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Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives.

Longhi S, Giongo L, Buti M, Surbanovski N, Viola R, Velasco R, Ward JA, Sargent DJ - Hortic Res (2014)

Bottom Line: Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus.These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering.In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

View Article: PubMed Central - PubMed

Affiliation: Research and Innovation Centre , Fondazione Edmund Mach, San Michele all'Adige, Italy.

ABSTRACT
The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance, including the soft fruit species strawberry (Fragaria ×ananassa), red (Rubus idaeus) and black (Rubus occidentalis) raspberries, blackberries (Rubus spp.) and one of the most economically important cut flower genera, the roses (Rosa spp.). Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus. These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering. In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

No MeSH data available.


The chloroplast genome of Potentilla micrantha assembled from PacBio RS and Illumina HiSeq2000 data144 detailing genes transcribed clockwise (inside circle) and counterclockwise (outside circle). Genes are coloured according to functional categorisation, IRA and IRB denote inverted repeats and LSC and SSC denote long and short single copy regions, respectively.
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fig3: The chloroplast genome of Potentilla micrantha assembled from PacBio RS and Illumina HiSeq2000 data144 detailing genes transcribed clockwise (inside circle) and counterclockwise (outside circle). Genes are coloured according to functional categorisation, IRA and IRB denote inverted repeats and LSC and SSC denote long and short single copy regions, respectively.

Mentions: Recently, the whole chloroplast genome sequence of Potentilla micrantha was sequenced using the Pacific Biosciences PacBio RS sequencing platform.144 The genome spanned a total of 154 959 bp and was structurally similar to the F. vesca chloroplast genome, containing the two expected inverted repeats spanning 25 530 bp in length each, a large single copy and small single copy region covering 85 137 bp and 18 762 bp, respectively, and 120 genes, 21 of which were duplicated in the inverted repeats, giving a total of 141 genes of known function (Figure 3). Through comparison with the F. vesca chloroplast genome sequence, the authors determined that gene order within the chloroplasts of the two species was identical. The chloroplast genome of P.micrantha was the first to be sequenced using the PacBio RS platform, which, following de novo assembly, yielded a single, highly accurate contiguous sequence spanning the entire chloroplast, and suggesting that PacBio RS data may be of immense utility in whole-genome shotgun sequencing and BAC-sequencing projects.


Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives.

Longhi S, Giongo L, Buti M, Surbanovski N, Viola R, Velasco R, Ward JA, Sargent DJ - Hortic Res (2014)

The chloroplast genome of Potentilla micrantha assembled from PacBio RS and Illumina HiSeq2000 data144 detailing genes transcribed clockwise (inside circle) and counterclockwise (outside circle). Genes are coloured according to functional categorisation, IRA and IRB denote inverted repeats and LSC and SSC denote long and short single copy regions, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591673&req=5

fig3: The chloroplast genome of Potentilla micrantha assembled from PacBio RS and Illumina HiSeq2000 data144 detailing genes transcribed clockwise (inside circle) and counterclockwise (outside circle). Genes are coloured according to functional categorisation, IRA and IRB denote inverted repeats and LSC and SSC denote long and short single copy regions, respectively.
Mentions: Recently, the whole chloroplast genome sequence of Potentilla micrantha was sequenced using the Pacific Biosciences PacBio RS sequencing platform.144 The genome spanned a total of 154 959 bp and was structurally similar to the F. vesca chloroplast genome, containing the two expected inverted repeats spanning 25 530 bp in length each, a large single copy and small single copy region covering 85 137 bp and 18 762 bp, respectively, and 120 genes, 21 of which were duplicated in the inverted repeats, giving a total of 141 genes of known function (Figure 3). Through comparison with the F. vesca chloroplast genome sequence, the authors determined that gene order within the chloroplasts of the two species was identical. The chloroplast genome of P.micrantha was the first to be sequenced using the PacBio RS platform, which, following de novo assembly, yielded a single, highly accurate contiguous sequence spanning the entire chloroplast, and suggesting that PacBio RS data may be of immense utility in whole-genome shotgun sequencing and BAC-sequencing projects.

Bottom Line: Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus.These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering.In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

View Article: PubMed Central - PubMed

Affiliation: Research and Innovation Centre , Fondazione Edmund Mach, San Michele all'Adige, Italy.

ABSTRACT
The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance, including the soft fruit species strawberry (Fragaria ×ananassa), red (Rubus idaeus) and black (Rubus occidentalis) raspberries, blackberries (Rubus spp.) and one of the most economically important cut flower genera, the roses (Rosa spp.). Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus. These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering. In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

No MeSH data available.