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

Souleyre EJF, Bowen JK, Matich AJ, Tomes S, Chen X, Hunt MB, Wang MY, Ileperuma NR, Richards K, Rowan DD, Chagné D, Atkinson RG.

Plant J. 2019 Aug 22. doi: 10.1111/tpj.14504. [Epub ahead of print]


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

Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB.

BMC Genomics. 2019 May 2;20(1):331. doi: 10.1186/s12864-019-5712-3.


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

Pilkington SM, Tahir J, Hilario E, Gardiner SE, Chagné D, Catanach A, McCallum J, Jesson L, Fraser LG, McNeilage MA, Deng C, Crowhurst RN, Datson PM, Zhang Q.

BMC Plant Biol. 2019 Apr 30;19(1):172. doi: 10.1186/s12870-019-1766-2.


Indigenous Perspectives and Gene Editing in Aotearoa New Zealand.

Hudson M, Mead ATP, Chagné D, Roskruge N, Morrison S, Wilcox PL, Allan AC.

Front Bioeng Biotechnol. 2019 Apr 11;7:70. doi: 10.3389/fbioe.2019.00070. eCollection 2019.


Apple whole genome sequences: recent advances and new prospects.

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.

Hortic Res. 2019 Apr 5;6:59. doi: 10.1038/s41438-019-0141-7. eCollection 2019. Review.


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

Chagné D, Vanderzande S, Kirk C, Profitt N, Weskett R, Gardiner SE, Peace CP, Volz RK, Bassil NV.

Hortic Res. 2019 Mar 1;6:30. doi: 10.1038/s41438-018-0114-2. eCollection 2019.


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

VanBuren R, Wai CM, Colle M, Wang J, Sullivan S, Bushakra JM, Liachko I, Vining KJ, Dossett M, Finn CE, Jibran R, Chagné D, Childs K, Edger PP, Mockler TC, Bassil NV.

Gigascience. 2018 Aug 1;7(8). doi: 10.1093/gigascience/giy094.


Diversification and independent domestication of Asian and European pears.

Wu J, Wang Y, Xu J, Korban SS, Fei Z, Tao S, Ming R, Tai S, Khan AM, Postman JD, Gu C, Yin H, Zheng D, Qi K, Li Y, Wang R, Deng CH, Kumar S, Chagné D, Li X, Wu J, Huang X, Zhang H, Xie Z, Li X, Zhang M, Li Y, Yue Z, Fang X, Li J, Li L, Jin C, Qin M, Zhang J, Wu X, Ke Y, Wang J, Yang H, Zhang S.

Genome Biol. 2018 Jun 11;19(1):77. doi: 10.1186/s13059-018-1452-y.


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

Pilkington SM, Crowhurst R, Hilario E, Nardozza S, Fraser L, Peng Y, Gunaseelan K, Simpson R, Tahir J, Deroles SC, Templeton K, Luo Z, Davy M, Cheng C, McNeilage M, Scaglione D, Liu Y, Zhang Q, Datson P, De Silva N, Gardiner SE, Bassett H, Chagné D, McCallum J, Dzierzon H, Deng C, Wang YY, Barron L, Manako K, Bowen J, Foster TM, Erridge ZA, Tiffin H, Waite CN, Davies KM, Grierson EP, Laing WA, Kirk R, Chen X, Wood M, Montefiori M, Brummell DA, Schwinn KE, Catanach A, Fullerton C, Li D, Meiyalaghan S, Nieuwenhuizen N, Read N, Prakash R, Hunter D, Zhang H, McKenzie M, Knäbel M, Harris A, Allan AC, Gleave A, Chen A, Janssen BJ, Plunkett B, Ampomah-Dwamena C, Voogd C, Leif D, Lafferty D, Souleyre EJF, Varkonyi-Gasic E, Gambi F, Hanley J, Yao JL, Cheung J, David KM, Warren B, Marsh K, Snowden KC, Lin-Wang K, Brian L, Martinez-Sanchez M, Wang M, Ileperuma N, Macnee N, Campin R, McAtee P, Drummond RSM, Espley RV, Ireland HS, Wu R, Atkinson RG, Karunairetnam S, Bulley S, Chunkath S, Hanley Z, Storey R, Thrimawithana AH, Thomson S, David C, Testolin R, Huang H, Hellens RP, Schaffer RJ.

BMC Genomics. 2018 Apr 16;19(1):257. doi: 10.1186/s12864-018-4656-3.


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

Bilton TP, Schofield MR, Black MA, Chagné D, Wilcox PL, Dodds KG.

Genetics. 2018 May;209(1):65-76. doi: 10.1534/genetics.117.300627. Epub 2018 Feb 27.


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

Jibran R, Dzierzon H, Bassil N, Bushakra JM, Edger PP, Sullivan S, Finn CE, Dossett M, Vining KJ, VanBuren R, Mockler TC, Liachko I, Davies KM, Foster TM, Chagné D.

Hortic Res. 2018 Feb 7;5:8. doi: 10.1038/s41438-017-0013-y. eCollection 2018.


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

Hunter DA, Jibran R, Dijkwel P, Chagné D, Sullivan K, Kanojia A, Crowhurst R.

Methods Mol Biol. 2018;1744:195-220. doi: 10.1007/978-1-4939-7672-0_17.


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

Yauk YK, Souleyre EJF, Matich AJ, Chen X, Wang MY, Plunkett B, Dare AP, Espley RV, Tomes S, Chagné D, Atkinson RG.

Plant J. 2017 Jul;91(2):292-305. doi: 10.1111/tpj.13564. Epub 2017 Jun 1.


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

Li L, Deng CH, Knäbel M, Chagné D, Kumar S, Sun J, Zhang S, Wu J.

DNA Res. 2017 Jun 1;24(3):289-301. doi: 10.1093/dnares/dsw063.


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

Guitton B, Kelner JJ, Celton JM, Sabau X, Renou JP, Chagné D, Costes E.

BMC Plant Biol. 2016 Feb 29;16:55. doi: 10.1186/s12870-016-0739-y.


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

Montanari S, Brewer L, Lamberts R, Velasco R, Malnoy M, Perchepied L, Guérif P, Durel CE, Bus VG, Gardiner SE, Chagné D.

Hortic Res. 2016 Jan 6;3:15064. doi: 10.1038/hortres.2015.64. eCollection 2016.


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

Foster TM, Celton JM, Chagné D, Tustin DS, Gardiner SE.

Hortic Res. 2015 Feb 11;2:15001. doi: 10.1038/hortres.2015.1. eCollection 2015.


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

Kumar S, Molloy C, Muñoz P, Daetwyler H, Chagné D, Volz R.

G3 (Bethesda). 2015 Oct 23;5(12):2711-8. doi: 10.1534/g3.115.021105.


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

Boocock J, Chagné D, Merriman TR, Black MA.

BMC Genomics. 2015 Oct 23;16:848. doi: 10.1186/s12864-015-2096-x.


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

Knäbel M, Friend AP, Palmer JW, Diack R, Wiedow C, Alspach P, Deng C, Gardiner SE, Tustin DS, Schaffer R, Foster T, Chagné D.

BMC Plant Biol. 2015 Sep 22;15:230. doi: 10.1186/s12870-015-0620-4.


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

Yao JL, Xu J, Cornille A, Tomes S, Karunairetnam S, Luo Z, Bassett H, Whitworth C, Rees-George J, Ranatunga C, Snirc A, Crowhurst R, de Silva N, Warren B, Deng C, Kumar S, Chagné D, Bus VG, Volz RK, Rikkerink EH, Gardiner SE, Giraud T, MacDiarmid R, Gleave AP.

Plant J. 2015 Oct;84(2):417-27. doi: 10.1111/tpj.13021.


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

Jibran R, Sullivan KL, Crowhurst R, Erridge ZA, Chagné D, McLachlan AR, Brummell DA, Dijkwel PP, Hunter DA.

J Exp Bot. 2015 Nov;66(21):6849-62. doi: 10.1093/jxb/erv390. Epub 2015 Aug 10.


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

Yauk YK, Chagné D, Tomes S, Matich AJ, Wang MY, Chen X, Maddumage R, Hunt MB, Rowan DD, Atkinson RG.

Plant J. 2015 Jun;82(6):937-50. doi: 10.1111/tpj.12861. Epub 2015 May 20.


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

Bastiaanse H, Bassett HC, Kirk C, Gardiner SE, Deng C, Groenworld R, Chagné D, Bus VG.

Mol Plant Pathol. 2016 Feb;17(2):159-72. doi: 10.1111/mpp.12269. Epub 2015 Jun 7.


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

Chagné D, Bianco L, Lawley C, Micheletti D, Jacobs JM.

Methods Mol Biol. 2015;1245:281-98. doi: 10.1007/978-1-4939-1966-6_21.


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

Chagné D.

Methods Mol Biol. 2015;1245:151-9. doi: 10.1007/978-1-4939-1966-6_11.


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

Bianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M.

PLoS One. 2014 Oct 10;9(10):e110377. doi: 10.1371/journal.pone.0110377. eCollection 2014.


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

Saeed M, Brewer L, Johnston J, McGhie TK, Gardiner SE, Heyes JA, Chagné D.

BMC Plant Biol. 2014 Sep 16;14:241. doi: 10.1186/s12870-014-0241-3.


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

Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, Knäbel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VG, Schaffer RJ, Gardiner SE, Velasco R.

PLoS One. 2014 Apr 3;9(4):e92644. doi: 10.1371/journal.pone.0092644. eCollection 2014.


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

Souleyre EJ, Chagné D, Chen X, Tomes S, Turner RM, Wang MY, Maddumage R, Hunt MB, Winz RA, Wiedow C, Hamiaux C, Gardiner SE, Rowan DD, Atkinson RG.

Plant J. 2014 Jun;78(6):903-15. doi: 10.1111/tpj.12518. Epub 2014 May 23.


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

Chagné D, Dayatilake D, Diack R, Oliver M, Ireland H, Watson A, Gardiner SE, Johnston JW, Schaffer RJ, Tustin S.

Hortic Res. 2014 Sep 17;1:14046. doi: 10.1038/hortres.2014.46. eCollection 2014.


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

Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D.

PLoS One. 2013 Oct 14;8(10):e77022. doi: 10.1371/journal.pone.0077022. eCollection 2013.


Novel genomic approaches unravel genetic architecture of complex traits in apple.

Kumar S, Garrick DJ, Bink MC, Whitworth C, Chagné D, Volz RK.

BMC Genomics. 2013 Jun 12;14:393. doi: 10.1186/1471-2164-14-393.


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

Bushakra JM, Krieger C, Deng D, Stephens MJ, Allan AC, Storey R, Symonds VV, Stevenson D, McGhie T, Chagné D, Buck EJ, Gardiner SE.

Theor Appl Genet. 2013 Mar;126(3):847-65. doi: 10.1007/s00122-012-2022-4. Epub 2012 Dec 9.


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

Chagné D, Lin-Wang K, Espley RV, Volz RK, How NM, Rouse S, Brendolise C, Carlisle CM, Kumar S, De Silva N, Micheletti D, McGhie T, Crowhurst RN, Storey RD, Velasco R, Hellens RP, Gardiner SE, Allan AC.

Plant Physiol. 2013 Jan;161(1):225-39. doi: 10.1104/pp.112.206771. Epub 2012 Oct 24.


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

Mellidou I, Chagné D, Laing WA, Keulemans J, Davey MW.

Plant Physiol. 2012 Nov;160(3):1613-29. doi: 10.1104/pp.112.203786. Epub 2012 Sep 21.


Genomic selection for fruit quality traits in apple (Malus×domestica Borkh.).

Kumar S, Chagné D, Bink MC, Volz RK, Whitworth C, Carlisle C.

PLoS One. 2012;7(5):e36674. doi: 10.1371/journal.pone.0036674. Epub 2012 May 4.


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

Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE.

Theor Appl Genet. 2012 Jul;125(2):311-27. doi: 10.1007/s00122-012-1835-5. Epub 2012 Mar 8.


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

Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C.

PLoS One. 2012;7(2):e31745. doi: 10.1371/journal.pone.0031745. Epub 2012 Feb 21.


QTL and candidate gene mapping for polyphenolic composition in apple fruit.

Chagné D, Krieger C, Rassam M, Sullivan M, Fraser J, André C, Pindo M, Troggio M, Gardiner SE, Henry RA, Allan AC, McGhie TK, Laing WA.

BMC Plant Biol. 2012 Jan 23;12:12. doi: 10.1186/1471-2229-12-12.


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

Devoghalaere F, Doucen T, Guitton B, Keeling J, Payne W, Ling TJ, Ross JJ, Hallett IC, Gunaseelan K, Dayatilake GA, Diak R, Breen KC, Tustin DS, Costes E, Chagné D, Schaffer RJ, David KM.

BMC Plant Biol. 2012 Jan 13;12:7. doi: 10.1186/1471-2229-12-7.


Genetic control of biennial bearing in apple.

Guitton B, Kelner JJ, Velasco R, Gardiner SE, Chagné D, Costes E.

J Exp Bot. 2012 Jan;63(1):131-49. doi: 10.1093/jxb/err261. Epub 2011 Sep 30.


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

Brendolise C, Yauk YK, Eberhard ED, Wang M, Chagne D, Andre C, Greenwood DR, Beuning LL.

FEBS J. 2011 Jul;278(14):2485-99. doi: 10.1111/j.1742-4658.2011.08175.x. Epub 2011 Jun 24.


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

Lin-Wang K, Micheletti D, Palmer J, Volz R, Lozano L, Espley R, Hellens RP, Chagnè D, Rowan DD, Troggio M, Iglesias I, Allan AC.

Plant Cell Environ. 2011 Jul;34(7):1176-90. doi: 10.1111/j.1365-3040.2011.02316.x. Epub 2011 Apr 21.


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

Illa E, Sargent DJ, Lopez Girona E, Bushakra J, Cestaro A, Crowhurst R, Pindo M, Cabrera A, van der Knaap E, Iezzoni A, Gardiner S, Velasco R, Arús P, Chagné D, Troggio M.

BMC Evol Biol. 2011 Jan 12;11:9. doi: 10.1186/1471-2148-11-9.


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

Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R.

Nat Genet. 2010 Oct;42(10):833-9. doi: 10.1038/ng.654. Epub 2010 Aug 29.


Update on comparative genome mapping between Malus and Pyrus.

Celton JM, Chagné D, Tustin SD, Terakami S, Nishitani C, Yamamoto T, Gardiner SE.

BMC Res Notes. 2009 Sep 14;2:182. doi: 10.1186/1756-0500-2-182.


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

Rowan DD, Hunt MB, Dimouro A, Alspach PA, Weskett R, Volz RK, Gardiner SE, Chagné D.

J Agric Food Chem. 2009 Sep 9;57(17):7953-61. doi: 10.1021/jf901678v.


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

Espley RV, Brendolise C, Chagné D, Kutty-Amma S, Green S, Volz R, Putterill J, Schouten HJ, Gardiner SE, Hellens RP, Allan AC.

Plant Cell. 2009 Jan;21(1):168-83. doi: 10.1105/tpc.108.059329. Epub 2009 Jan 16.


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

Han Y, Chagné D, Gasic K, Rikkerink EH, Beever JE, Gardiner SE, Korban SS.

Genomics. 2009 Mar;93(3):282-8. doi: 10.1016/j.ygeno.2008.11.005. Epub 2008 Dec 21.

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