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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 seven pseudochromosomes (yellow) of the Fragaria vesca ‘Hawaii 4’ (FvH4) genome sequence as anchored to the FV×FB reference map (red).93 The pseudochromosomes are composed of a total of 222 sequencing scaffolds covering 197.7 Mb of sequence, representing 94% of the F. vesca genome. cM, centiMorgan.
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fig4: The seven pseudochromosomes (yellow) of the Fragaria vesca ‘Hawaii 4’ (FvH4) genome sequence as anchored to the FV×FB reference map (red).93 The pseudochromosomes are composed of a total of 222 sequencing scaffolds covering 197.7 Mb of sequence, representing 94% of the F. vesca genome. cM, centiMorgan.

Mentions: The first whole-genome sequencing initiative in the Rosoideae was the genome of the woodland strawberry, F. vesca. The genome of F. vesca cultivar Hawaii 4 (FvH4) was sequenced by an international consortium, and since it was the first genome to be characterised using exclusively short-read technology, the project represented a significant milestone in plant genomics.145 The 39× average depth of sequence coverage of the genome was achieved using predominantly data generated with the Roche 454 platform, supplemented with Illumina GAII and ABI/SOLiD data, and was assembled de novo into ∼3200 sequencing scaffolds with an N50 of 1.3 Mb. The majority of the sequenced genome (209.8 Mb, representing in excess of 95% of the total assembled genome length) was contained in 272 scaffolds of which 222, covering 197.7 Mb (94%), were anchored to the diploid Fragaria reference map to create seven pseudo-chromosomes (Figure 4).93


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 seven pseudochromosomes (yellow) of the Fragaria vesca ‘Hawaii 4’ (FvH4) genome sequence as anchored to the FV×FB reference map (red).93 The pseudochromosomes are composed of a total of 222 sequencing scaffolds covering 197.7 Mb of sequence, representing 94% of the F. vesca genome. cM, centiMorgan.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: The seven pseudochromosomes (yellow) of the Fragaria vesca ‘Hawaii 4’ (FvH4) genome sequence as anchored to the FV×FB reference map (red).93 The pseudochromosomes are composed of a total of 222 sequencing scaffolds covering 197.7 Mb of sequence, representing 94% of the F. vesca genome. cM, centiMorgan.
Mentions: The first whole-genome sequencing initiative in the Rosoideae was the genome of the woodland strawberry, F. vesca. The genome of F. vesca cultivar Hawaii 4 (FvH4) was sequenced by an international consortium, and since it was the first genome to be characterised using exclusively short-read technology, the project represented a significant milestone in plant genomics.145 The 39× average depth of sequence coverage of the genome was achieved using predominantly data generated with the Roche 454 platform, supplemented with Illumina GAII and ABI/SOLiD data, and was assembled de novo into ∼3200 sequencing scaffolds with an N50 of 1.3 Mb. The majority of the sequenced genome (209.8 Mb, representing in excess of 95% of the total assembled genome length) was contained in 272 scaffolds of which 222, covering 197.7 Mb (94%), were anchored to the diploid Fragaria reference map to create seven pseudo-chromosomes (Figure 4).93

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.