Whole-genome analysis of diversity and SNP-major gene association in peach germplasm

PLoS ONE

Volumn 10, Issue 9, 2015, Pages

  Micheletti, Diego ^a,e   Dettori, Maria Teresa ^b   Micali, Sabrina ^b   Aramini, Valeria ^b   Pacheco, Igor ^c,p   Da Silva Linge, Cassia ^c   Foschi, Stefano ^d   Banchi, Elisa ^e   Barreneche, Teresa ^f,g   Quilot Turion, Bénédicte ^h   Lambert, Patrick ^h   Pascal, Thierry ^h   Iglesias, Ignasi ⁱ   Carbó, Joaquim ⁱ   Wang, Li Rong ^j   Ma, Rui Juan ^k   Li, Xiong Wei ^l   Gao, Zhong Shan ^l   Nazzicari, Nelson ^m   Troggio, Michela ^e   Bassi, Daniele ^c   Rossini, Laura ^c,m   Verde, Ignazio ^b   Laurens, François ^n,o   Arús, Pere ^a   Joséaranzana, Maria ^a   more..

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

^c UNIVERSITY OF MILAN   (Italy)

^d Centro Ricerche Produzioni Vegetali   (Italy)

^e RESEARCH AND INNOVATION CENTRE   (Italy)

^f Univ Bordeaux   (France)

^g UNIVERSITÉ DE BORDEAUX   (France)

^h Researches Center of Avignon   (France)

ⁱ IRTA   (Spain)

^j INSTITUTE OF PLANT PROTECTION   (China)

^k INSTITUTE OF PLANT PROTECTION   (China)

^l ZHEJIANG UNIVERSITY   (China)

^m PARCO TECNOLOGICO PADANO   (Italy)

ⁿ Universite d'Angers   (France)

^o UNIVERSITÉ D'ANGERS   (France)

^p UNIVERSITY OF CHILE   (Chile)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CULTIVAR; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENOME ANALYSIS; GERMPLASM; HAPLOTYPE; LANDRACE; LINKAGE ANALYSIS; NONHUMAN; PEACH; PLANT GENOME; POPULATION STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; VARIETAS; CHROMOSOMAL MAPPING; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; PHENOTYPE; PHYLOGENY; PLANT CHROMOSOME;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENETIC VARIATION; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOTYPES; PHENOTYPE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRUNUS PERSICA;

EID: 84944753710     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0136803     Document Type: Article

References (49)

1. Faust M, Timon B. Origin and Dissemination of Peach. In: Janik J, editor. Horticultural Reviews. New York: John Wiley & Sons, Inc.; 1995. p. 331-79.
2. Byrne DH. Isozyme variability in four diploid stone fruits compared with other woody perennial plants. The Journal of Heredity 1990;81(1):68-71.
3. Mnejja M, Garcia-Mas J, Audergon J-M, Arús P. Prunus microsatellite markertransferability across rosaceous crops. Tree Genetics & Genomes 2010;6(5):689-700.
4. Scorza R, Mehlenbacher SA, Lightner GW. Inbreeding and coancestry of freestone peach cultivars of the eastern united states and implications for peach germplasm improvement. J Amer Soc Hort Sci 1985;110(4):547-52.
5. Hesse CO. Peaches. Advances in Fruit Breeding 1975:285-335.
6. Li X-w, MengX-q, Jia H-j, Yu M-l, Ma R-j, Wang L-r, et al. Peach genetic resources: diversity, population structure and linkage disequilibrium. BMC Genetics 2013;14(1):84.
7. Aranzana MJ, Carbó J, Arús P. Microsatellite variability in peach [Prunus persica (L.) Batsch]: cultivar identification, marker mutation, pedigree inferences and population structure. Theor Appl Genet 2003;106(8):1341-52. PMID: 12750778
8. Verde I, Abbott AG, Scalabrin S, JungS, Shu S, Marroni F, 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(5):487-94. doi: 10.1038/ng.2586 PMID: 23525075
9. 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 Biology 2014;15(7):415. doi: 10.1186/s13059-014-0415-1 PMID: 25079967
10. Monet R, Guye A, Roy M, Dachary N. Peach mendelian genetics: a short review and new results. Agro-nomie 1996;16:321-9.
11. Abbott AG, Georgi L, Yvergniaux D, Wang Y, Blenda A, Reighard G, et al. Peach: the model genome for Rosaceae. Acta Hort 2002;575:145-55.
12. Dirlewanger E, Graziano E, JoobeurT, Garriga-Calderé F, Cosson P, Howad W, et al. Comparative mapping and marker-assisted selection in Rosaceae fruit crops. PNAS 2004;101(23):9891-6.
13. Abbott AG, Arús P, Scorza R. Genetic engineering and genomics. In: Bassi DRLaD, editor. The peach Botany, production and uses London: CAB International; 2008. pp. 85-105.
14. Arús P, YamamotoT, Dirlewanger E, Abbott AG. Synteny in the Rosaceae. In: JanikJ, editor. Plant Breeding Reviews. Hoboken, NJ: John Wiley & Sons; 2005. pp. 175-211.
15. AranzanaM, IllaE, Howad W, Arus P. A first insight into peach [Prunus persica (L.) Batsch] SNP variability. Tree Genetics & Genomes 2012;8(6):1359-69.
16. Ahmad R, Parfitt DE, Fass J, Ogundiwin E, DhingraA, GradzielTM, et al. Whole genome sequencing of peach (Prunuspersica L.) for SNP identification and selection. BMC Genomics 2011;12:569. doi: 10.1186/1471-2164-12-569 PMID: 22108025
17. 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(4):e35668. doi: 10.1371/journal.pone.0035668 PMID: 22536421
18. Eduardo I, ChieteraG, PironaR, Pacheco I, TroggioM, Banchi E, et al. Genetic dissection of aroma volatile compounds from the essential oil of peach fruit: QTL analysis and identification of candidate genes using dense SNP maps. Tree Genetics & Genomes 2013;9(1):189-204.
19. Yang N, Reighard G, Ritchie D, Okie W, Gasic K. Mapping quantitative trait loci associated with resistance to bacterial spot (Xanthomonas arboricola pv. pruni) in peach. Tree Genetics & Genomes 2013;9(2):573-86.
20. FrettT, Reighard G, Okie W, Gasic K. Mapping quantitative trait loci associated with blush in peach [Prunus persica (L.) Batsch]. Tree Genetics & Genomes 2014;10(2):367-81.
21. Pacheco I, Bassi D, Eduardo I, Ciacciulli A, PironaR, Rossini L, et al. QTL mapping for brown rot (Moni-liniafructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny. Tree Genetics & Genomes 2014;10(5):1223-42.
22. Romeu J, Monforte A, Sanchez G, Granell A, Garcia-Brunton J, BadenesM, et al. Quantitative trait loci affecting reproductive phenology in peach. BMC Plant Biology 2014;14(1):52.
23. Pritchard JK, Stephens M, Donnelly P. Inference of Population Structure Using Multilocus Genotype Data. Genetics 2000 June 1, 2000;155(2):945-59. PMID: 10835412
24. Mangin B, SiberchicotA, Nicolas S, DoligezA, This P, Cierco-Ayrolles C. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity 2012;108(3):285-91. doi: 10.1038/hdy.2011.73 PMID: 21878986
25. Dirlewanger E, Pronier V, Parvery C, Rothan C, Guye A, Monet R. Genetic linkage map of peach [Prunus persica (L.) Batsch] using morphological and molecular markers. Theoretical and Applied Genetics 1998;97(5-6):888-95.
26. Eduardo I, López-Girona E, BatlIe I, Reig G, Iglesias I, Howad W, et al. Development of diagnostic markers for selection of the subacid trait in peach. Tree Genetics & Genomes 2014;10(6):1695-709.
27. Scheet P, Stephens M. A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase. American Journal of Human Genetics 2006;78(4):629-44. PMID: 16532393
28. 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. The Plant Journal 2013;76(2):175-87. doi: 10.1111/tpj.12283 PMID: 23855972
29. Vendramin E, PeaG, Dondini L, Pacheco I, Dettori MT, Gazza L, et al. A Unique Mutation in aMYB Gene Cosegregates with the Nectarine Phenotype in Peach. PLOS ONE 2014;9(3):e90574. doi: 10. 1371/journal.pone.0090574 PMID: 24595269
30. Dirlewanger E, Cosson P, Boudehri K, RenaudC, CapdevilleG, Tauzin Y, et al. Development of a second-generation genetic linkage map for peach [Prunuspersica (L.) Batsch] and characterization of morphological traits affecting flower and fruit. Tree Genetics & Genomes 2006;3(1):1-13.
31. Peace CP, Crisosto CH, GradzielTM. Endopolygalacturonase: a Candidate Gene for Freestone and Melting Fleshin Peach. Molecular Breeding 2005;16(1):21-31.
32. Ogundiwin E, Peace C, Gradziel T, Parfitt D, Bliss F, Crisosto C. A fruit quality gene map of Prunus. BMC Genomics 2009;10(1):587.
33. Dettori MT, Quarta R, Verde I. A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome 2001;44:783-90. PMID: 11681601
34. AranzanaM, Abbassi E-K, Howad W, Arus P. Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genetics 2010;11(1):69.
35. Jáuregui B, de Vicente MC, Messeguer R, Felipe A, Bonnet A, Salesses G, et al. A reciprocal translocation between 'Garfi' almond and 'Nemared' peach. TheorAppl Genet 2001;102:1169-76
36. Yamamoto T, Yamaguchi M, Hayashi T. An integrated genetic linkage map of peach by SSR, STS, AFLP and RAPD. J Jpn Soc Hort Sci 2005;74(3):204-13.
37. Lambert P, Pascal T. Mapping Rm2 gene conferring resistance to the green peach aphid (Myzus persi-cae Sulzer) in the peach cultivar 'Rubira'. Tree Genetics & Genomes 2011;7(5):1057-68.
38. Cao K, Wang L, Zhu G, Fang W, Chen C, Luo J. Genetic diversity, linkage disequilibrium, and association mapping analyses of peach (Prunus persica) landraces in China. Tree Genetics & Genomes 2012;8(5):975-90.
39. Pfaff CL, Parra EJ, BonillaC, Hiester K, McKeigue PM, Kamboh MI, et al. Population Structure in Admixed Populations: Effect of Admixture Dynamics on the Pattern of Linkage Disequilibrium. Amer J Hum Genet 2001;68:198-207. PMID: 11112661
40. Xie R, LiX, Chai M, Song L, JiaH, Wu D, et al. Evaluation ofthe genetic diversity of Asian peach accessions using a selected set of SSR markers. Scientia Horticulturae 2010;125(4):622-9.
41. Soto-CerdaBJ, CloutierS. Association mapping in plant genomes. In: Caliskan M Editor. Genetic Diversity in Plants; 2012. pp. 29-54.
42. Bradbury PJ, Zhang Z, Kroon DE, CasstevensTM, RamdossY, Buckler ES. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 2007;23:2633-2635. PMID: 17586829
43. Purcell S, Neale B, Todd-Brown K, Thomas L, FerreiraMAR, Bender D, et al. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics 2007;81(3):559-75. PMID: 17701901
44. EvannoG, RegnautS, GoudetJ. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005;14:2611-20. PMID: 15969739
45. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. Interrogating a High-Density SNP Map for Signatures of Natural Selection. Genome Research. 2002;12(12):1805-1814. PMID: 12466284
46. VanRaden P. Efficient methods to compute genomic predictions. Journal of dairy science 2008;91(11):4414-23. doi: 10.3168/jds.2007-0980 PMID: 18946147
47. LipkaAE, Tian F, WangQ, Peiffer J, Li M, Bradbury PJ, et al. GAPIT: genome association and prediction integrated tool. Bioinformatics 2012;28(18):2397-9. PMID: 22796960
48. Zhang Z, Ersoz E, Lai C-Q, TodhunterRJ, Tiwari HK, Gore MA, et al. Mixed linear model approach adapted for genome-wide association studies. Nature genetics 2010;42(4):355-60. doi: 10.1038/ng. 546 PMID: 20208535
49. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Statist 2001;29(4):1165-88.