Apple whole genome sequences

recent advances and new prospects

Cameron P. Peace*, Luca Bianco, Michela Troggio, Eric van de Weg, Nicholas P. Howard, Amandine Cornille, Charles Eric Durel, Sean Myles, Zoë Migicovsky, Robert J. Schaffer, Evelyne Costes, Gennaro Fazio, Hisayo Yamane, Steve van Nocker, Chris Gottschalk, Fabrizio Costa, David Chagné, Xinzhong Zhang, Andrea Patocchi, Susan E. Gardiner & 7 others Craig Hardner, Satish Kumar, Francois Laurens, Etienne Bucher, Dorrie Main, Sook Jung, Stijn Vanderzande

*Corresponding author for this work

Research output: Contribution to journalReview articleAcademicpeer-review

2 Citations (Scopus)

Abstract

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Original languageEnglish
Article number59
JournalHorticulture Research
Volume6
Issue number1
DOIs
Publication statusPublished - 5 Apr 2019

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Malus
apples
Genes
Genome
genome
Crops
genomics
tree fruits
fruit crops
wild relatives
Malus domestica
crops
Quantitative Trait Loci
Physiology
Genetic Association Studies
pedigree
Pedigree
diagnostic techniques
Fruits
Genomics

Cite this

Peace, C. P., Bianco, L., Troggio, M., van de Weg, E., Howard, N. P., Cornille, A., ... Vanderzande, S. (2019). Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6(1), [59]. https://doi.org/10.1038/s41438-019-0141-7
Peace, Cameron P. ; Bianco, Luca ; Troggio, Michela ; van de Weg, Eric ; Howard, Nicholas P. ; Cornille, Amandine ; Durel, Charles Eric ; Myles, Sean ; Migicovsky, Zoë ; Schaffer, Robert J. ; Costes, Evelyne ; Fazio, Gennaro ; Yamane, Hisayo ; van Nocker, Steve ; Gottschalk, Chris ; Costa, Fabrizio ; Chagné, David ; Zhang, Xinzhong ; Patocchi, Andrea ; Gardiner, Susan E. ; Hardner, Craig ; Kumar, Satish ; Laurens, Francois ; Bucher, Etienne ; Main, Dorrie ; Jung, Sook ; Vanderzande, Stijn. / Apple whole genome sequences : recent advances and new prospects. In: Horticulture Research. 2019 ; Vol. 6, No. 1.
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title = "Apple whole genome sequences: recent advances and new prospects",
abstract = "In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.",
author = "Peace, {Cameron P.} and Luca Bianco and Michela Troggio and {van de Weg}, Eric and Howard, {Nicholas P.} and Amandine Cornille and Durel, {Charles Eric} and Sean Myles and Zo{\"e} Migicovsky and Schaffer, {Robert J.} and Evelyne Costes and Gennaro Fazio and Hisayo Yamane and {van Nocker}, Steve and Chris Gottschalk and Fabrizio Costa and David Chagn{\'e} and Xinzhong Zhang and Andrea Patocchi and Gardiner, {Susan E.} and Craig Hardner and Satish Kumar and Francois Laurens and Etienne Bucher and Dorrie Main and Sook Jung and Stijn Vanderzande",
year = "2019",
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day = "5",
doi = "10.1038/s41438-019-0141-7",
language = "English",
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journal = "Horticulture Research",
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Peace, CP, Bianco, L, Troggio, M, van de Weg, E, Howard, NP, Cornille, A, Durel, CE, Myles, S, Migicovsky, Z, Schaffer, RJ, Costes, E, Fazio, G, Yamane, H, van Nocker, S, Gottschalk, C, Costa, F, Chagné, D, Zhang, X, Patocchi, A, Gardiner, SE, Hardner, C, Kumar, S, Laurens, F, Bucher, E, Main, D, Jung, S & Vanderzande, S 2019, 'Apple whole genome sequences: recent advances and new prospects', Horticulture Research, vol. 6, no. 1, 59. https://doi.org/10.1038/s41438-019-0141-7

Apple whole genome sequences : recent advances and new prospects. / Peace, Cameron P.; Bianco, Luca; Troggio, Michela; van de Weg, Eric; Howard, Nicholas P.; Cornille, Amandine; Durel, Charles Eric; Myles, Sean; Migicovsky, Zoë; Schaffer, Robert J.; Costes, Evelyne; Fazio, Gennaro; Yamane, Hisayo; van Nocker, Steve; Gottschalk, Chris; Costa, Fabrizio; Chagné, David; Zhang, Xinzhong; Patocchi, Andrea; Gardiner, Susan E.; Hardner, Craig; Kumar, Satish; Laurens, Francois; Bucher, Etienne; Main, Dorrie; Jung, Sook; Vanderzande, Stijn.

In: Horticulture Research, Vol. 6, No. 1, 59, 05.04.2019.

Research output: Contribution to journalReview articleAcademicpeer-review

TY - JOUR

T1 - Apple whole genome sequences

T2 - recent advances and new prospects

AU - Peace, Cameron P.

AU - Bianco, Luca

AU - Troggio, Michela

AU - van de Weg, Eric

AU - Howard, Nicholas P.

AU - Cornille, Amandine

AU - Durel, Charles Eric

AU - Myles, Sean

AU - Migicovsky, Zoë

AU - Schaffer, Robert J.

AU - Costes, Evelyne

AU - Fazio, Gennaro

AU - Yamane, Hisayo

AU - van Nocker, Steve

AU - Gottschalk, Chris

AU - Costa, Fabrizio

AU - Chagné, David

AU - Zhang, Xinzhong

AU - Patocchi, Andrea

AU - Gardiner, Susan E.

AU - Hardner, Craig

AU - Kumar, Satish

AU - Laurens, Francois

AU - Bucher, Etienne

AU - Main, Dorrie

AU - Jung, Sook

AU - Vanderzande, Stijn

PY - 2019/4/5

Y1 - 2019/4/5

N2 - In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

AB - In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

U2 - 10.1038/s41438-019-0141-7

DO - 10.1038/s41438-019-0141-7

M3 - Review article

VL - 6

JO - Horticulture Research

JF - Horticulture Research

SN - 2052-7276

IS - 1

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ER -