Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

B. Denoyes, I. Amaya, A. Liston, J. Tennessen, T.L. Ashman, V.M. Whitaker, T. Hytönen, E. van de Weg, S. Osorio, K.M. Folta, J. Slovin, R.J. Harrison, A. Monfort, N.V. Bassil

Research output: Chapter in Book/Report/Conference proceedingConference paper

1 Citation (Scopus)

Abstract

In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequence obtained in the Rosoideae sub-family. This genome has a high level of synteny with genomes of other species of diploid and polyploid Fragaria, but it also provides a reference for species like Rubus and Rosa for functional genomics. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. For genotyping, many studies have used simple sequence repeats (SSRs) but whole genome sequencing is now a mature technology and facilitates the development of genotyping chips and other genetic approaches such as genome wide association studies (GWAS). Furthermore, microarray-based technologies have been eclipsed by RNA-seq, the high-throughput sequencing of RNA. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses such as NILs and EMS have appeared in addition to the classical segregating population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. Selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.

Original languageEnglish
Title of host publication8th International Strawberry Symposium
PublisherInternational Society for Horticultural Science
Pages13-24
Volume1156
ISBN (Electronic)9789462611528
DOIs
Publication statusPublished - 2017
EventVIII International Strawberry Symposium - Québec City, Canada
Duration: 13 Aug 201617 Aug 2017

Publication series

NameActa Horticulturae
Volume1156
ISSN (Print)0567-7572

Conference

ConferenceVIII International Strawberry Symposium
CountryCanada
CityQuébec City
Period13/08/1617/08/17

Fingerprint

strawberries
genomics
genotyping
genome
Fragaria vesca
Fragaria
Rubus
plant biology
plant physiology
polyploidy
fruit quality
Rosa
diploidy
microsatellite repeats
RNA
genotype

Keywords

  • Fragaria
  • Functional genomics
  • Omics
  • Polyploidy

Cite this

Denoyes, B., Amaya, I., Liston, A., Tennessen, J., Ashman, T. L., Whitaker, V. M., ... Bassil, N. V. (2017). Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. In 8th International Strawberry Symposium (Vol. 1156, pp. 13-24). (Acta Horticulturae; Vol. 1156). International Society for Horticultural Science. https://doi.org/10.17660/ActaHortic.2017.1156.3
Denoyes, B. ; Amaya, I. ; Liston, A. ; Tennessen, J. ; Ashman, T.L. ; Whitaker, V.M. ; Hytönen, T. ; van de Weg, E. ; Osorio, S. ; Folta, K.M. ; Slovin, J. ; Harrison, R.J. ; Monfort, A. ; Bassil, N.V. / Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. 8th International Strawberry Symposium. Vol. 1156 International Society for Horticultural Science, 2017. pp. 13-24 (Acta Horticulturae).
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title = "Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come",
abstract = "In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequence obtained in the Rosoideae sub-family. This genome has a high level of synteny with genomes of other species of diploid and polyploid Fragaria, but it also provides a reference for species like Rubus and Rosa for functional genomics. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. For genotyping, many studies have used simple sequence repeats (SSRs) but whole genome sequencing is now a mature technology and facilitates the development of genotyping chips and other genetic approaches such as genome wide association studies (GWAS). Furthermore, microarray-based technologies have been eclipsed by RNA-seq, the high-throughput sequencing of RNA. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses such as NILs and EMS have appeared in addition to the classical segregating population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. Selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.",
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Denoyes, B, Amaya, I, Liston, A, Tennessen, J, Ashman, TL, Whitaker, VM, Hytönen, T, van de Weg, E, Osorio, S, Folta, KM, Slovin, J, Harrison, RJ, Monfort, A & Bassil, NV 2017, Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. in 8th International Strawberry Symposium. vol. 1156, Acta Horticulturae, vol. 1156, International Society for Horticultural Science, pp. 13-24, VIII International Strawberry Symposium , Québec City, Canada, 13/08/16. https://doi.org/10.17660/ActaHortic.2017.1156.3

Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. / Denoyes, B.; Amaya, I.; Liston, A.; Tennessen, J.; Ashman, T.L.; Whitaker, V.M.; Hytönen, T.; van de Weg, E.; Osorio, S.; Folta, K.M.; Slovin, J.; Harrison, R.J.; Monfort, A.; Bassil, N.V.

8th International Strawberry Symposium. Vol. 1156 International Society for Horticultural Science, 2017. p. 13-24 (Acta Horticulturae; Vol. 1156).

Research output: Chapter in Book/Report/Conference proceedingConference paper

TY - GEN

T1 - Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

AU - Denoyes, B.

AU - Amaya, I.

AU - Liston, A.

AU - Tennessen, J.

AU - Ashman, T.L.

AU - Whitaker, V.M.

AU - Hytönen, T.

AU - van de Weg, E.

AU - Osorio, S.

AU - Folta, K.M.

AU - Slovin, J.

AU - Harrison, R.J.

AU - Monfort, A.

AU - Bassil, N.V.

PY - 2017

Y1 - 2017

N2 - In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequence obtained in the Rosoideae sub-family. This genome has a high level of synteny with genomes of other species of diploid and polyploid Fragaria, but it also provides a reference for species like Rubus and Rosa for functional genomics. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. For genotyping, many studies have used simple sequence repeats (SSRs) but whole genome sequencing is now a mature technology and facilitates the development of genotyping chips and other genetic approaches such as genome wide association studies (GWAS). Furthermore, microarray-based technologies have been eclipsed by RNA-seq, the high-throughput sequencing of RNA. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses such as NILs and EMS have appeared in addition to the classical segregating population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. Selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.

AB - In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequence obtained in the Rosoideae sub-family. This genome has a high level of synteny with genomes of other species of diploid and polyploid Fragaria, but it also provides a reference for species like Rubus and Rosa for functional genomics. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. For genotyping, many studies have used simple sequence repeats (SSRs) but whole genome sequencing is now a mature technology and facilitates the development of genotyping chips and other genetic approaches such as genome wide association studies (GWAS). Furthermore, microarray-based technologies have been eclipsed by RNA-seq, the high-throughput sequencing of RNA. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses such as NILs and EMS have appeared in addition to the classical segregating population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. Selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.

KW - Fragaria

KW - Functional genomics

KW - Omics

KW - Polyploidy

U2 - 10.17660/ActaHortic.2017.1156.3

DO - 10.17660/ActaHortic.2017.1156.3

M3 - Conference paper

VL - 1156

T3 - Acta Horticulturae

SP - 13

EP - 24

BT - 8th International Strawberry Symposium

PB - International Society for Horticultural Science

ER -

Denoyes B, Amaya I, Liston A, Tennessen J, Ashman TL, Whitaker VM et al. Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. In 8th International Strawberry Symposium. Vol. 1156. International Society for Horticultural Science. 2017. p. 13-24. (Acta Horticulturae). https://doi.org/10.17660/ActaHortic.2017.1156.3