Dr David Chagné

Honorary Senior Research Fellow, Otago & Scientist, Plant & Food Research
David Chagne
  • Biochemistry Department
  • School of Biomedical Sciences
  • University of Otago
  • P.O. Box 56
  • 710 Cumberland St
  • Dunedin 9054 , New Zealand
  • Tel.: 64 3 479-7872
  • Fax: 64 3 479-7866
  • Email:david.chagne@plantandfood.co.nz

My research focuses on the application of genetic mapping and genomics to elucidate the genetic control of important plant characters. I have a strong underpinning interest in the study of DNA variations in plant genomes.

I have catalogued single nucleotide polymorphisms (SNPs) in the apple and pear genomes and led an international project that has sequenced the European pear genome. Using this information, I have identified markers linked to significant traits, including fruit antioxidant content, red flesh and peel, crispness and aroma. I designed a SNP assay that has been used to accurately predict fruit quality of young apple seedlings using genome-wide selection, years before they first set fruit.

Selected Publications

Boocock J, Chagné D, Merriman T, Black M 2015 The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh. BMC Genomics 10.1186/s12864-015-2096-x.

Kumar S, Molloy C, Munoz P, Daetwyler H, Chagné D, Volz R 2015 Genome-enabled estimates of additive and non-additive genetic variances and prediction of apple phenotypes across environments. Genes, Genomes, Genetics (G3) 10.1534/g3.115.021105.

Chagné D, Kirk C, Whitworth C, Erasmusson S, Bicknell R, Sargent D, Kumar S, Troggio M 2015 Polyploid and aneuploid detection in apple using a single nucleotide polymorphism array. Tree Genetics & Genomes 11:94.

Yao JL, Xu J, Cornille A, Tomes S, Karunairetnam S, Luo Z, Bassett H, Whitwoirth C, Ress-George J, Ranatunga C, Snirc A, Crowhurst R, de Silva N, Warren B, Deng C, Kumar S, Chagné D, Bus V, Volz R, Rikkerink E, Gardiner S, Giraud T, MacDiarmid R, Gleave A 2015 A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal 10.1111/tpj.13021

Jibran R, Sullivan K, Crowhurst R, Erridge Z, Chagné D, McLachlan A, Brummell D, Dijkwel P, Hunter D 2015 Staying green postharvest: how three mutations in the Arabidopsis chlorophyll b reductase gene NYC1 delay degreening by distinct mechanisms. Journal of Experimental Botany 10.1093/jxb/erv390

Knäbel M, Friend AP, Palmer JW, Diack R, Wiedow C, Alspach P, Deng C, Gardiner SE, Tustin DS, Schaffer R, Foster T, Chagné D 2015 Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci. BMC Plant Biology 15:230.

Marshall CW, Chagné D, Deusch O, Gruenheit N, McCallum J, Bergin D, Lockhart P, Wilcox P 2015 A DNA-based diagnostic for differentiating among New Zealand endemic Podocarpus. Tree Genetics & Genomes 11(4):1-16.

Montanari S, Guérif P, Ravon E, Denancé C, Muranty H, Velasco R, Chagné D, Bus VGM, Robert P, Perchepied L, Durel C-E 2015 Genetic mapping of Cacopsylla pyri resistance in an interspecific pear (Pyrus spp.) population. Tree Genetics & Genomes 11(4):1-14

Foster TM, Celton J-M, Chagné D, Tustin DS, Gardiner SE 2015 Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple. Horticulture Research

Kumar S, Rowan D, Hunt M, Chagné D, Whitworth C, Souleyre E 2015 Genome-wide scans reveal genetic architecture of apple flavour volatiles. Molecular Breeding 35(5):1-16.

Yauk YK, Chagné D, Tomes S, Matich A, Wang M, Chen X, Maddumage R, Hunt M, Rowan D, Atkinson R 2015 The O-methyltransferase MdoOMT1 is required for biosynthesis of methylated phenylpropenes in ripe apple fruit. Plant Journal, DOI: 10.1111/tpj.12861

Bastiaanse H, Bassett H, Kirk C, Gardiner S, Deng C, Remmelt G, Chagné D, Bus V 2015 Scab resistance in ‘Geneva’ apple is conditioned by a resistance gene cluster with complex genetic control. Molecular Plant Pathology, DOI: 10.1111/mpp.12269.

Chagné D, Dayatilake D, Diack R, Oliver M, Ireland H, Watson A, Gardiner SE, Johnston J, Schaffer R, Tustin S 2014 Genetic and environmental control of fruit maturation, dry matter and firmness in apple (Malus x domestica Borkh.). Horticulture Research 1:14046.

Won K, Bastiaanse H, Kim YK, Song JH, Kang SS, Lee HC, Cho KH, Brewer L, Singla G, Gardiner SE, Chagné D, Bus V 2014 Genetic mapping of polygenic scab (Venturia pirina) resistance in an interspecific pear family. Molecular Breeding 34(4): 2179-2189.

Saeed M, Brewer L, Johnston J, McGhie T, Gardiner SE, Heyes JA, Chagné D 2014 Genetic metabolite and developmental determinism of fruit friction discolouration in pear. BMC Plant Biology 14:241.

Lozano L, Micheletti D, Kumar S, Volz RK, Gardiner SE, Allan AC, Iglesias I, Troggio M, Chagné D 2014 Feasibility of genome-wide association analysis using a small SNP panel in an apple breeding population. Journal of the American Society of Horticulture Science 139(6):619-626.

Souleyre EJF, 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 (2014) The AAT1 locus is critical for the biosynthesis of esters contributing to 'ripe apple' flavour in 'Royal Gala' and 'Granny Smith' apples. Plant Journal 78(6): 903-915.

Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, et al. 2014 The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’) PLoS ONE 9(4)

Kumar S, Raulier P, Chagné D, Whitworth C 2014 Genetic differentiation between Malus domestica and Malus sieversii at genome-wide single nucleotide polymorphic (SNP) markers and quantitative traits. Plant Genetic Resources 12(3):330-340.

Montanari S, Saeed M, Knabel 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 2013 Identification of Pyrus Single Nucleotide Polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus. PLoS ONE 8(10):e77022.

Kumar S, Garrick DJ, Bink MC, Whitworth C, Chagné D, Volz RK 2013. Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics 14:393

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 2013. An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiology 161(1): 225–239.

Bushakra J, Krieger C, Deng D, Stephens J, Allan A, Storey R, Symonds V, Stevenson D, McGhie T, Chagné D, Buck E, Gardiner S 2012. QTL involved in the modification of cyanidin compounds in black and red raspberry fruit. Theoretical and Applied Genetics 126(3):847-865.

Mellidou I, Chagné D, Laing WA, Keulemans J, Davey MW 2012. Allelic variation in paralogs of GDP-l-Galactose Phosphorylase is a major determinant of vitamin C concentrations in apple fruit. Plant Physiology 160(3):1613–1629.

Kumar S, Chagné D, Bink MCAM, Volz RK, Witworth C, Carlisle CM 2012. Genomic selection for complex fruit quality traits in apple (Malus x domestica Borkh). PLoS ONE 7(5): e36674.

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 2012. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7(2): e31745.

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 2012. QTL and candidate gene mapping for polyphenolic composition in apple fruit. BMC Plant Biology 12: 12

Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE 2012. Construction of black (Rubus occidentalis) and red (R. Idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple and peach. Theoretical and Applied Genetics 125(2): 311–327.

Guitton B, Kelner JJ, Velasco R, Gardiner SE, Chagné D, Costes E 2012. Genetic control of biennial bearing in apple. Journal of Experimental Botany 63(1): 131–149.

Bushakra JM, Sargent DJ, Cabrera A, Crowhurst R, Girona EL, Velasco R, Symonds VV, van der Knaap E, Troggio M, Gardiner SE, Chagné D 2012. Rosaceae conserved orthologous set (RosCOS) markers as a tool to assess genome synteny between Malus and Fragaria. Tree Genetics & Genomes 8(4):643-658.

Kumar S, Bink MCAM, Volz RK, Bus VGM, Chagné D 2012. Towards genomic selection in apple (Malus x domestica Borkh.) breeding programmes: Prospects, challenges and strategies. Tree Genetics & Genomes 8(1): 1–14.

Troggio M, Gleave A, Salvi S, Chagné D, Cestaro A, Kumar S, Crowhurst RN, Gardiner SE 2012. Apple, from genome to breeding. Tree Genetics & Genomes 8(3): 509-529.

Sarkhosh A, Zamani Z, Fatahi R, Wiedow C, Chagné D, Gardiner SE 2012. A pomegranate (Punica granatum L.) linkage map based on AFLP markers. Journal of Horticultural Science and Biotechnology 87(1):1-6.

Devoghalaere F, Doucen T, Guitton B, Keeling J, Payne W, Ling TJ, Ross JJ, Hallett IC, Gunaseelan K, Dayatilake DGA, Diack R, Breen KC, Tustin DS, Costes E, Chagné D, Schaffer RJ, David KM 2012. A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control. BMC Plant Biology DOI: 10.1186/1471-2229-12-7.

Lin-Wang K, Micheletti D, Palmer J, Volz R, Lozano L, Espley R, Hellens R, Chagné D, Rowan D, Troggio M, Iglesias I, Allan A 2011. Temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex. Plant Cell & Environment 34(7): 1176–1190.

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 2011. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evolutionary Biology 11: 9.

Brendolise C, Yauk YK, Eberhard ED, Wang M, Chagné D, Andre C, Greenwood DR, Beuning LL 2011. An unusual plant triterpene synthase with predominant alpha-amyrin-producing activity identified by characterizing oxidosqualene cyclases from Malus x domestica. FEBS Journal 278(14):2485-2499.

Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar S, Troggio M, Pruss D, et al., Chagné D, et al. 2010. The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics 42(10): 833–839.

Sooriyapathirana SS, Khan A, Sebolt AM, Wang DC, Bushakra JM, Lin-Wang K, Allan AC, Gardiner SE, Chagné D, Iezzoni AF 2010. QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.) Tree Genetics & Genomes 6(6): 821-832.

Bus VGM, Bassett HCM, Bowatte D, Chagné D, Ranatunga CA, Ulluwishewa D, Wiedow C, Gardiner SE 2010. Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated Mildew Immune Selection. Tree Genetics & Genomes 6(3): 477-487.