Abstract
Apple is one of the most widely cultivated tree fruits in the temperate regions of the world. Development of new apple cultivars is generally based on eating quality, appearance, marketability, health/wellbeing and more recently, on environmental sustainability. A range of new technologies that will both reduce unit costs and increase production are being integrated in apple breeding programmes. Also, molecular breeding is opening an opportunity to significantly reduce the time to incorporate new traits from wild relatives into established crops; enhancing nutritional value, and enabling adaptation to new environmental conditions. The availability of genome sequence along with high throughput genotyping platforms is transforming the strategies for developing new cultivars. Now a range of genome-based selection strategies are providing opportunities to accelerate cultivar breeding. Genomic selection (GS) can be used to obtain genomic breeding values for choosing next-generation parents or selections for further testing as potential commercial cultivars. An empirical study in a New Zealand apple cultivar breeding programme showed that the selection response per unit time using GS compared with the conventional selection were very high (> 100 %) especially for low-heritability traits. The cost for highly paralleled targeted genotyping (e.g. single nucleotide polymorphism assays) is constantly decreasing, which would make implementation of GS affordable in near future.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Albrecht A, Wimmer V, Auinger H-J et al (2011) Genome based prediction of testcross values in maize. Theor Appl Genet 123:339–350
Alston FH, Phillips KL, Evans KM (2000) A Malus gene list. Acta Hort 538:561–570
Andersson L (2001) Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet 2:130–138
Aranzana MJ, Abbassi EK, Howad W, Arús P (2010) Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genet 11:69
Basil N, Lewers K (2009) Genomics opportunities, new crops and new products. In: Folta KM, Gardiner SE (eds) Genetics and genomics of the Rosaceae. Springer, New York, pp 55–70
Batlle I, Lozano L, Iglesias I et al (2009) The IRTA-HortResearch apple scion breeding programme: aiming for high fruit quality under warm growing conditions. Acta Hort 814:209–214
Baumgartner IO, Leumann LR, Frey JE et al (2012) Breeding apples to withstand infection pressure by fireblight and other diseases. In: 15th International Conference on Organic Fruit-Growing, Hohenheim, Germany, 20th–22nd February. www.ecofruit.net
Bernardo R, Yu J (2007) Prospects for genome-wide selection for quantitative traits in maize. Crop Sci 47:1082–1090
Berry DP, Kearney F, Harris BL (2009) Genomic Selection in Ireland. Proceedings of the interbull international workshop—genomic information in genetic evaluations, Uppsala, Sweden, Bulletin no. 39
Bringhurst RS (1983) Breeding strategy. In: Janick J, Moore JN (eds). Methods in fruit breeding. Purdue University Press, West Lafayette, pp 147–153
Brown AG (1975) Apples. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue University Press, West Lafayette, pp 3–37
Brown AG, Harvey DM (1971) The nature and inheritance of sweetness and acidity in the cultivated apple. Euphytica 20:68–80
Bus VGM, Chagne D, Bassett HCM et al (2008) Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.). Tree Genet Genomes 4:223–236
Bus VGM, Esmenjaud D, Buck E, Laurens F (2009) Application of genetic markers in rosaceous crops. In: Folta KM, Gardiner SE (eds) Genetics and genomics of the rosaceae. Springer, New York, pp 563–600
Bus VGM, Bassett H, Bowatte D et al (2010) Genome mapping of an apple scab, a powdery mildew and a woolly apple aphid resistance gene from open-pollinated mildew immune selection. Tree Genet Genomes 6:477–487
Calus M (2010) Genomic breeding value prediction: methods and procedures. Animal 4:157–164
Calus M, Veerkamp R (2007) Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. J Anim Breed Genet 124:362–368
Celton JM, Tustin DS, Chagne D, Gardiner SE (2009) Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genet Genomes 5:93–107
Celton JM, Martinez S, Jammes MJ et al (2011) Deciphering the genetic determinism of bud phenology in apple progenies: a new insight into chilling and heat requirement effects on flowering dates and positional candidate genes. New Phytol 192:378–392
Cevik V, Ryder CD, Popovich A et al (2009) A FRUITFULL-like gene is associated with genetic variation for fruit flesh firmness in apple (Malus domestica Borkh.). Tree Genet Genomes 6:271–279
Chagné D, Carlisle C, Blond C et al (2007) Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple. BMC Genomics 8:212
Chagné D, Gasic K, Crowhurst RN et al (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics 92:353–358
Chagné D, Crowhurst RN, Troggio M et al (2012a) Genome-Wide SNP Detection, Validation, and Development of an 8 K SNP Array for Apple. PLoS ONE 7(2):e31745
Coart E, Vekemans X, Smulders MJM et al (2003) Genetic variation in the endangered wild apple (Malus sylvestris (L.) Mill.) in Belgium as revealed by amplified fragment length polymorphism and microsatellite markers. Mol Ecol 12:845–857
Coart E, Van Glabeke S, De Loose M et al (2006) Chloroplast diversity in the genus Malus: new insights into the relationship between the European wild apple (Malus sylvestris (L.) Mill.) and the domesticated apple (Malus domestica Borkh.). Mol Ecol 15:2171–2182
Cook M, Gardiner S (2004) Development of a fully automated system to extract DNA from difficult plant tissues for genomics research. In: Plant & Animal Genome XII Conference, San Diego, CA (Abstract P180)
Coster A, Bastiaansen JWM, Calus MPL et al (2010) Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance. Genet Sel Evol 42:9
Crossa J, de los CG, Pérez P et al (2010) Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186:713–724
Daetwyler HD, Pong-Wong R, Villanueva B, Woolliams JA (2010) The impact of genetic architecture on genome-wide evaluation methods. Genetics 185:1021–1031
Daillant-Spinnler B, MacFie HJH, Beyts PK, Hedderley D (1996) Relationships between perceived sensory properties and major preference directions of 12 varieties of apples from the Southern Hemisphere. Food Qual Pref 7:113–126
De Roos APW, Schrooten C, Mullaart E et al (2009) Genomic selection at CRV. Proceedings of the interbull international workshop—genomic information in genetic evaluations. Uppsala, Sweden, Bulletin no. 39
Dekkers JCM (2004) Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J Anim Sci 82:E313–E328
Devoghalaere F, Doucen T, Guitton B et al (2012) A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control. BMC Plant Biol 12. DOI 10.1186/1471–2229-12–7
Dunemann F, Ulrich D, Malysheva-Otto L et al (2012) Functional allelic diversity of the apple alcohol acyl-transferase gene MdAAT1 associated with fruit ester volatile contents in apple cultivars. Mol Breeding 29:609–625
Durel C-E, Laurens F, Fouillet A, Lespinasse Y (1998) Utilisation of pedigree information to estimate genetic parameters from large, unbalanced data sets in apple. Theor Appl Genet 96:1077–1085
Espley RV, Brendolise C, Chagne D et al (2009) Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. Plant Cell 21:168–183
Evans K (2012) Apple breeding in the pacific northwest. Acta Hort (in press)
Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th ed. Longman, Harlow
Fernando R, Grossman M (1989) Marker assisted selection using best linear unbiased prediction. Genet Select E 21:467–477
Fischer C (1994) Shortening of the juvenile period in apple breeding. In: Schmidt H, Kellerhals M (eds) Progress in temperate fruit breeding. Kluwer, Dordrecht, pp 161–164
Fischer M, Fischer C (2004) 75 years of tradition in classical pillnitz fruit breeding—aims, results. Acta Hort 663:699–706
Flachowsky H, Peil A, Sopanen T et al (2007) Overexpression of BpMADS4 from silver birch (Betula pendula Roth.) induces early flowering in apple (Malus x domestica Borkh.). Plant Breed 126:137–145
Flachowsky H, Hanke M-V, Peil A et al (2009) A review on transgenic approaches to accelerate breeding of woody plants. Plant Breed 128:217–226
Flachowsky H, Le Roux P-M, Peil A et al (2011) Application of a high-speed breeding technology to apple (Malus x domestica) based on transgenic early flowering plants and marker-assisted selection. New Phytol 192:364–377
Forsline PL, Aldwinckle HS, Dickson EE et al (2003) Collection, maintenance, characterization, and utilization of wild apples of central Asia. Hortic Rev 29:1–61
Frey JE, Frey B, Sauer C, Kellerhals M (2004) Efficient low-cost DNA extraction and multiplex fluorescent PCR method for marker-assisted selection in breeding. Plant Breed 123:554–557
Gardiner S, Norelli J, de Silva N et al (2012) Candidate gene markers associated with quantitative trait loci for fireblight resistance in Malus ’Robusta 5’ accessions. BMC Genet 13:25. doi: 10.1186/1471–2156-13–25
Gardiner SE, Bus VGM, Rusholme RL et al (2007) Apple. In: Kole C (ed) Genome mapping and molecular breeding in plants, Vol. 4, fruits and nuts. Springer, Heidelberg, pp 1–62
Gasic K, Gonzalez DO, Thimmapuram J et al (2009) Comparative analysis and functional annotation of a large expressed sequence tag collection of apple. Plant Genome 2:23–38
Goddard ME (2009) Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136:245–257
Guitton B, Kelner J-J, Velasco R et al (2012) Genetic control of biennial bearing in apple. J Exp Bot 63:131–149
Habier D, Fernando RL, Dekkers JC (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389–2397
Habier D, Tetens J, Seefried F-R et al (2010) The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet Sel Evol 42:5
Harker FR, Gunson FA, Jaeger SR (2003) The case for fruit quality: an interpretive review of consumer attitudes and preferences. Postharvest Biol Tec 28:333–347
Harris BL, Johnson DL, Spelman RJ (2008) Genomic selection in New Zealand and the implications for national genetic evaluation. Proceedings of the 36th ICAR Session, Niagara Falls (USA), pp 325–331
Harris SA, Robinson JP, Juniper BE (2002) Genetic clues to the origin of the apple. Trends Genet 18:426–430
Harrison N, Harrison R (2011) On the evolutionary history of the domesticated apple. Nat Genet 43:1043–1044
Hayes BJ, Visscher PM, Goddard ME (2009a) Increased accuracy of artificial selection by using the realized relationship matrix. Genet Res 91:47–60
Hayes BJ, Daetwyler HD, Bowman P et al (2009b) Accuracy of genomic selection: comparing theory and results. Proc Assoc Advmt Ani Breed Genet 18:34–37
Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009c) Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92:433–443
Heffner EL, Lorenz AJ, Jannink JL, Sorrells ME (2010) Plant breeding with genomic selection: gain per unit time and cost. Crop Sci 50:1681–1690
Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12
Henderson CR (1984) Application of linear models in animal breeding. University of Guelph
Heslot N, Yang H-P, Sorrells ME, Jannink J-L (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52:146–160
Iwata H, Hayashi T, Tsumura Y (2011) Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica. Tree Genet Genomes 7:1–12
Jaeger SR, Andani Z, Wakeling IN, MacFie HJH (1998) Consumer preferences for fresh and aged apples: a crosscultural comparison. Food Qual Pref 9:355–366
Janick J, Cummins JN, Brown SK, Hemmat M (1996) Apples. In: Janick J, Moore JN (eds) Fruit breeding. Vol I. Tree and tropical fruits. John Wiley & Sons Inc., New York, pp 1–77
Jannink JL (2010) Dynamics of long-term genomic selection. Genet Sel Evol 42:35
Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177
Janse J, Verhaegh JJ, den Nijs APM (1994) Early selection of partial resistance to powdery mildew, Podosphaera leucotricha (Ell. et EV.) Salm. in apple progenies. Euphytica 77:7–9
Kellerhals M, Bamgartner I, Leumann L et al (2012) Progress in pyramiding disease resistances in apple breeding. Acta Hort (in press)
Khan SA, Chibon P-Y, de Vos RCH et al (2012) Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16. J Expt Bot 8:895–2908
Kizilkaya K, Fernando RL, Garrick DJ (2010) Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J Anim Sci 88:544–551.
Korban SS, Tartarini S (2009) Apple structural genomics. In: Folta KM, Gardiner SE (eds) Genetics and genomics of the rosaceae. Springer, New York, pp 85–119
Kouassi AB, Durel C-E, Costa F et al (2009) Estimation of genetic parameters and prediction of breeding values for apple fruit-quality traits using pedigreed plant material in Europe. Tree Genet Genomes 5:659–672
Kumar S, Volz RK, Alspach PA, Bus VGM (2010) Development of a recurrent apple breeding programme in New Zealand: a synthesis of results, and a proposed revised breeding strategy. Euphytica 173:207–222
Kumar S, Volz RK, Weskett R (2011) Genetic architecture of fruit quality traits in Malus x domestica (Borkh.) compared between own-rooted seedlings and vegetative propagules on ‘M. 9’ rootstock. Tree Genet Genomes 7:1079–1088
Kumar S, Bink MCAM, Volz RK et al (2012a) Towards genomic selection in apple (Malus × domestica Borkh.) breeding programs: prospects, challenges and strategies. Tree Genet Genomes 8:1–14
Kumar S, Chagné D, Bink MCAM et al (2012b) Genomic selection for fruit quality traits in apple (Malus × domestica Borkh.). PLoS ONE 7(5):e36674
Labuschagné IF (2004) Budbreak number as selection criteria for breeding apples adapted to mild winter climatic conditions: a review. Acta Hort 663:775–781
Laurens F (1999) Review of the current apple breeding programs in the world: objectives for scion cultivar improvement. Acta Hort 484:163–170
Le Roux P-M, Flachowsky H, Hanke M-V et al (2012) Development of apple pre-breeding genotypes highly resistant to fireblight by early flowering In: BiotechFruit 2012, Nelson, New Zealand, 25th-29th March, pp 133. www.biotechfruit.com
Legarra A, Robert-Granie C, Manfredi E, Elsen J-M (2008) Performance of genomic selection in mice. Genetics 180:611–618
Lespinasse Y (2009) Review of pome fruit breeding in Europe: which strategies for the near future? Acta Hort 824:865–871
Lespinasse Y, Alston FH, Watkins R (1976) Cytological techniques for use in apple breeding. Ann Appl Biol 82:349–353
Liebhard R, Kellerhals M, Pfammatter W et al (2003) Mapping quantitative physiological traits in apple (Malus × domestica Borkh.). Plant Mol Biol 52:511–526
Longhi S, Moretto M, Viola R et al (2012) Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus × domestica Borkh.). J Expt Bot 63:1107–1121
Lorenz AJ, Hamblin MT, Jannink J-L (2010) Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley. PLoS ONE 5: e14079.
Lorenz AJ, Chao S, Asoro FG et al (2011) Genomic selection in plant breeding: knowledge and prospects. Adv Agron 110:77–123
Lorenzana RE, Bernardo R (2009) Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet 120:151–161
Luby JJ, Shaw DV (2001) Does marker-assisted selection make dollars and sense in a fruit breeding program? HortScience 36:872–879
Lund M, Su G (2009) Genomic selection in the Nordic countries. Proceedings of the interbull international workshop—genomic information in genetic evaluations. Uppsala, Sweden, Bulletin no. 39
Meuwissen THE (2009) Accuracy of breeding values of ’unrelated’ individuals predicted by dense SNP genotyping. Genet Sel Evol 41:35–43
Meuwissen THE, Goddard ME (1996) The use of marker haplotypes in animal breeding schemes. Genet Sel Evol 28:161–176
Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
Micheletti D, Troggio M, Zharkikh A et al (2011) Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genet Genomes 7:11
Montes JM, Melchinger AE, Reif JC (2007) Novel throughput phenotyping platforms in plant genetic studies. Trends Plant Sci 12:433–436
Morgan J, Richards A (1993) The book of apples. Ebury Press, London
Moser G, Tier B, Crump R et al (2009) A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers. Genet Sel Evol 41:56
Newcomb RD, Crowhurst RN, Gleave AP et al (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141:147–166
Noiton DAM, Alspach PA (1996) Founding clones, inbreeding, coancestry, and status number of modern apple cultivars. J Am Soc Hortic Sci 121:773–782.
O’Rourke D (2011) World apple review. Belrose Inc, Pullman, Washington
Oraguzie NC, Iwanami H, Soejima J et al (2004) Inheritance of the Md-ACS1 gene and its relationship to fruit softening in apple (Malus × domestica Borkh.). Theor Appl Genet 108:1526–1533
Patocchi A, Frei A, Frey JE, Kellerhals M (2009) Towards improvement of marker assisted selection of apple scab resistant cultivars: Venturia inaequalis virulence surveys and standardization of molecular marker alleles associated with resistance genes. Mol Breeding 24:337–347
Pindo M, Vezzulli S, Coppola G et al (2008) SNP high-throughput screening in grapevine using the SNPlexTM genotyping system. BMC Plant Biol 8:12
Rehder A (1940) Manual of cultivated trees and shrubs. MacMillan, New York, NY, pp 389–399
Resende MDV, Resende MFRJ, Sansaloni CP et al (2012c) Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytol 194:116–128
Resende MFRJ, Muñoz P, Resende MDV et al (2012a) Accuracy of genomic selection methods in a standard dataset of loblolly pine (Pinus taeda L.). Genetics 190:1503–1510
Resende MFRJ, Muñoz P, Acosta JJ et al (2012b) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytol 193:617–624
Robinson JP, Harris SA, Juniper BE (2001) Taxonomy of the genus Malus Mill. (Rosaceae) with emphasis on the cultivated apple, Malus x domestica Borkh. Plant Syst Evol 226:35–58
Rothschild MF, Soller M (1997) Candidate gene analysis to detect genes controlling traits of economic importance in domestic livestock. Probe 8:13–20
Schenkel FS, Sargolzaei M, Kistemaker G et al (2009) Reliability of genomic evaluation of Holstein cattle in Canada. Proceedings of the interbull international workshop—genomic information in genetic evaluations. Uppsala, Sweden, Bulletin no. 39
Silfverberg-Dilworth E, Matasci CL, Van de Weg WE et al (2006) Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes 2:202–224
Sved JA (1971) Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol 2:125–141
Toosi A, Fernando RL, Dekkers JCM (2009) Genomic selection in admixed and crossbred populations. J Anim Sci 88:32–46
VanRaden PM, Van Tassell CP, Wiggans GR et al (2009) Invited review: reliability of genomic predictions for North American Holstein bulls. J Dairy Sci 92:16–24
Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42:833–839
Volz RK, Alspach PA, White AG, Ferguson IB (2001) Genetic variability in apple fruit storage disorders. Acta Hort 553:241–244
Volz RK, Rikkerink E, Austin P et al (2009) “Fast Breeding” in apple: a strategy to accelerate introgression of new traits into elite germplasm. Acta Hort 814:163–168
Wiedow C, Chagné D, Souleyre E et al (2010) QTL and candidate gene mapping of ‘ripe apple’ aroma. In: Plant & Animal Genome XVIII Conference, San Diego, CA, January 9–13
Wong C, Bernardo R (2008) Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations. Theor Appl Genet 116:815–824
Xu S (2007) An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 63:513–521.
Yang JA, Benyamin B, McEvoy BP et al (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42:565–131
Yi N, Xu S (2008) Bayesian LASSO for quantitative trait loci mapping. Genetics 179:1045–1055.
Zhong S, Dekkers JCM, Fernando RL, Jannink J-L (2009) Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182:355–364
Zhu Y, Barritt BH (2008) Md-ACS1 and Md-ACO1 genotyping of apple (Malus x domestica Borkh.) breeding parents and suitability for marker-assisted selection. Tree Genet Genomes 4:555–562
Zhu Y, Evans K, Peace C (2011) Utility testing of an apple skin color MdMYB1 marker in two progenies. Mol Breeding 27:525–532
Zimmerman RH (1991) Flowering in crabapple seedlings: methods of shortening the juvenile phase. J Am Soc Hort Sci 96:404–411
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Kumar, S., Volz, R., Chagné, D., Gardiner, S. (2014). Breeding for Apple (Malus × domestica Borkh.) Fruit Quality Traits in the Genomics Era. In: Tuberosa, R., Graner, A., Frison, E. (eds) Genomics of Plant Genetic Resources. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7575-6_16
Download citation
DOI: https://doi.org/10.1007/978-94-007-7575-6_16
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-7574-9
Online ISBN: 978-94-007-7575-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)