D. Barabaschi

Emerging Knowledge from Genome Sequencing of Crop Species

Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population’s viability.

Inside the CBF locus in Poaceae.

Several molecular evidences have been gathered in Poaceae that point out a central role of the CBF/DREB1 transcription factors in the signal transduction pathways leading to low-temperature tolerance, although to a quite different extent between crops originating from either temperate or tropical climates. A common feature of the CBF/DREB1 genes in Poaceae is their structural organization at the genome level in clusters of tandemly duplicated genes. In temperate cereals such as barley and wheat, expansion of specific multigene phylogenetic clades of CBFs that map at the Frost Resistance-2 locus has been exclusively observed. In addition, copy number variants of CBF genes between frost resistant and frost sensitive genotypes raise the question if multiple copies of the CBF/DREB1s are required to ensure freezing tolerance. On the other hand, in crops of tropical origin such as rice and maize, a smaller or less-responsive CBF regulon may have evolved, and different mechanisms might determine chilling tolerance. In this review, recent advances on the organization and diversity at the CBF cluster locus in the grasses are provided and discussed.

Integrated views in plant breeding: from the perspective of biotechnology

Conventional plant breeding has typically used phenotypic observations and statistical analysis to select for improved germplasm in segregating populations and the improvements in yield were likely associated with the unconscious pyramiding of yield-related traits. Modern breeding relies on genetics and genomics to identify superior alleles and to introduce them into new high-yielding varieties and hybrids. The recent advances in genomics and the diffusion of low-cost sequencing platforms have implications for both current and future plant breeding. New high-throughput genotyping facilities are allowing a fast identification of marker-trait associations and make possible a genome-wide selection process (genomic selection). Resequencing projects, leading to the discovery of new alleles and new molecular breeding methods based on site specific mutagenesis in combination with the knowledge on gene functions, open new perspectives for genetically modified (GM) and non-GM plant improvement.