Skip to main content
SpringerLink
Log in

A DNA test for routine prediction in breeding of peach blush, Ppe-Rf-SSR

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Blush, the proportion of red overcolor on the skin surface of fruit, is highly variable in peach breeding germplasm and is important in the marketing of peach fruit. The fresh market peach industry demands a high level of blush to entice consumers, while the processing peach industry requires minimal blush. Therefore, blush is a major selection criterion in breeding programs. The use of DNA-based information could improve breeding efficiency and accuracy for fruit blush coverage, but a predictive DNA test is required. The objective of this study was to develop a DNA test for the prediction of blush coverage by targeting the major locus, R f , associated with blush variation. Initially, haplotypes were developed based on five SNP markers associated with variation in blush coverage. To convert the 5-SNP haplotype test into a single, simple PCR-based assay, 11 simple sequence repeat markers were designed and used to screen individuals representing all SNP haplotypes. The most informative assay, named Ppe-Rf-SSR, was chosen to screen 200 individuals of the RosBREED peach reference germplasm set that incorporated germplasm from four breeding programs. Ppe-Rf-SSR accurately differentiated individuals with high-, medium-, and low-blush coverage in most lineages. Outcomes highlighted that DNA tests can be quite predictive for some breeding programs or specific germplasm sets, while for others the predictiveness can falter. Therefore, the confirmation of genotype effects for any DNA test is recommended in new germplasm before routine use. The prediction accuracy and breeding utility of Ppe-Rf-SSR in the University of Arkansas breeding program were subsequently confirmed by screening 443 seedlings, independent of the initial DNA test development process, derived from 18 cross-combinations of 28 parents. Ppe-Rf-SSR can be used to efficiently and accurately predict fruit blush coverage, especially in fresh market germplasm, and has been deployed for routine use in the University of Arkansas peach breeding program.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Arús P, Yamamoto T, Dirlewanger E, Abbott AG (2006) Synteny in the Rosaceae. In: Janick J (ed) Plant Breeding Reviews Volume 25. Wiley, New York, pp 175–211

    Google Scholar 

  • Bassi D, Monet R (2008) Botany and taxonomy. In: Layne DR, Bassi D (eds) The peach, botany, production and uses. CAB International Press, Wallingford, UK, pp 1–36

    Chapter  Google Scholar 

  • Beckman TG, Sherman WB (2003) Probable qualitative inheritance of full red skin color in peach. Hortscience 38:1184–1185

    Google Scholar 

  • Beckman TG, Alcazar JR, Sherman WB, Werner DJ (2005) Evidence for qualitative suppression of red skin color in peach. Hortscience 40:523–524

    Google Scholar 

  • Bink MCAM, Boer MP, ter Braak CJF, Jansen J, Voorrips RE, van de Weg W (2008) Bayesian analysis of complex traits in pedigreed plant populations. Euphytica 161:85–96

    Article  Google Scholar 

  • Blake MA (1932) The J.H. Hale as a parent in peach crosses. Proc Amer Soc Hort Sci 29:131–136

    Google Scholar 

  • Blake MA (1940) Some results of crosses of early ripening varieties of peaches. Proc Amer Soc Hort Sci 37:232–241

    Google Scholar 

  • Bliss F (2010) Marker-assisted breeding in horticultural crops. Acta Hort 859:339–350

    Article  Google Scholar 

  • Byrne DH (2007) Molecular marker use in perennial plant breeding. Acta Hort 751:163–167

    Article  Google Scholar 

  • Byrne D, Bassols M, Bassi D, Piagnani M, Gasic K, Reighard G, Moreno M, Pérez S (2012) Peach. In: Badenes M, Byrne D (eds) Fruit Breeding. Springer, New York, pp 505–570

    Chapter  Google Scholar 

  • Cantín CM, Crisosto CH, Ogundiwin EA, Gradziel T, Torrents J, Moreno MA, Gogorcena Y (2010) Chilling injury susceptibility in an intraspecific peach [Prunus persica (L.) Bastch] progeny. Postharvest Biol Technol 58:79–87

    Article  Google Scholar 

  • Chagné D, Carlisle CM, Blong C, Volz RK, Whitworth CJ, Oraguzie NC, Crowhurst RN, Allan AC, Espley RV, Hellens RP, Gardiner SE (2007) Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple. BMC Genomics 8:212

    Article  PubMed  PubMed Central  Google Scholar 

  • Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc Lond B Biol Sci 363:557–572

    Article  CAS  Google Scholar 

  • Crisosto CH, Costa G (2008) Preharvest factors affecting peach quality. In: Layne DR, Bassi D (eds) The peach, botany, production and uses. CAB International Press, Wallingford, UK, pp 536–549

    Chapter  Google Scholar 

  • de Souza VAB, Byrne DH, Taylor JF (1998) Heritability, genetic and phenotypic correlations, and predicted selection response quantitative traits in peach. II. An analysis of several fruit traits. J Amer Soc Hort Sci 123:604–611

    Google Scholar 

  • Decroocq S, Chague A, Lambert P, Roch G, Audergon JM, Geuna F, Chiozzotto R, Bassi D, Dondini L, Tartarini S, Salava J, Krska B, Palmisano F, Karayiannis I, Decroocq V (2014) 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 10:1161–1170

    Article  Google Scholar 

  • Doerksen TK, Herbinger CM (2010) Impact of reconstructed pedigrees on progeny-test breeding values in red spruce. Tree Genet Genomes 6:591–600

    Article  Google Scholar 

  • Edge-Garza D, Rowland T, Haendiges S, Peace C (2014) A high-throughput and cost-efficient DNA extraction protocol for the tree fruit crops apple, sweet cherry, and peach relying on silica beads during tissue sampling. Mol Breed 34:2225–2228

    Article  CAS  Google Scholar 

  • Edge-Garza D, Luby J, Peace C (2015) Decision support for cost-efficient and logistically feasible markerassisted seedling selection in fruit breeding. Mol Breed 35:223

  • 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 7:323–335

    Article  Google Scholar 

  • Eduardo I, López-Girona E, Batlle I, Reig F, Iglesias I, Howad W, Arús P, Aranzana MJ (2014) Development of diagnostic markers for selection of the subacid trait in peach. Tree Genet Genomes 10:1695–1709

    Article  Google Scholar 

  • Eduardo I, Picañol R, Rojas E, Batlle I, Howad W, Aranzana MH, 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 205:627–636

    Article  CAS  Google Scholar 

  • Espley RV, Hellens RP, Putterill J, Stevenson DE, Kutty-Amma S, Allan AC (2007) Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10. Plant J 49:414–427

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Falchi R, Vendramin E, Zanon L, Scalabrin S, Cipriani G, Verde I, Vizzotto G, Morgante M (2013) Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach. Plant J 76:175–187

    CAS  PubMed  PubMed Central  Google Scholar 

  • Food and Agriculture Organization of the United Nations (2015) FAOSTAT. FAOSTAT (Database). http://faostat3.fao.org/browse/Q/QC/E. Accessed 5 Nov 2015

  • Frett TJ, Reighard GL, Okie WR, Gasic K (2014) Mapping quantitative trait loci association with blush in peach [Prunus persica (L.) Batsch]. Tree Genet Genomes 10:367–381

    Article  Google Scholar 

  • Frett TJ, Gasic K, Clark JR, Byrne D, Gradziel T, Crisosto C (2012) Standardized phenotyping for fruit quality in peach [Prunus persica (L.) Batsch]. J Amer Pom Soc 66:214–219

    Google Scholar 

  • Gasic K, Quick R, Abdelghafar A, Frett TJ, Rauh B, Reighard G (2014) Marker assisted breeding for red skin coloration in peach. XXII Plant and Animal Genome conference, January 11–15, San Diego, p 435

  • Giraudoux P (2015) Pgirmess: data analysis in ecology. R package version 1.6.2. http://CRAN.R-project.org/package=pgirmess. Accessed 28 Sept 2015

  • Gradziel TM, McCaa JP (2008) Processing peach cultivar development. In: Layne DR, Bassi D (eds) The peach, botany, production and uses. CAB International Press, Wallingford, UK, pp 175–192

    Chapter  Google Scholar 

  • Hansche PE (1986) Heritability of fruit quality traits in peach and nectarine breeding stocks dwarfed by dw gene. Hortscience 21:1193–1195

    Google Scholar 

  • Iezzoni A, Weebadde C, Luby J, Yue CY, van de Weg E, Fazio G, Main D, Peace CP, Bassil N, McFerson J (2010) RosBREED: enabling marker-assisted breeding in Rosaceae. Acta Hort 859:389–394

    Article  Google Scholar 

  • Janick J (2005) The origins of fruits, fruit growing, and fruit breeding. In: Janick J (ed) Plant breeding reviews, volume 25. Wiley & Sons, Oxford, UK, pp 255–320

    Google Scholar 

  • Jordan JL, Shewfelt RL, Prussia SE (1986) The value of peach quality characteristics in the postharvest system. Acta Hort 203:175–182

    Google Scholar 

  • Jung S, Ficklin S, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Bombarely A, Cho L, Ru S, Evans K, Peace C, Abbott A, Mueller L, Olmstead MA, Main D (2014) The genome database for Rosaceae (GDR): year 10 update. Nucl Acids Res 42:D1237–D1244

    Article  CAS  PubMed  Google Scholar 

  • Lin-Wang KL, Bolitho K, Garryn K, Kortstee A, Karunairetnam S, McGhie TK, Espley RV, Hellens RP, Allan AC (2010) An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biol 10:50

    Article  PubMed  PubMed Central  Google Scholar 

  • Luby J, Shaw D (2001) Does marker-assisted selection make dollars and sense in a fruit breeding program? Hortscience 36:872–879

    Google Scholar 

  • Luchsinger L, Ortin P, Reginato G, Infante R (2002) Influence of canopy fruit position on the maturity and quality of Angelus peaches. Acta Hort 592:515–521

    Article  Google Scholar 

  • Munoz PR, Resende MFR, Huber DA, Quesada T, Resende MDV, Neale DB, Wegrzyn JL, Kirst M, Peter GF (2014) Genomic relationship matrix for correcting pedigree errors in breeding populations: impact on genetic parameters and genomic selection accuracy. Crop Sci 53:1115–1123

    Article  Google Scholar 

  • Okie WR, Bacon T, Bassi D (2008) Fresh-market cultivar development. In: Layne DR, Bassi D (eds) The peach, botany, production and uses. CAB International Press, Wallingford, UK, pp 139–174

    Chapter  Google Scholar 

  • Olmstead MA, Gilbert JL, Colquhoun TA, Clark DG, Kluson R, Moskowitz HR (2015) In pursuit of the perfect peach: consumer-assisted selection of peach fruit traits. Hortscience 50:1202–1212

    Google Scholar 

  • Parker D, Zilberman D, Moulton K (1991) How quality relates to price in California fresh peaches. Calif Agric 45:14–16

    Google Scholar 

  • Peace C, Norelli J (2009) Genomics approaches to crop improvement in the Rosaceae. In: Folta KM, Gardiner SE (eds) Genetics and genomics of Rosaceae. Springer, NY, pp 19–54

    Chapter  Google Scholar 

  • Peace CP, Luby JJ, van de Weg WE, Bink MCAM, Iezzoni AF (2014) A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry. Tree Genet Genomes 10:1679–1694

    Article  Google Scholar 

  • Picañol R, Eduardo I, Aranzana MJ, Howad W, Batlle I, Iglesias I, Alonso JM, Arús P (2013) Combinging linkage and association mapping to search for markers linked to the flat fruit character in peach. Euphytica 190:279–288

    Article  Google Scholar 

  • 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 109:884–897

    Article  CAS  PubMed  Google Scholar 

  • R Core Team (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. http://www.R-project.org/. Accessed 28 Sept 2015

  • Rahim MA, Busatto N, Trainotti L (2014) Regulation of anthocyanin biosynthesis in peach fruits. Planta 240:913–929

    Article  CAS  PubMed  Google Scholar 

  • Ramkumar G, Prahalada GD, Hechanova SL, Vinarao R, Jena KK (2015) Development and validation of SNP-based functional codominant markers for two major disease resistance genes in rice (O. sativa L.). Mol Breed 35:129

    Article  Google Scholar 

  • Ravaglia D, Espley R, Hendry-Kirk RA, Andreotti C, Ziosi V, Hellens R, Cost G, Allan A (2013) Transcriptional regulation of flavonoid biosynthesis in nectarine (Prunus persica) by a set of R2R3 MYB transcription factors. BMC Plant Biol 13:68

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ru S, Main D, Peace C (2015) Current applications, challenges, and perspectives of marker-assisted seedling selection in Rosaceae tree fruit breeding. Tree Genet Genomes 11:1–12

    Article  Google Scholar 

  • Sandefur P, Oraguzie N, Peace C (2016) A DNA test for routine prediction in breeding of sweet cherry fruit color, Pav-Rf-SSR. Mol Breed 36:33

    Article  Google Scholar 

  • Sansavini S, Gamberini A, Bassi D (2006) Peach breeding, genetics and new cultivar trends. Acta Hort 713:23–48

    Article  Google Scholar 

  • Scorza R, Sherman WB (1996) Peaches. In: Janick J, Moore JN (eds) Fruit Breeding. Wiley, New York, pp 325–440

    Google Scholar 

  • Sooriyapathirana SS, Khan A, Sebolt AM, Wang D, 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 Genet Genomes 6:821–832

    Article  Google Scholar 

  • Stegmeir T, Schuster M, Sebolt A, Rosyara U, Sundin G, Iezzoni A (2014) Cherry leaf spot resistance in cherry (Prunus) is associated with a quantitative trait locus on linkage group 4 inherited from P. canescens. Mol Breed 34:927–935

    Article  CAS  Google Scholar 

  • Takos AM, Jaffe FW, Jacob SR, Bogs J, Robinson SP, Walker AR (2006) Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol 142:1216–1232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • United State Department of Agriculture (2004) United States standards for grades of peaches. http://www.agmrc.org/media/cms/peaches_4EFAEFAA6947E.pdf. Accessed 21 Oct 2015

  • Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40:e115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vendramin E, Pea G, Dondini L, Pacheco I, Dettori MT, Gazza L, Scalabrin S, Strozzi F, Tartarini S, Bassi D, Verde I, Rossini L (2014) A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach. PLoS One 9(3):e90574

    Article  PubMed  PubMed Central  Google Scholar 

  • Verde I, Quarta R, Cedrola C, Dettori MT (2002) QTL analysis of agronomic traits in a BC1 peach population. Acta Hort 592:291–295

    Article  CAS  Google Scholar 

  • 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 9 k SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 7(4):e35668

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Ralchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS (2013) The high-quality draft of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genet 45:487–494

    Article  CAS  PubMed  Google Scholar 

  • Weinberger JH (1944) Characteristics of the progeny of certain peach varieties. Proc Amer Soc Hort Sci 45:233–238

    Google Scholar 

  • Yamamoto T, Shimada T, Imai T, Yaegaki H, Haji T, Matsuta N, Yamaguchi M, Hayashi T (2001) Characterization of morphological traits based on a genetic linkage map in peach. Breed Sci 51:271–278

    Article  CAS  Google Scholar 

  • Yamamoto T, Yamaguchi M, Hayashi T (2005) An integrated genetic linkage map of peach by SSR, STS, AFLP, and RAPD. J Jap Soc Hort Sci 74:204–213

    Article  CAS  Google Scholar 

  • You FM, Huo H, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253

    Article  PubMed  PubMed Central  Google Scholar 

  • Yuan K, Wang C, Wang J, Xin L, Zhou G, Li L, Shen G (2014) Analysis of the MdMYB1 gene sequence and development of new molecular markers related to apple skin color and fruit-bearing traits. Mol Gen Genomics 289:1257–1265

    Article  CAS  Google Scholar 

  • Zhou Y, Zhou H, Lin-Wang K, Vimolmangkang S, Espley RV, Wang L, Allan AC, Han Y (2014) Transcriptome analysis and transient transformation suggest an ancient duplicated MYB transcription factor as a candidate gene for leaf red coloration in peach. BMC Plant Biol 14:338

    Article  Google Scholar 

Download references

Acknowledgments

The authors thank Alejandra Salgado, Jonathan Fresnedo, Tim Hartmann, David Byrne, Tom Gradziel, Andrew Jecmen, Terry Rowland, and Daniel Edge-Garza for their technical support and suggestions and thank all reviewers for their comments. This work was partially supported by the USDA National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808) and “RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars” (2014-51181-22378) and with USDA Hatch funds provided to the Department of Horticulture, Washington State University.

Author information

Authors and Affiliations

  1. Washington State University, Pullman, WA, 99163, USA

    Paul Sandefur & Cameron Peace

  2. University of Arkansas, Fayetteville, AR, 72701, USA

    Terrence Frett & John Clark

  3. Clemson University, Clemson, SC, 29634, USA

    Ksenija Gasic

Authors
  1. Paul Sandefur
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Terrence Frett
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John Clark
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ksenija Gasic
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Cameron Peace
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Cameron Peace.

Electronic supplementary material

Online Resource 1

(PDF 605 kb)

Online Resource 2

(PDF 211 kb)

Online Resource 3

(PDF 17 kb)

Online Resource 4

(PDF 112 kb)

Online Resource 5

(PDF 209 kb)

Online Resource 6

(PDF 141 kb)

Online Resource 7

(PDF 158 kb)

Online Resource 8

(PDF 136 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sandefur, P., Frett, T., Clark, J. et al. A DNA test for routine prediction in breeding of peach blush, Ppe-Rf-SSR. Mol Breeding 37, 11 (2017). https://doi.org/10.1007/s11032-016-0615-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-016-0615-3

Keywords

Search

Navigation