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Items: 46

1.

A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource.

Mosca E, Cruz F, Gómez-Garrido J, Bianco L, Rellstab C, Brodbeck S, Csilléry K, Fady B, Fladung M, Fussi B, Gömöry D, González-Martínez SC, Grivet D, Gut M, Hansen OK, Heer K, Kaya Z, Krutovsky KV, Kersten B, Liepelt S, Opgenoorth L, Sperisen C, Ullrich KK, Vendramin GG, Westergren M, Ziegenhagen B, Alioto T, Gugerli F, Heinze B, Höhn M, Troggio M, Neale DB.

G3 (Bethesda). 2019 Jul 9;9(7):2039-2049. doi: 10.1534/g3.119.400083.

2.

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.

3.

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.

4.

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array.

Marrano A, Martínez-García PJ, Bianco L, Sideli GM, Di Pierro EA, Leslie CA, Stevens KA, Crepeau MW, Troggio M, Langley CH, Neale DB.

Plant Biotechnol J. 2019 Jun;17(6):1027-1036. doi: 10.1111/pbi.13034. Epub 2018 Dec 4.

5.

An integrated approach for increasing breeding efficiency in apple and peach in Europe.

Laurens F, Aranzana MJ, Arus P, Bassi D, Bink M, Bonany J, Caprera A, Corelli-Grappadelli L, Costes E, Durel CE, Mauroux JB, Muranty H, Nazzicari N, Pascal T, Patocchi A, Peil A, Quilot-Turion B, Rossini L, Stella A, Troggio M, Velasco R, van de Weg E.

Hortic Res. 2018 Mar 1;5:11. doi: 10.1038/s41438-018-0016-3. eCollection 2018. Review.

6.

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple.

Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE.

Front Plant Sci. 2017 Nov 10;8:1923. doi: 10.3389/fpls.2017.01923. eCollection 2017.

7.

Integrated QTL detection for key breeding traits in multiple peach progenies.

Hernández Mora JR, Micheletti D, Bink M, Van de Weg E, Cantín C, Nazzicari N, Caprera A, Dettori MT, Micali S, Banchi E, Campoy JA, Dirlewanger E, Lambert P, Pascal T, Troggio M, Bassi D, Rossini L, Verde I, Quilot-Turion B, Laurens F, Arús P, Aranzana MJ.

BMC Genomics. 2017 Jun 6;18(1):404. doi: 10.1186/s12864-017-3783-6.

8.

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development.

Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro EA, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E.

Nat Genet. 2017 Jul;49(7):1099-1106. doi: 10.1038/ng.3886. Epub 2017 Jun 5.

PMID:
28581499
9.

The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.

Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori MT, Schmutz J.

BMC Genomics. 2017 Mar 11;18(1):225. doi: 10.1186/s12864-017-3606-9.

10.

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species.

Di Pierro EA, Gianfranceschi L, Di Guardo M, Koehorst-van Putten HJ, Kruisselbrink JW, Longhi S, Troggio M, Bianco L, Muranty H, Pagliarani G, Tartarini S, Letschka T, Lozano Luis L, Garkava-Gustavsson L, Micheletti D, Bink MC, Voorrips RE, Aziz E, Velasco R, Laurens F, van de Weg WE.

Hortic Res. 2016 Nov 23;3:16057. eCollection 2016.

11.

Development and validation of the Axiom(®) Apple480K SNP genotyping array.

Bianco L, Cestaro A, Linsmith G, Muranty H, Denancé C, Théron A, Poncet C, Micheletti D, Kerschbamer E, Di Pierro EA, Larger S, Pindo M, Van de Weg E, Davassi A, Laurens F, Velasco R, Durel CE, Troggio M.

Plant J. 2016 Apr;86(1):62-74. doi: 10.1111/tpj.13145.

12.

Accuracy and responses of genomic selection on key traits in apple breeding.

Muranty H, Troggio M, Sadok IB, Rifaï MA, Auwerkerken A, Banchi E, Velasco R, Stevanato P, van de Weg WE, Di Guardo M, Kumar S, Laurens F, Bink MC.

Hortic Res. 2015 Dec 23;2:15060. doi: 10.1038/hortres.2015.60. eCollection 2015.

13.

Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm.

Micheletti D, Dettori MT, Micali S, Aramini V, Pacheco I, Da Silva Linge C, Foschi S, Banchi E, Barreneche T, Quilot-Turion B, Lambert P, Pascal T, Iglesias I, Carbó J, Wang LR, Ma RJ, Li XW, Gao ZS, Nazzicari N, Troggio M, Bassi D, Rossini L, Verde I, Laurens F, Arús P, Aranzana MJ.

PLoS One. 2015 Sep 9;10(9):e0136803. doi: 10.1371/journal.pone.0136803. eCollection 2015.

14.

ASSIsT: an automatic SNP scoring tool for in- and outbreeding species.

Di Guardo M, Micheletti D, Bianco L, Koehorst-van Putten HJ, Longhi S, Costa F, Aranzana MJ, Velasco R, Arús P, Troggio M, van de Weg EW.

Bioinformatics. 2015 Dec 1;31(23):3873-4. doi: 10.1093/bioinformatics/btv446. Epub 2015 Aug 6.

15.

A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'.

Falginella L, Cipriani G, Monte C, Gregori R, Testolin R, Velasco R, Troggio M, Tartarini S.

BMC Plant Biol. 2015 Jun 19;15:150. doi: 10.1186/s12870-015-0507-4.

16.

New candidate genes for the fine regulation of the colour of grapes.

Costantini L, Malacarne G, Lorenzi S, Troggio M, Mattivi F, Moser C, Grando MS.

J Exp Bot. 2015 Aug;66(15):4427-40. doi: 10.1093/jxb/erv159. Epub 2015 Jun 12.

17.

Micro- and macro-geographic scale effect on the molecular imprint of selection and adaptation in Norway spruce.

Scalfi M, Mosca E, Di Pierro EA, Troggio M, Vendramin GG, Sperisen C, La Porta N, Neale DB.

PLoS One. 2014 Dec 31;9(12):e115499. doi: 10.1371/journal.pone.0115499. eCollection 2014.

18.

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.

19.

QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

Verdu CF, Guyot S, Childebrand N, Bahut M, Celton JM, Gaillard S, Lasserre-Zuber P, Troggio M, Guilet D, Laurens F.

PLoS One. 2014 Oct 1;9(10):e107103. doi: 10.1371/journal.pone.0107103. eCollection 2014.

20.

Fast and cost-effective genetic mapping in apple using next-generation sequencing.

Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, Velasco R, Troggio M, Myles S.

G3 (Bethesda). 2014 Jul 16;4(9):1681-7. doi: 10.1534/g3.114.011023.

21.

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.

22.

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.

23.

Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin.

Troggio M, Surbanovski N, Bianco L, Moretto M, Giongo L, Banchi E, Viola R, Fernández FF, Costa F, Velasco R, Cestaro A, Sargent DJ.

PLoS One. 2013 Jun 27;8(6):e67407. doi: 10.1371/journal.pone.0067407. Print 2013.

24.

Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape.

Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS.

BMC Plant Biol. 2013 Mar 7;13:39. doi: 10.1186/1471-2229-13-39.

25.

A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome.

Khan MA, Han Y, Zhao YF, Troggio M, Korban SS.

PLoS One. 2012;7(11):e47864. doi: 10.1371/journal.pone.0047864. Epub 2012 Nov 5.

26.

Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.

Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ.

BMC Genomics. 2012 May 25;13:203. doi: 10.1186/1471-2164-13-203.

27.

Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm.

Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C.

PLoS One. 2012;7(4):e35668. doi: 10.1371/journal.pone.0035668. Epub 2012 Apr 20. Erratum in: PLoS One. 2012;7(6). doi:10.1371/annotation/33f1ba92-c304-4757-91aa-555de64a0768.

28.

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.

Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta KM, Sosinski B, Abbott A, Celton JM, Arús P, Shulaev V, Verde I, Morgante M, Rokhsar D, Velasco R, Sargent DJ.

BMC Genomics. 2012 Apr 4;13:129. doi: 10.1186/1471-2164-13-129.

29.

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.

30.

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.

31.

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.

32.

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.

33.

The genome of woodland strawberry (Fragaria vesca).

Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM.

Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26.

34.

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.

PMID:
20802477
35.

Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar.

Scalabrin S, Troggio M, Moroldo M, Pindo M, Felice N, Coppola G, Prete G, Malacarne G, Marconi R, Faes G, Jurman I, Grando S, Jesse T, Segala C, Valle G, Policriti A, Fontana P, Morgante M, Velasco R.

BMC Genomics. 2010 Mar 26;11:204. doi: 10.1186/1471-2164-11-204.

36.

A SNP transferability survey within the genus Vitis.

Vezzulli S, Micheletti D, Riaz S, Pindo M, Viola R, This P, Walker MA, Troggio M, Velasco R.

BMC Plant Biol. 2008 Dec 16;8:128. doi: 10.1186/1471-2229-8-128.

37.

Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: problems and solutions.

Zharkikh A, Troggio M, Pruss D, Cestaro A, Eldrdge G, Pindo M, Mitchell JT, Vezzulli S, Bhatnagar S, Fontana P, Viola R, Gutin A, Salamini F, Skolnick M, Velasco R.

J Biotechnol. 2008 Aug 31;136(1-2):38-43. doi: 10.1016/j.jbiotec.2008.04.013. Epub 2008 May 3.

PMID:
18538432
38.

A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers.

Vezzulli S, Troggio M, Coppola G, Jermakow A, Cartwright D, Zharkikh A, Stefanini M, Grando MS, Viola R, Adam-Blondon AF, Thomas M, This P, Velasco R.

Theor Appl Genet. 2008 Aug;117(4):499-511. doi: 10.1007/s00122-008-0794-3. Epub 2008 May 27.

PMID:
18504538
39.

A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes.

Salmaso M, Malacarne G, Troggio M, Faes G, Stefanini M, Grando MS, Velasco R.

Theor Appl Genet. 2008 May;116(8):1129-43. doi: 10.1007/s00122-008-0741-3.

PMID:
18347774
40.

SNP high-throughput screening in grapevine using the SNPlex genotyping system.

Pindo M, Vezzulli S, Coppola G, Cartwright DA, Zharkikh A, Velasco R, Troggio M.

BMC Plant Biol. 2008 Jan 28;8:12. doi: 10.1186/1471-2229-8-12.

41.

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety.

Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R.

PLoS One. 2007 Dec 19;2(12):e1326.

42.

A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs.

Troggio M, Malacarne G, Coppola G, Segala C, Cartwright DA, Pindo M, Stefanini M, Mank R, Moroldo M, Morgante M, Grando MS, Velasco R.

Genetics. 2007 Aug;176(4):2637-50. Epub 2007 Jul 1.

43.

Genetic mapping in the presence of genotyping errors.

Cartwright DA, Troggio M, Velasco R, Gutin A.

Genetics. 2007 Aug;176(4):2521-7. Epub 2007 Feb 4.

44.

An improved protocol for the production of AFLP markers in complex genomes by means of capillary electrophoresis.

Papa R, Troggio M, Ajmone-Marsan P, Nonnis Marzano F.

J Anim Breed Genet. 2005 Feb;122(1):62-8.

PMID:
16130490
45.

Comparative mapping in the Pinaceae.

Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB.

Genetics. 2004 Sep;168(1):447-61.

46.

A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.).

Scalfi M, Troggio M, Piovani P, Leonardi S, Magnaschi G, Vendramin GG, Menozzi P.

Theor Appl Genet. 2004 Feb;108(3):433-41. Epub 2003 Oct 22. Erratum in: Theor Appl Genet. 2004 Mar;108(5):967.

PMID:
14574454

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