Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

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• 作者：José Luis Zeballos ; Walid Abidi ; Rosa Giménez…
• 关键词：Peach physical map ; Vitamin C ; Total phenolics ; Flavonoids ; Anthocyanins ; Sugars
• 刊名：Tree Genetics & Genomes
• 出版年：2016
• 出版时间：June 2016
• 年：2016
• 卷：12
• 期：3
• 全文大小：1,797 KB
• 参考文献：Abbott AG, Rajapakse S, Sosinski B, Lu ZX, Sossey-Alaoui K, Gannavarapu M, Reighard G, Ballard RE, Baird WV, Scorza R, Callahan A (1998) Construction of saturated linkage maps of peach crosses segregating for characters controlling fruit quality, tree architecture and pest resistance. Acta Hortic 465:41–50CrossRef
  Abidi W, Jiménez S, Moreno MÁ, Gogorcena Y (2011) Evaluation of antioxidant compounds and total sugar content in a nectarine [Prunus persica (L.) Batsch] progeny. Int J Mol Sci 12:6919–6935CrossRef PubMed PubMedCentral
  Abidi W, Cantín C, Gonzalo MJ, Moreno MA, Gogorcena Y (2012) Genetic control and location of QTLs involved in antioxidant capacity and fruit quality traits in peach [Prunus persica (L.) Batch]. Acta Hortic 962:129–134CrossRef
  Abidi W, Cantín CM, Jiménez S, Giménez R, Moreno MA, Gogorcena Y (2015) Effect of antioxidant compounds and total sugars and genetic background on the chilling injury susceptibility of a non-melting peach [Prunus persica (L.) Batsch] progeny. J Sci Food Agric 95:351–358CrossRef PubMed
  Albrechtsen A, Nielsen FC, Nielsen R (2010) Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol 11:2534–2547CrossRef
  Arús P, Verde I, Sosinski B, Zhebentyayeva T, Abbott AG (2012) The peach genome. Tree Genet Genomes 8:531–547CrossRef
  Boeing H, Bechthold A, Bub A, Ellinger S, Haller D, Kroke A, Leschik-Bonnet E, Müller MJ et al (2012) Critical review: vegetables and fruit in the prevention of chronic diseases. Eur J Nutr 51:637–663CrossRef PubMed PubMedCentral
  Brem RB, Kruglyak L (2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A 102:1572–1577CrossRef PubMed PubMedCentral
  Broman KW, Saunak S (2009) A guide to QTL mapping with R/qtl. Statistic for biology and health. Springer, New York. doi:10.​1007/​978-0-387-92125-9 CrossRef
  Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890CrossRef PubMed
  Byrne DH, Raseira MB, Bassi D, Piagnani MC, Gasic K, Moreno MA, Pérez S (2012) Peach. In: Badenes ML, Byrne DH (eds) Fruit breeding, vol 8. Handbook of plant breeding, vol 8. Springer, New York, pp 505–569
  Cantín CM, Gogorcena Y, Moreno MA (2009a) Analysis of phenotypic variation of sugar profile in different peach and nectarine [Prunus persica (L.) Batsch] breeding progenies. J Sci Food Agric 89:1909–1917CrossRef
  Cantín CM, Moreno MA, Gogorcena Y (2009b) Evaluation of the antioxidant capacity, phenolic compounds, and vitamin C content of different peach and nectarine [Prunus persica (L.) Batsch] breeding progenies. J Agric Food Chem 57:4586–4592CrossRef PubMed
  Cantín CM, Crisosto CH, Ogundiwin EA, Gradziel T, Torrents J, Moreno MA, Gogorcena Y (2010a) Chilling injury susceptibility in an intra-specific peach [Prunus persica (L.) Batsch] progeny. Postharvest Biol Technol 58:79–87CrossRef
  Cantín CM, Gogorcena Y, Moreno MA (2010b) Phenotypic diversity and relationships of fruit quality traits in peach and nectarine [Prunus persica (L.) Batsch] breeding progenies. Euphytica 171:211–226CrossRef
  Crisosto CH (2002) How do we increase peach consumption? Acta Hortic 592:601–605CrossRef
  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 Biol 12:1–16CrossRef
  Chaparro JX, Werner DJ, O’Malley D, Sederoff RR (1994) Targeted mapping and linkage analysis of morphological isozyme, and RAPD markers in peach. Theor Appl Genet 87:805–815CrossRef PubMed
  Da Silva Linge C, Bassi D, Bianco L, Pacheco I, Pirona R, Rossini L (2015) Genetic dissection of fruit weight and size in an F2 peach (Prunus persica (L.) Batsch) progeny. Mol Breed 35:71CrossRef
  Davey MW, Kenis K, Keulemans J (2006) Genetic control of fruit vitamin C contents. Plant Physiol 142:343–351CrossRef PubMed PubMedCentral
  Dirlewanger E, Pronier V, Parvery C, Rothan C, Guye A, Monet R (1998) Genetic linkage map of peach [Prunus persica (L.) Batsch] using morphological and molecular markers. Theor Appl Genet 97:888–895CrossRef
  Dirlewanger E, Moing A, Rothan C, Svanella L, Pronier V, Guye A, Plomion C, Monet R (1999) Mapping QTLs controlling fruit quality in peach (Prunus persica (L.) Batsch). Theor Appl Genet 98(1):18–31CrossRef
  Dirlewanger E, Graziano E, Joobeur T, Garriga-Calderé F, Cosson P, Howad W, Arús P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci U S A 101:9891–9896CrossRef PubMed PubMedCentral
  Dirlewanger E, Cosson P, Renaud C, Monet R, Poëssel JL, Moing A (2006) New detection of QTLs controlling major fruit quality components in peach. Acta Hortic 713:65–72CrossRef
  Dirlewanger E, Quero-García J, Le Dantec L, Lambert P, Ruiz D, Dondini L, Illa E, Quilot-Turion B, Audergon JM, Tartarini S, Letourmy P, Arús P (2012) Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry. Heredity 109:280–292CrossRef PubMed PubMedCentral
  Eduardo I, Pacheco I, Chietera G, Bassi D, Pozzi C, Vecchietti A, Rossini L (2011) QTL analysis of fruit quality traits in two peach intraspecific populations and importance of maturity date pleiotropic effect. Tree Genet Genomes 7:323–335CrossRef
  Eduardo I, Chietera G, Pirona R, Pacheco I, Troggio M, Banchi E, Bassi D, Rossini L, Vecchietti A, Pozzi C (2013) 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 Genet Genomes 9:189–204CrossRef
  Eduardo I, López-Girona E, BatlIe I, Reig G, Iglesias I, Howad W, Arús P, Aranzana MJ (2014) Development of diagnostic markers for selection of the subacid trait in peach. Tree Genet Genomes 10:1695–1709CrossRef
  Eduardo I, Picañol R, Rojas E, BatlIe I, Howad W, Aranzana MJ, Arús P (2015) Mapping of a major gene for the slow ripening character in peach: co-location with the maturity date gene and development of a candidate gene-based diagnostic marker for its selection. Euphytica 205:627–636CrossRef
  Etienne C, Rothan C, Moing A, Plomion C, Bodénès C, Svanella-Dumas L, Cosson P, Pronier V, Monet R, Dirlewanger E (2002) Candidate genes and QTLs for sugar and organic acid content in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 105:145–159CrossRef PubMed
  FAOSTAT (2015) Food and Agriculture Organization of the United Nations. http://​faostat.​fao.​org/​site/​291/​default.​aspx . Accessed 1 August 2015
  Font i Forcada C, Oraguzie N, Igartua E, Moreno MA, Gogorcena Y (2013) Population structure and marker-trait associations for pomological traits in peach and nectarine cultivars. Tree Genet Genomes 9:331–349CrossRef
  Fresnedo-Ramírez J, Bink MCAM, van der Weg E, Famula TR, Crisosto CH, Frett TJ, Gasic K, Peace CP, Gradziel TM (2015) QTL mapping of pomological traits in peach and related species breeding germplasm. Mol Breed 35:166CrossRef
  Frett T, Reighard G, Okie W, Gasic K (2014) Mapping quantitative trait loci associated with blush in peach [Prunus persica (L.) Batsch]. Tree Genet Genomes 10:367–381CrossRef
  GDR (2015) Genome database for Rosaceae. http://​www.​rosaceae.​org/​species/​prunus_​persica/​genome_​v1.​0 . Accessed 13 Nov 2015
  Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137PubMed PubMedCentral
  Illa E, Eduardo I, Audergon JM, Barale F, Dirlewanger E, Li X, Moing A, Lambert P, Le Dantec L, Gao Z, Poëssel JL, Pozzi C, Rossini L, Vecchietti A, Arús P, Howad W (2011) Saturating the Prunus (stone fruits) genome with candidate genes for fruit quality. Mol Breed 28(4):667–682CrossRef
  Infante R, Farcuh M, Meneses C (2008) Monitoring the sensorial quality and aroma through an electronic nose in peaches during cold storage. J Sci Food Agric 88:2073–2078CrossRef
  Jáuregui B, De Vicente MC, Messeguer R, Felipe A, Bonnet A, Salesses G, Arús P (2001) A reciprocal translocation between ‘Garfi’ almond and ‘Nemared’ peach. Theor Appl Genet 102:1169–1176CrossRef
  Martin C, Zhang Y, Tonelli C, Petroni K (2013) Plants, diet, and health. Annu Rev Plant Biol 64:19–46CrossRef PubMed
  Martínez-García PJ, Fresnedo-Ramírez J, Parfitt DE, Gradziel TM, Crisosto CH (2013a) Effect prediction of identified SNPs linked to fruit quality and chilling injury in peach [Prunus persica (L.) Batsch]. Plant Mol Biol 81:161–174CrossRef PubMed
  Martínez-García PJ, Parfitt DE, Ogundiwin EA, Fass J, Chan HM, Ahmad R, Lurie S, Dandekar A, Gradziel TM, Crisosto CH (2013b) High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.). Tree Genet Genomes 9:19–36CrossRef
  Nielsen R, Hubisz MJ, Clark AG (2004) Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics 168:2373–2382CrossRef PubMed PubMedCentral
  Nuñez-Lillo G, Cifuentes-Esquivel A, Troggio M, Micheletti D, Rodrigo Infante R, Campos-Vargas R, Orellana A, Blanco-Herrera F, Meneses C (2015) Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing. Tree Genet Genomes 1:86CrossRef
  Ogundiwin EA, Peace CP, Gradziel TM, Parfitt DE, Bliss FA, Crisosto CH (2009) A fruit quality gene map of Prunus. BMC Genomics 10:587CrossRef PubMed PubMedCentral
  Orazem P, Stampar F, Hudina M (2011) Quality analysis of ‘Redhaven’ peach fruit grafted on 11 rootstocks of different genetic origin in a replant soil. Food Chem 124(4):1691–1698CrossRef
  Pacheco I, Bassi D, Eduardo I, Ciacciulli A, Pirona R, Rossini L, Vecchietti A (2014) QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny. Tree Genet Genomes 10:1223–1242. doi:10.​1007/​s11295-014-0756-7 CrossRef
  Peace C, Norelli J (2009) Genomics approaches to crop improvement in the Rosaceae. In: Folta KM, Gardiner SE (eds) Genetics and genomics of Rosaceae, vol 6. Plant genetics and genomics: crops and models. Springer, New York, pp 19–53CrossRef
  Pirona R, Eduardo I, Pacheco I, Da Silva Linge C, Miculan M, Verde I, Tartarini S, Dondini L, Giorgio Pea G, Daniele Bassi D, Rossini L (2013) Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach. BMC Plant Biol 3:166CrossRef
  Quarta R, Dettori MT, Sartori A, Verde I (2000) Genetic linkage map and QTL analysis in peach. Acta Hortic 521:233–242CrossRef
  Quilot B, Wu BH, Kervella J, Génard M, Foulongne M, Moreau K (2004) QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana. Theor Appl Genet 109:884–897CrossRef PubMed
  Romeu J, Monforte AJ, Sánchez G, Granell A, García-Brunton J, Badenes M, Ríos G (2014) Quantitative trait loci affecting reproductive phenology in peach. BMC Plant Biol 14:52CrossRef PubMed PubMedCentral
  Ru S, Main D, Evans K, Peace C (2015) Current applications, challenges, and perspectives of marker-assisted seedling selection in Rosaceae tree fruit breeding. Tree Genet Genomes 11:8CrossRef
  Salazar JA, Ruiz D, Egea J, Martínez-Gómez P (2013) Transmission of fruit quality traits in apricot (Prunus armeniaca L.) and analysis of linked quantitative trait loci (QTLs) using simple sequence repeat (SSR) markers. Plant Mol Biol Rep 31:1506–1517. doi:10.​1007/​s11105-013-0625-9 CrossRef
  Sánchez G, Besada C, Badenes ML, Monforte AJ, Granell A (2012) A non-targeted approach unravels the volatile network in peach fruit. PLoS One 7(6), e38992CrossRef PubMed PubMedCentral
  Sánchez G, Romeu J, García J, Monforte AJ, Badenes M, Granell A (2014) The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population. BMC Plant Biology 14:137CrossRef PubMed PubMedCentral
  Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL (2006) Whole-genome genotyping with the single-base extension assay. Nat Methods 3(1):31–33. doi:10.​1038/​nmeth842 CrossRef PubMed
  Van Ooijen JW (1992) Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803–811CrossRef PubMed
  Van Ooijen JW (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen, Netherlands
  Verde I, Quarta R, Cedrola C, Dettori MT (2002) QTL analysis of agronomic traits in a BC1 peach population. Acta Hortic 592:291–297CrossRef
  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 (2012) Development and evaluation of a 9k SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 7(4), e35668CrossRef PubMed PubMedCentral
  Verde I, Abbott AG, Scalabrin S, Jung S, Shu SQ, Marroni F, Zhebentyayeva T, et al. (Int Peach Genome I) (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487-U447
  Verdu CF, Guyot S, Childebrand N, Bahut M, Celton JM, Gaillard S, Lasserre-Zuber P, Troggio M, Guilet D, Laurens F (2014) QTL analysis and candidate gene mapping for the polyphenol content in cider apple. PLoS One 9(10), e107103CrossRef PubMed PubMedCentral
  Vizzotto M, Porter W, Byrne D, Luis Cisneros-Zevallos L (2014) Polyphenols of selected peach and plum genotypes reduce cell viability and inhibit proliferation of breast cancer cells while not affecting normal cells. Food Chem 164:363–370CrossRef PubMed
  Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRef PubMed
  Wargovich MJ, Morris J, Moseley V, Weber R, Byrne DH (2012) Developing fruit cultivars with enhanced health properties, in fruit breeding. In: Badenes ML, Byrne DH (eds) Fruit breeding, vol 8, Handbook of plant breeding. Springer, New York, pp 37–68CrossRef
  Yang J, Hu Ch, Hu H, Yu R, Xia Z, Ye X, Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24(5):721–723
  Yang N, Reighard G, Ritchie D, Okie W, Gasic K (2013) Mapping quantitative trait loci associated with resistance to bacterial spot (Xanthomonas arboricola pv. pruni) in peach. Tree Genet Genomes 9:573–586CrossRef
  Zeballos J (2012) Identification of genomic region related to fruit quality traits in peach. Universidad de Lleida, Zaragoza, Spain
  Zeballos J, Abidi W, Giménez R, Monforte AJ, Moreno MA, Gogorcena Y (2015) QTL analysis of fruit quality traits in peach [Prunus persica (L.) Batsch] using dense SNP maps. Acta Hortic 1084:703–710
  Zhebentyayeva TN, Swire-Clark G, Georgi LL, Garay L, Jung S, Forrest S, Blenda AV, Blackmon B, Mook J, Horn R, Howad W, Arús P, Main D, Tomkins JP, Sosinski B, Baird WV, Reighard GL, Abbott AG (2008) A framework physical map for peach, a model Rosaceae species. Tree Genet Genomes 4:745–756CrossRef
  Zhebentyayeva TN, Fan S, Chandra A, Bielenberg DG, Reighard GL, Okie WR, Abbott AG (2014) Dissection of chilling requirement and bloom date QTLs in peach using a whole genome sequencing of sibling trees from an F2 mapping population. Tree Genet Genomes 10:35–51CrossRef
  
• 作者单位：José Luis Zeballos (1)
  Walid Abidi (1)
  Rosa Giménez (1)
  Antonio J. Monforte (2)
  María Ángeles Moreno (1)
  Yolanda Gogorcena (1)
  
  1. Department of Pomology, Estación Experimental de Aula Dei-CSIC, P.O. Box 13034, 50080, Zaragoza, Spain
  2. Instituto de Biología Molecular y Celular de Plantas-(CSIC-UPV), 46022, Valencia, Spain
  
• 刊物主题：Forestry; Plant Genetics & Genomics; Plant Breeding/Biotechnology; Tree Biology; Biotechnology;
• 出版者：Springer Berlin Heidelberg
• ISSN：1614-2950

文摘

Fruit quality is an essential criterion used to select new cultivars in peach breeding programs and is determined based on a combination of organoleptic and nutritional traits. The aim of this study was to identify quantitative trait loci (QTLs) for fruit quality traits in an F₁ nectarine population derived from ‘Venus’ and ‘Big Top’ cultivars. The progeny were evaluated over 4 years for agronomical and biochemical characteristics and genotyped using simple sequence repeat (SSR) markers and ‘IPSC 9K peach SNP array v1’. Two genetic maps were constructed using 411 markers. The ‘Venus’ map spanned 259 cM on nine linkage groups (LGs) with 104 markers. The ‘Big Top’ map spanned 464 cM on 10 LGs with 122 markers. Single or Multiple QTL models mapping was applied separately for each year and all years combined. A total of 54 QTLs mapped over 12 LGs belonged to seven peach chromosomes. Most of the QTLs were consistent over the 4 years of study and were validated with the multi-year analysis. QTLs for total phenolic, flavonoid, and anthocyanin contents were reported for the first time in peach. LG 4 in ‘Venus’ and LG 5 in ‘Big Top’ showed the highest numbers of QTLs. This work represents the first study in an F₁ nectarine family to identify peach genomic regions that control fruit quality traits using ‘IPSC 9K SNP array v1’ and provides useful information for marker-assisted breeding to produce peaches with better antioxidant content and healthy attributes.