List of works - David Chagné

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

scientific article published in 2020

A QTL detected in an interspecific pear population confers stable fire blight resistance across different environments and genetic backgrounds

scholarly article

A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control.

scientific article

A high density linkage map and quantitative trait loci for tree growth for New Zealand mānuka (Leptospermum scoparium)

scientific article published in 2018

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

scientific article published on 16 April 2018

A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution.

scientific article published on 10 September 2015

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

article by Robert VanBuren et al published 1 August 2018 in GigaScience

Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations

scientific article published on 27 February 2018

Alcohol acyl transferase 1 links two distinct volatile pathways that produce esters and phenylpropenes in apple fruit

scientific article published on 5 April 2017

Allelic variation in paralogs of GDP-L-galactose phosphorylase is a major determinant of vitamin C concentrations in apple fruit

scientific article published on 21 September 2012

An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes.

scientific article published on 24 October 2012

An exploration of assembly strategies and quality metrics on the accuracy of the Knightia excelsa (rewarewa) genome

scientific article published on 28 October 2020

An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa ( Knightia excelsa ) genome

scientific article published on 19 June 2021

An unusual plant triterpene synthase with predominant α-amyrin-producing activity identified by characterizing oxidosqualene cyclases from Malus × domestica

scientific article

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

scientific article

Analysis of transcripts differentially expressed between fruited and deflowered 'Gala' adult trees: a contribution to biennial bearing understanding in apple

scientific article

Apple whole genome sequences: recent advances and new prospects

scientific article published on 05 April 2019

Application of the high-resolution melting technique for gene mapping and SNP detection in plants

scientific article published on 01 January 2015

Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences

scientific article published in February 2004

BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple

scientific article published on 21 December 2008

Biosynthesis of the Dihydrochalcone Sweetener Trilobatin Requires Phloretin Glycosyltransferase 2

scientific article published on 30 July 2020

CRISPR-Cas9 enrichment and long read sequencing for fine mapping in plants

scientific article published on 01 September 2020

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data.

scientific article published on 7 February 2018

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family.

scientific article

Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences

article by J.-M. Celton et al published 2 August 2008 in Tree Genetics and Genomes

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach.

scientific article published on 8 March 2012

Cross-species transferability and mapping of genomic and cDNA SSRs in pines

article

Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).

scientific article

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

article

Development of a set of SNP markers present in expressed genes of the apple

scientific article

Diversification and independent domestication of Asian and European pears. ⬇️

scientific article published on 11 June 2018

Evolution and function of red pigmentation in land plants

scientific article published in 2022

Expressed sequence tags from the midgut of Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae).

scientific article

Fast construction of a reference genome: challenges and opportunities using ‘Royal Gala’ apple as a case study

scholarly article

First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit

publication published on 16 May 2022

Genetic and cytological analyses reveal the recombination landscape of a partially differentiated plant sex chromosome in kiwifruit

article

Genetic and environmental control of fruit maturation, dry matter and firmness in apple (Malus × domestica Borkh.).

scientific article

Genetic control of biennial bearing in apple

scientific article

Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

scientific article published on 22 September 2015

Genetic control of α-farnesene production in apple fruit and its role in fungal pathogenesis

scientific article published on 19 September 2019

Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers

scientific article published on 01 April 2001

Genetic mapping of pear sawfly (Caliroa cerasi) and pear blister mite (Eriophyes pyri) resistance in an interspecific pear family

scholarly article published on 20 May 2018

Genetic mapping of polygenic scab (Venturia pirina) resistance in an interspecific pear family

article published in 2014

Genetic mapping of the European canker (Neonectria ditissima) resistance locus Rnd1 from Malus ‘Robusta 5’

scholarly article

Genetic, metabolite and developmental determinism of fruit friction discolouration in pear

scientific article

Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated Mildew Immune Selection

article

Genome mapping of postzygotic hybrid necrosis in an interspecific pear population.

scientific article

Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.)

article

Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

scientific article

Genome-wide SNP detection, validation, and development of an 8K SNP array for apple

scientific article (publication date: 2012)

Genome-wide scans reveal genetic architecture of apple flavour volatiles

article by Satish Kumar et al published 22 April 2015 in Molecular Breeding

Genome‐wide analysis reveals the genetic stock structure of hoki ( Macruronus novaezelandiae )

scientific article published on 23 November 2021

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.) ⬇️

scientific article (publication date: 2012)

High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex

scientific article published on 21 April 2011

High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content

scientific article published in 2022

Identification of Postharvest Senescence Regulators Through Map-Based Cloning Using Detached Arabidopsis Inflorescences as a Model Tissue.

scientific article published in January 2018

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids

scientific article

Indigenous Perspectives and Gene Editing in Aotearoa New Zealand

article

Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome.

scientific article

Isolation and characterization of nuclear microsatellite loci in Pinus pinaster Ait

scientific article published in 2005

Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple

scientific article

Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation

scientific article published on 02 December 2019

Methods for the design, implementation, and analysis of illumina infinium™ SNP assays in plants.

scientific article published in January 2015

Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis)

scientific article published on 01 September 2019

Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples.

scientific article

Novel genomic approaches unravel genetic architecture of complex traits in apple

scientific article

Profiling fruit volatiles in the progeny of a 'Royal Gala' x 'Granny Smith' apple (Malus x domestica) cross.

scientific article published in September 2009

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).

scientific article published on 01 December 2019

QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population

scientific article published on 20 November 2020

QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.)

article

QTL and candidate gene mapping for polyphenolic composition in apple fruit

scientific article

QTL involved in the modification of cyanidin compounds in black and red raspberry fruit

scientific article published on 9 December 2012

Quantitative trait loci controlling vegetative propagation traits mapped in European pear (Pyrus communis L.)

scientific article published in 2017

Quantitative trait loci influencing pentacyclic triterpene composition in apple fruit peel

scientific article published on 06 December 2019

Resistance of New Zealand Provenance Leptospermum scoparium, Kunzea robusta, Kunzea linearis, and Metrosideros excelsa to Austropuccinia psidii

scientific article published on 09 April 2020

Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data

scientific article published on 06 April 2020

Scab resistance in 'Geneva' apple is conditioned by a resistance gene cluster with complex genetic control.

scientific article

Single nucleotide polymorphism analysis in Leptospermum scoparium (Myrtaceae) supports two highly differentiated endemic species in Aotearoa New Zealand and Australia

scientific article published in 2023

Staying green postharvest: how three mutations in the Arabidopsis chlorophyll b reductase gene NYC1 delay degreening by distinct mechanisms

scientific article published on 10 August 2015

Stress, senescence, and specialized metabolites in bryophytes

scientific article published in 2022

The AAT1 locus is critical for the biosynthesis of esters contributing to 'ripe apple' flavour in 'Royal Gala' and 'Granny Smith' apples.

scientific article published on 23 May 2014

The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

scientific article published on 01 November 2021

The O-methyltransferase gene MdoOMT1 is required for biosynthesis of methylated phenylpropenes in ripe apple fruit.

scientific article published on 22 April 2015

The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh.

scientific article published on 23 October 2015

The draft genome sequence of European pear (Pyrus communis L. 'Bartlett')

scientific article

The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus

scientific article published on 02 November 2021

The genome of the domesticated apple (Malus × domestica Borkh.)

scientific article

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

scientific article published on 12 April 2022

Two Loci, RiAF3 and RiAF4, Contribute to the Annual-Fruiting Trait in Rubus

scientific article published on 25 October 2019

Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple.

scientific article published on 11 February 2015

Update on comparative genome mapping between Malus and Pyrus

scientific article

Validation of SNP markers for fruit quality and disease resistance loci in apple ( × Borkh.) using the OpenArray® platform

article by David Chagné et al published 2019 in Horticulture research

List of works by David Chagné

<i>Austropuccinia psidii</i>, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

A QTL detected in an interspecific pear population confers stable fire blight resistance across different environments and genetic backgrounds

A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control.

A high density linkage map and quantitative trait loci for tree growth for New Zealand mānuka (<i>Leptospermum scoparium</i>)

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution.

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations

Alcohol acyl transferase 1 links two distinct volatile pathways that produce esters and phenylpropenes in apple fruit

Allelic variation in paralogs of GDP-L-galactose phosphorylase is a major determinant of vitamin C concentrations in apple fruit

An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes.

An exploration of assembly strategies and quality metrics on the accuracy of the Knightia excelsa (rewarewa) genome

An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa ( Knightia excelsa ) genome

An unusual plant triterpene synthase with predominant α-amyrin-producing activity identified by characterizing oxidosqualene cyclases from Malus × domestica

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

Analysis of transcripts differentially expressed between fruited and deflowered 'Gala' adult trees: a contribution to biennial bearing understanding in apple

Apple whole genome sequences: recent advances and new prospects

Application of the high-resolution melting technique for gene mapping and SNP detection in plants

Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences

BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple

Biosynthesis of the Dihydrochalcone Sweetener Trilobatin Requires Phloretin Glycosyltransferase 2

CRISPR-Cas9 enrichment and long read sequencing for fine mapping in plants

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data.

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family.

Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach.

Cross-species transferability and mapping of genomic and cDNA SSRs in pines

Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

Development of a set of SNP markers present in expressed genes of the apple

Diversification and independent domestication of Asian and European pears. ⬇️

Evolution and function of red pigmentation in land plants

Expressed sequence tags from the midgut of Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae).

Fast construction of a reference genome: challenges and opportunities using ‘Royal Gala’ apple as a case study

First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit

Genetic and cytological analyses reveal the recombination landscape of a partially differentiated plant sex chromosome in kiwifruit

Genetic and environmental control of fruit maturation, dry matter and firmness in apple (Malus × domestica Borkh.).

Genetic control of biennial bearing in apple

Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

Genetic control of α-farnesene production in apple fruit and its role in fungal pathogenesis

Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers

Genetic mapping of pear sawfly (Caliroa cerasi) and pear blister mite (Eriophyes pyri) resistance in an interspecific pear family

Genetic mapping of polygenic scab (Venturia pirina) resistance in an interspecific pear family

Genetic mapping of the European canker (Neonectria ditissima) resistance locus Rnd1 from Malus ‘Robusta 5’

Genetic, metabolite and developmental determinism of fruit friction discolouration in pear

Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated Mildew Immune Selection

Genome mapping of postzygotic hybrid necrosis in an interspecific pear population.

Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.)

Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

Genome-wide SNP detection, validation, and development of an 8K SNP array for apple

Genome-wide scans reveal genetic architecture of apple flavour volatiles

Genome‐wide analysis reveals the genetic stock structure of hoki ( Macruronus novaezelandiae )

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.) ⬇️

High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex

High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content

Identification of Postharvest Senescence Regulators Through Map-Based Cloning Using Detached Arabidopsis Inflorescences as a Model Tissue.

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids

Indigenous Perspectives and Gene Editing in Aotearoa New Zealand

Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome.

Isolation and characterization of nuclear microsatellite loci in Pinus pinaster Ait

Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple

Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation

Methods for the design, implementation, and analysis of illumina infinium™ SNP assays in plants.

Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis)

Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples.

Novel genomic approaches unravel genetic architecture of complex traits in apple

Profiling fruit volatiles in the progeny of a 'Royal Gala' x 'Granny Smith' apple (Malus x domestica) cross.

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).

QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population

QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.)

QTL and candidate gene mapping for polyphenolic composition in apple fruit

QTL involved in the modification of cyanidin compounds in black and red raspberry fruit

Quantitative trait loci controlling vegetative propagation traits mapped in European pear (Pyrus communis L.)

Quantitative trait loci influencing pentacyclic triterpene composition in apple fruit peel

Resistance of New Zealand Provenance Leptospermum scoparium, Kunzea robusta, Kunzea linearis, and Metrosideros excelsa to Austropuccinia psidii

Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data

Scab resistance in 'Geneva' apple is conditioned by a resistance gene cluster with complex genetic control.

Single nucleotide polymorphism analysis in Leptospermum scoparium (Myrtaceae) supports two highly differentiated endemic species in Aotearoa New Zealand and Australia

Staying green postharvest: how three mutations in the Arabidopsis chlorophyll b reductase gene NYC1 delay degreening by distinct mechanisms