Atanasoff D. Plum pox. A new virus disease. In: Yearbook University of Sofia, University of Sofia, F.o.A. Ed. Sofia. 1932;11:49–69.
Google Scholar
EPPO. Current Status of plum pox virus and sharka disease worldwide. Bulletin. OEPP/EPPO Bull. 2006;36:205–18.
Google Scholar
Rimbaud L, Dallot S, Gottwald T, Decroocq V, Jacquot E, Soubeyrand S, et al. Sharka epidemiology and worldwide management strategies: learning lessons to optimize disease control in perennial plants. Annu Rev Phytopathol. 2015;53:357–78.
Article
CAS
PubMed
Google Scholar
Decroocq V, Badenes ML, Neumüller M. Breeding for resistance to plum pox virus. In: Hadidi A, M Barba M, T Candresse T, Jelkmann W, editors. . Virus and virus-like diseases of pome and stone fruits. St Paul, MN, USA: The American Phytopathological Society Press; 2011. p. 401–6.
Google Scholar
Martínez-Gómez P, Rubio M, Dicenta F, Gradziel TM. Resistance to plum pox virus (RB3.30 isolate) in a group of California almonds and transfer of resistance to peach. Journal of the am. Soc. Hortic Sci. 2004;129:544–8.
Google Scholar
Pascal T, Pfeiffer F, Kervella J. Preliminary observations on the resistance to sharka in peach and related species. Acta Hortic. 2002;592:699–704.
Article
Google Scholar
Mainou A, Syringianidis GD. Evaluation of peach and nectarine varieties according to resistance to Sharka (plum pox) virus. Acta Hortic. 1992;309:221–8.
Article
Google Scholar
Polak J, Outropec I, Krska B, Pivalova J, Miller W. Difference in reactions of apricot and peach cultivars to plum pox virus: serological and symptomatological evaluation. Hort Sci. 2003;30:129–34.
Google Scholar
Rubio M, Martínez-Gómez P, García-Brunton J, Pascal T, García-Ibarra A, Dicenta F. Sensitivity of peach cultivars against a Dideron isolate of plum pox virus. Sci Hortic. 2012;144:81–6.
Article
Google Scholar
Liverani A, Babini AR, Bassi D. Il miglioramento genetico per la resistenza a sharka in pesco: risultati del progetto italiano PPVCON. Italus Hortus. 2011;35-44(Italian):18.
Google Scholar
Cirilli M, Geuna F, Babini AR, Bozhkova V, Catalano L, Cavagna B, et al. Fighting Sharka in peach: current limitations and future perspectives. Front Plant Sci. 2016;7:1290.
Article
PubMed
PubMed Central
Google Scholar
Decroocq V, Foulogne M, Lambert P, Le Gall P, Mantin C, Pascal T, et al. Analogues of virus resistance genes map to QTLs for resistance to sharka disease in Prunus Davidiana. Mol Gen Genomics. 2005;272:680–9.
Article
CAS
Google Scholar
Marandel G, Pascal T, Candresse T, Decroocq V. Quantitative resistance to plum pox virus in Prunus Davidiana P1908 linked to components of the eukaryotic translation initiation complex. Plant Pathol. 2009;58:425–35.
Article
CAS
Google Scholar
Rubio M, Pascal T, Bachellez A, Lambert P. Quantitative trait loci analysis of PPV resistance in P. Davidiana: new insights on the organization of genomic resistance regions. Tree genet. Genomes. 2010;6:291–304.
Google Scholar
Zuriaga E, Soriano JM, Zhebentyayeva T, Romero C, Dardick C, Cañizares J, et al. Genomic analysis reveals MATH gene (s) as candidate (s) for plum pox virus (PPV) resistance in apricot (Prunus Armeniaca L.). Mol Plant Pathol. 2013;14:663–77.
Article
CAS
PubMed
Google Scholar
Decroocq S, Chague A, Lambert P, Roch G, Audergon JM, Geuna F, et al. Selecting with markers linked to the PPVres major QTL is not sufficient to predict resistance to plum pox virus (PPV) in apricot. Tree genet. Genomes. 2014;10:1161–70.
Google Scholar
Cosson P, Sofer L, Le QH, Léger V, Schurdi-Levraud V, Whitham SA, et al. RTM3, which controls long-distance movement of potyviruses, is a member of a new plant gene family encoding a meprin and TRAF homology domain-containing protein. Plant Physiol. 2010;154:222–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Decroocq V, Sicard O, Alamillo JM, Lansac M, Eyquard JP, Garcia JA, et al. Multiple resistance traits control plum pox virus infection in Arabidopsis Thaliana. Mol Plant-Microbe Interact. 2006;19:541–9.
Article
CAS
PubMed
Google Scholar
Nicaise V. Crop immunity against viruses: outcomes and future challenges. Front Plant Sci. 2014;5:660.
Article
PubMed
PubMed Central
Google Scholar
Wang X, Kohalmi SE, Svircev A, Wang A, Sanfaçon H, Tian L. Silencing of the host factor eIF(iso)4E gene confers plum pox virus resistance in plum. PLoS One. 2013;8:e50627.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cui H, Wang A. An efficient viral vector for functional genomics studies of Prunus fruit trees and its induced resistance to plum pox virus via silencing of a host factor gene. Plant Biotechnol. 2016;15(3):344–56.
Article
Google Scholar
Korte A, Farlow A. The advantages and limitations of trait analysis with GWAS: a review. Plant Methods. 2013;9:29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Slatkin M. Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nat Rev Genet. 2008;9:477–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price AL, Zaitlen NA, Reich D, Patterson N. New approaches to population stratification in genome-wide association studies. Nat. Rev. Genet. 2010;11:459–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Faust M, Timon B. Origin and dissemination of peach. Hortic Rev. 1995;17:331–79.
Google Scholar
Aranzana MJ, Abbassi EK, Howad W, Arus P. Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genet. 2010;11:69.
Article
PubMed
PubMed Central
Google Scholar
Akagi T, Hanada T, Yaegaki H, Gradziel TM, Tao R. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication. DNA Res. 2016;23(3):271–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cao K, Zheng Z, Wang L, Liu X, Zhu G, Fang W, et al. Comparative population genomics reveals the domestication history of the peach, Prunus Persica, and human influences on perennial fruit crops. Genome Biol. 2014;15:415.
PubMed
PubMed Central
Google Scholar
Li XW, Meng XQ, Jia HJ, ML Y, Ma RJ, Wang LR, et al. Peach genetic resources: diversity, population structure and linkage disequilibrium. BMC Genet. 2013;14:84.
Article
PubMed
PubMed Central
Google Scholar
Verde I, Abbott AG, Scalabrin S, et al. The high-quality draft genome of peach (Prunus Persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 2013;45:487–94.
Article
CAS
PubMed
Google Scholar
Fresnedo-Ramírez J, Bink MCAM, van de Weg E, Famula TR, Crisosto CH, Frett TJ, et al. QTL mapping of pomological traits in peach and related species breeding germplasm. Mol. Breeding. 2015;35:166.
Article
Google Scholar
Micheletti D, Dettori MT, Micali S, Aramini V, Pacheco I, Da Silva Linge C, et al. Whole-genome analysis of diversity and SNP-major gene association in peach germplasm. PLoS One. 2015;10:e0136803.
Article
PubMed
PubMed Central
Google Scholar
Casati P, Bassi D, Spadone P, Bianco PA. Preliminary results on resistance to PPV-M in Prunus Persica (L.) Batsch. Julius-Kühn-Archives. 2010;427:323–6.
Google Scholar
Falchi R, Vendramin E, Zanon L, Scalabrin S, Cipriani G, Verde I, et al. Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach. Plant J. 2013;76:175–87.
CAS
PubMed
PubMed Central
Google Scholar
Vendramin E, Pea G, Dondini L, Pacheco I, Dettori MT, Gazza LA, et al. Unique mutation in a MYB gene Cosegregates with the nectarine phenotype in peach. PLoS One. 2014;9(3):e90574.
Article
PubMed
PubMed Central
Google Scholar
Chisholm ST, Parra MA, Anderberg RJ, Carrington JC. Arabidopsis RTM1 and RTM2 genes function in phloem to restrict long-distance movement of tobacco etch virus. Plant Physiol. 2001;127:1667–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liverani A, Brandi F, Sirri S, Giovannini D, Baroni G, Lonardi F. Preliminary evaluation on susceptibility to natural infections of putative resistant peach breeding selections in a PPV endemic site. Acta Hortic. 2015;1084:585–90.
Article
Google Scholar
Clemente-Moreno MJ, Hernández JA, Díaz-Vivancos P. Sharka: how do plants respond to plum pox virus infection? J Exp Bot. 2015;66:25–35.
Article
CAS
PubMed
Google Scholar
Rafalski JA. Association genetics in crop improvement. Curr Opin Plant Biol. 2010;13:174–80.
Article
CAS
PubMed
Google Scholar
St. Clair DA. Quantitative disease resistance and quantitative resistance loci in breeding. Annu Rev Phytopathol. 2010;48:247–68.
Article
CAS
PubMed
Google Scholar
Dondini L, Lain O, Vendramin V, Rizzo M, Vivoli D, Adami M, et al. Identification of QTL for resistance to plum pox virus strains M and D in Lito and Harcot apricot cultivars. Mol. Breeding. 2011;27:289–99.
Article
Google Scholar
Mariette S, Wong Jun tai F, Roch G, Barre a, Chague a, Decroocq S, et al. genome-wide association links candidate genes to resistance to plum pox virus in apricot (Prunus Armeniaca). New Phytol 2016; 209:773–784.
Soriano JM, Domingo ML, Zuriaga E, Romero C, Zhebentyayeva T, Abbott AG, et al. Identification of simple sequence repeat markers tightly linked to plum pox virus resistance in apricot. Mol. Breeding. 2012;30:1017–26.
Article
CAS
Google Scholar
Brachi B, Morris GP, Borevitz JO. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol. 2011;12:232.
Article
PubMed
PubMed Central
Google Scholar
Louthan AM, Kay KM. Comparing the adaptive landscape across trait types: larger QTL effect size in traits under biotic selection. BMC Evol Biol. 2011;11:60–10.
Article
PubMed
PubMed Central
Google Scholar
Flint-Garcia SA, Thornsberry JM, Buckler ES. Structure of linkage disequilibrium in plants. Annu Rev Plant Biol. 2003;54:357–74.
Article
CAS
PubMed
Google Scholar
Gupta PK, Rustgi S, Kulwal PL. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol. 2005;57:461–85.
Article
CAS
PubMed
Google Scholar
Whitham SA, Anderberg RJ, Chisholm ST, Carrington JC. Arabidopsis RTM2 gene is necessary for specific restriction of tobacco etch virus and encodes an unusual small heat shock-like protein. Plant Cell. 2000;12:569–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Decroocq V, Salvador B, Sicard O, Glasa M, Cosson P, Svanella-Dumas L, et al. The determinant of potyvirus ability to overcome the RTM resistance of Arabidopsis Thaliana maps to the N-terminal region of the coat protein. Mol Plant-Microbe Interact. 2009;22(10):1302–11.
Article
CAS
PubMed
Google Scholar
Kumar S, Bhatia S. A polymorphic (GA/CT)n- SSR influences promoter activity of tryptophan decarboxylase gene in Catharanthus Roseus L. Don Sci Rep. 2016;6:33280.
Article
CAS
PubMed
Google Scholar
Du Z, Chen A, Chen W, Westwood JH, Baulcombe DC, Carr JP. Using a viral vector to reveal the role of miR159 in disease symptom induction by a severe strain of cucumber mosaic virus. Plant Physiol. 2014;164:1378–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Denancé N, Szurek B, Noël LD. Emerging functions of nodulin-like proteins in non-nodulating plant species. Plant Cell Physiol. 2014;55:469–74.
Article
PubMed
Google Scholar
Benschop JJ, Mohammed S, O’Flaherty M, Heck AJ, Slijper M, Menke FL. Quantitative phosphoproteomics of early elicitor signalling in Arabidopsis. Mol Cell Proteomics. 2007;6:1198–214.
Article
CAS
PubMed
Google Scholar
Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, et al. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One. 2012;7:e35668.
Article
CAS
PubMed
PubMed Central
Google Scholar
Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, et al. The peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics. 2017;18:225.
Article
PubMed
PubMed Central
Google Scholar
Amenduni T, Bazzoni A, Minafra A, Savino V. Evaluation of the susceptibility of seedlings from apricot crosses to the Marcus strain of plum pox virus. Acta Hort. 2004;657:305–8.
Article
Google Scholar
Boscia D, Zeramdini H, Cambra M, Potere O, Gorris MT, Myrta A, et al. Production and characterization of a monoclonal antibody specific to the M serotype of plum pox potyvirus. Eur J Plant Pathol. 1997;103:477–80.
Article
CAS
Google Scholar
Wetzel T, Candresse T, Ravelonandro M, Dunez JA. Polymerase chain reaction assay adapted to plum pox potyvirus detection. J Virol Methods. 1991;33:355–65.
Article
CAS
PubMed
Google Scholar
Babini AR, Vicchi V, Poggi-Pollini C, Ratti C, Giunchedi L, Liverani A, et al. Valutazione del comportamento di cultivar e selezioni avanzate di drupacee nei confronti della sharka. In: Proceedings of conference: La sharka in Italia, stato dell’arte e prospettive per il futuro della peschicoltura, Verona (Italy), 25 November 2009, 16–18. (Italian).
Fontana F, Babini AR. Sharka delle drupacee: test sulle nuove cultivar. Agricoltura Emilia-Romagna 2014; 10:66-67. (Italian).
Poggi-Pollini C, Bianchi L, Babini AR, Vicchi V, Liverani A, Brandi F, et al. Evaluation of plum pox virus infection on different stone fruit tree varieties. J Plant Pathol. 2008;90:27–31.
Google Scholar
Gabova M. Evaluation of peach and nectarine cultivars in Bulgaria for their resistance to plum pox potyvirus. Bulletin. OEPP/EPPO Bull. 1994;24:755–60.
Article
Google Scholar
Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bradbury PJ, Zhang ZW, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ESTASSEL. Software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23:2633–5.
Article
CAS
PubMed
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21:263–5.
Article
CAS
PubMed
Google Scholar
Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, et al. GAPIT: genome association and prediction integrated tool. Bioinformatics. 2012;28:2397–9.
Article
CAS
PubMed
Google Scholar
Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB. Variance component model to account for sample structure in genome-wide association studies. Nat Genet. 2010;42:348–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu X, Huang M, Fan B, Buckler ES, Zhang Z. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genet. 2016;12(2):e1005767.
Article
PubMed
PubMed Central
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J Roy Stat Soc B. 1995;57:289–300.
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hoffman GE, Logsdon BA, Mezey JGPUMA. A unified framework for penalized multiple regression analysis of GWAS data. PLoS Comput Biol. 2013;9:e1003101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hahn LW, Ritchie MD, Moore JH. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics. 2003;19:376–82.
Article
CAS
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, et al. Using tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 2013;14:193–202.
Article
CAS
PubMed
Google Scholar
Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F. SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics. 2006;22:2183–5.
Article
CAS
PubMed
Google Scholar