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Antanaviciute L.,East Malling Research EMR | Fernandez-Fernandez F.,East Malling Research EMR | Jansen J.,Wageningen University | Banchi E.,Istituto Agrario San Michele allAdige | And 6 more authors.
BMC Genomics | Year: 2012

Background: A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny.Results: Of the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the 'Golden Delicious' genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the 'Golden Delicious' pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence.Conclusions: We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the 'Golden Delicious' reference sequence will assist in the continued improvement of the genome sequence assembly for that variety. © 2012 Antanaviciute et al.; licensee BioMed Central Ltd.

Jung S.,Washington State University | Cestaro A.,Istituto Agrario San Michele allAdige | Troggio M.,Istituto Agrario San Michele allAdige | Main D.,Washington State University | And 12 more authors.
BMC Genomics | Year: 2012

Background: Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes.Results: Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes.Conclusion: Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae. © 2012 Jung et al; licensee BioMed Central Ltd.

Dorigoni A.,Istituto Agrario San Michele allAdige | Lezzer P.,Istituto Agrario San Michele allAdige | Dallabetta N.,Istituto Agrario San Michele allAdige | Serra S.,University of Bologna | Musacchi S.,University of Bologna
Acta Horticulturae | Year: 2011

The use of the dwarfing M.9 rootstock is widespread in apple orchards due to the high tree efficiency it induces. Today it is possible to purchase a given type of tree congruent with the desired orchard design. Alongside the traditional chipbudded trees produced in a two-year cycle, there are types like two-year knip plants, trees obtained with the June bud (1-year-old) and bench-budded plants in a oneyear cycle. These different types of plants are suitable for the spindle training system. The innovative 'bi-a×is' system requires a pre-formed, split-branch tree produced in the nursery that obviates the need for heading in the orchard and the one-year delay in shoot-system formation. The spindle system is widely employed in apple orchards to boost planting densities up to 4,000 trees per hectare. The bi-a×is system utilizes the novel idea of training plants with 2 a×es so as to divide the vigour over more branches. Two sets of trials are underway with 'Fuji' in different environments, i.e. an upland orchard in Trento Province and a lowland one in the Po valley, to compare the vegetative and cropping traits of bi-a×es against the traditional spindle in high density plantings. The comparison of the two systems has so far shown some differences in tree growth patterns and yield. Vigour is distributed over two a×es in the Y- tree shape which helps control tree-growth. Shoot length is almost halved in the bi-a×is system compared to the spindle. No significant differences in yield and crop quality were found in the first 2-3 years, but the bi-a×is trees seem to produce better fruit red overcolour than spindle after fourfive years.

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