of this region has not been examined in a homoeologous series. To determine this, three Rht-1-containing bacterial artificial chromosome (BAC) sequences derived from the A, B, and D genomes of the bread wheat variety Chinese Spring (CS) were fully assembled and analyzed. This revealed that Rht-1 and two upstream genes were highly conserved among the homoeologs. In contrast, transposable elements (TEs) were not conserved among homoeologs with the exception of intronic miniature inverted-repeat TEs (MITEs). In relation to the Triticum urartu ancestral line, CS-A genic sequences were highly conserved and several colinear TEs were present. Comparative analysis of the CS wheat BAC sequences with assembled Poaceae genomes showed gene synteny and amino acid sequences were well preserved. Further 5' and 3' of the wheat BAC sequences, a high degree of gene colinearity is present among the assembled Poaceae genomes. In the 20 kb of sequence flanking Rht-1, five conserved non-coding sequences (CNSs) were present among the CS wheat homoeologs and among all the Poaceae members examined. Rht-A1 was mapped to the long arm of chromosome 4 and three closely flanking genetic markers were identified. The tools developed herein will enable detailed studies of Rht-1 and linked genes that affect abiotic and biotic stress response in wheat.

Involvement of disperse repetitive sequences in wheat/rye genome adjustment

The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploidization functional implications. We intend to attain a deeper knowledge of dispersed repetitive sequence involvement in parental genome reshuffle in triticale and in wheat-rye addition lines that have the entire wheat genome plus each rye chromosome pair. Through Random Amplified Polymorphic DNA (RAPD) analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. Moreover, the sequential nature of those events was revealed by the increased absence of rye-origin bands in wheat-rye addition lines in comparison with triticale. Remodeled band sequencing revealed that both repetitive and coding genome domains are affected in wheat-rye hybrid genotypes. Additionally, the amplification and sequencing of pSc20H internal segments showed that the disappearance of parental bands may result from restricted sequence alterations and unraveled the involvement of wheat/rye related repetitive sequences in genome adjustment needed for hybrid plant stabilization.

A customized gene expression microarray reveals that the brittle stem phenotype fs2 of barley is attributable to a retroelement in the HvCesA4 cellulose synthase gene

The barley (Hordeum vulgare) brittle stem mutants, fs2, designated X054 and M245, have reduced levels of crystalline cellulose compared with their parental lines Ohichi and Shiroseto. A custom-designed microarray, based on long oligonucleotide technology and including genes involved in cell wall metabolism, revealed that transcript levels of very few genes were altered in the elongation zone of stem internodes, but these included a marked decrease in mRNA for the HvCesA4 cellulose synthase gene of both mutants. In contrast, the abundance of several hundred transcripts changed in the upper, maturation zones of stem internodes, which presumably reflected pleiotropic responses to a weakened cell wall that resulted from the primary genetic lesion. Sequencing of the HvCesA4 genes revealed the presence of a 964-bp solo long terminal repeat of a Copia-like retroelement in the first intron of the HvCesA4 genes of both mutant lines. The retroelement appears to interfere with transcription of the HvCesA4 gene or with processing of the mRNA, and this is likely to account for the lower crystalline cellulose content and lower stem strength of the mutants. The HvCesA4 gene maps to a position on chromosome 1H of barley that coincides with the previously reported position of fs2.

Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity

To understand key mechanisms leading to stabilized allopolyploid species, we characterized the meiotic behaviour of wheat allohexaploids in relation to structural and genetic changes. For that purpose, we analysed first generations of synthetic allohexaploids obtained through interspecific hybridization, followed by spontaneous chromosome doubling, between several genotypes of Triticum turgidum and Aegilops tauschii wheat species, donors of AB and D genomes, respectively. As expected for these Ph1 (Pairing homoeologous 1) gene-carrying allopolyploids, chromosome pairing at metaphase I of meiosis essentially occurs between homologous chromosomes. However, the different synthetic allohexaploids exhibited progenitor-dependent meiotic irregularities, such as incomplete homologous pairing, resulting in univalent formation and leading to aneuploidy in the subsequent generation. Stability of the synthetic allohexaploids was shown to depend on the considered genotypes of both AB and D genome progenitors, where few combinations compare to the natural wheat allohexaploid in terms of regularity of meiosis and euploidy. Aneuploidy represents the only structural change observed in these synthetic allohexaploids, as no apparent DNA sequence elimination or rearrangement was observed when analysing euploid plants with molecular markers, developed from expressed sequence tags (ESTs) as well as simple sequence repeat (SSR) and transposable element sequences.

Recruitment of closely linked genes for divergent functions: the seed storage protein (Glu-3) and powdery mildew (Pm3) genes in wheat (Triticum aestivum L.)

Wheat seed storage protein gene loci (Glu-3) and powdery mildew resistance gene loci (Pm3 and Pm3-like) are closely linked on the short arms of homoeologous group 1 chromosomes. To study the structural organization of the Glu-3/Pm3 loci, three bacterial artificial chromosome clones were sequenced from the A, B, and D genomes of hexaploid wheat. The A and B genome clones contained a Glu-3 adjacent to a Pm3-like gene organized in a conserved Glu-3/SFR159/Pm3-like structure. The D genome clone contained clusters of resistance gene analogs but no Pm3. Its similarity to the A and B genome was limited to the Glu-3/SFR159 region. Comparison of the B genome PM3-like deduced amino acid sequence with known PM3 functional isotypes reinforced the hypothesis of allelic evolution via block exchange by gene conversion/recombination. The advent of glutenin genes and the formation of the Glu-3/SFR159/Pm3 locus occurred after divergence of wheat from rice and Brachypodium. Comparison of the A genome homologous sequences permitted an estimate of time of divergence of approximately 0.3 million years ago. The B genome sequences were not colinear indicating that they could either be paralogs or represent different B genome progenitors. Analysis of the 11 complete retrotransposons indicated a time of divergence ranging from 0.29 to 5.62 million years ago, consistent with their complex nested structure.

Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins

The wheat high molecular weight (HMW) glutenins are important seed storage proteins that determine bread-making quality in hexaploid wheat (Triticum aestivum). In this study, detailed comparative sequence analyses of large orthologous HMW glutenin genomic regions from eight grass species, representing a wide evolutionary history of grass genomes, reveal a number of lineage-specific sequence changes. These lineage-specific changes, which resulted in duplications, insertions, and deletions of genes, are the major forces disrupting gene colinearity among grass genomes. Our results indicate that the presence of the HMW glutenin gene in Triticeae genomes was caused by lineage-specific duplication of a globulin gene. This tandem duplication event is shared by Brachypodium and Triticeae genomes, but is absent in rice, maize, and sorghum, suggesting the duplication occurred after Brachypodium and Triticeae genomes diverged from the other grasses ~35 Ma ago. Aside from their physical location in tandem, the sequence similarity, expression pattern, and conserved cis-acting elements responsible for endosperm-specific expression further support the paralogous relationship between the HMW glutenin and globulin genes. While the duplicated copy in Brachypodium has apparently become nonfunctional, the duplicated copy in wheat has evolved to become the HMW glutenin gene by gaining a central prolamin repetitive domain.