Abstract
Most rosaceous tree fruit have long juvenility and large plant sizes, which makes traditional seedling selection (TSS), relying on phenotypic evaluation alone, relatively time-consuming and expensive. Limited predictiveness of phenotypic information also restricts the accuracy of TSS for traits with low heritability. Marker-assisted seedling selection (MASS) uses DNA markers to provide an early DNA-based evaluation of genetic performance potential of seedlings, with the aim of improving cost and/or genetic efficiency of seedling selection. MASS is still not widely adopted in rosaceous tree fruit breeding despite some successful examples. This review assesses reported MASS successes and identifies key elements and remaining challenges. Suggested solutions to widespread MASS adoption in Rosaceae tree fruit breeding are to (1) provide more breeding-program-specific DNA tests for high-impact attributes, (2) develop approaches to readily identify efficient MASS schemes, (3) increase access to service providers specialized in DNA testing for rosaceous tree fruit breeding programs, (4) obtain funds to initially implement MASS, and (5) develop software tools and provide training to apply DNA information. Overcoming current challenges of implementing MASS is likely to facilitate its adoption in scenarios already proven to be effective: where DNA testing is conducted at an early seedling stage for single or multiple traits without significant interactions between them and where trait loci targeted by DNA tests have a major influence on trait levels.
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References
Abalo G, Tongoona P, Derera J, Edema R (2009) A comparative analysis of conventional and marker-assisted selection methods in breeding maize streak virus resistance in maize. Crop Sci 49:509–520
Adami M, De Franceschi P, Brandi F, Liverani A, Giovannini D, Rosati C, Dondini L, Tartarini S (2013) Identifying a carotenoid cleavage dioxygenase (ccd4) gene controlling yellow/white fruit flesh color of peach. Plant Mol Biol Rep 31:1166–1175
Asea G, Vivek BS, Lipps PE, Pratt RC (2012) Genetic gain and cost efficiency of marker-assisted selection of maize for improved resistance to multiple foliar pathogens. Mol Breed 29:515–527
Asíns MJ (2002) Present and future of quantitative trait locus analysis in plant breeding. Plant Breed 121:281–291
Asins MJ, Bernet GP, Villalta I, Carbonell EA (2010) QTL analysis in plant breeding. In: Jain SM, Brar DS (eds) Molecular techniques in crop improvement. Springer, New York, pp 3–21
Badenes ML, Byrne DH (2012) Fruit breeding. Springer, New York
Bliss FA (2010) Marker-assisted breeding in horticultural crops. Acta Horticult 859:339–350
Bošković R, Tobutt KR (1996) Correlation of stylar ribonuclease zymograms with incompatibility alleles in sweet cherry. Euphytica 90:245–250
Bus V, Ranatunga C, Gardiner S, Bassett H, Rikkerink E (2000) Marker assisted selection for pest and disease resistance in the New Zealand apple breeding programme. Acta Horticult 538:541–547
Bus V, Rikkerink E, Aldwinckle HS, Caffier V, Durel CE, Gardiner S, Gessler C, Groenwold R, Laurens F, Le Cam B, Luby J, Meulenbroek B, Kellerhals M, Parisi L, Patocchi A, Plummer K, Schouten HJ, Tartarini S, van de Weg WE (2009) A proposal for the nomenclature of Venturiainaequalisraces. Acta Horticult 814:739–746
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 363:557–572
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196
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 101:9891–9896
Dwivedi SL, Crouch JH, Mackill DJ, Xu Y, Blair MW, Ragot M, Upadhyaya HD, Ortiz R (2007) The molecularization of public sector crop breeding: progress, problems, and prospects. Adv Agron 95:163–318
Edge-Garza DA, Zhu Y, Peace CP (2010) Enabling marker-assisted seedling selection in the Washington apple breeding program. Acta Horticult 859:369–373
Edge-Garza DA, Rowland TV, Konishi B, Brutcher L, Evans K, Peace CP (2012) Quality control improves resource savings in routine marker-assisted seedling selection for the Washington apple breeding program. Poster presentation at 6th Rosaceous Genomics Conference, Mezzocorona, Italy
Edge-Garza DA, Rowland TV, Haendiges S, Peace C (2014) A high-throughput and cost-efficient DNA extraction protocol for the tree fruit crops of apple, sweet cherry, and peach relying on silica beads during tissue sampling. Mol Breed. doi:10.1007/s11032-014-0160-x
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 10:1695–1709
Evans KM, James CM (2003) Identification of SCAR markers linked to Pl-w mildew resistance in apple. Theor Appl Genet 106:1178–1183
Evans KM, Hanrahan I, Auvil T (2011) WSU’s apple breeding program’s fruit evaluation system. Good Fruit Grow 62:30–31
Evans KM, Konishi B, Brutcher L, Edge-Garza DA, Rowland Jr T, Peace CP (2012) The logistical challenges of marker-assisted seedling selection in an apple breeding program. Poster presentation at 6th Rosaceous Genomics Conference Mezzocorona, Italy
Evans KM, Jung S, Lee T, Brutcher L, Cho I, Peace C, Main D (2013) Addition of a breeding database in the Genome Database for Rosaceae. Database 2013:bat078
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
Foolad MR, Panthee DR (2012) Marker-assisted selection in tomato breeding. Crit Rev Plant Sci 31:93–123
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
Gasic K, Peace CP (2013) First peach SNP mini-arrays developed and tested. RosBREED Q Newsl 4(3):2
Haldar S, Haendiges S, Edge-Garza DA, Oraguzie NC, Olmstead J, Peace CP (2010) Applying genetic markers for self-compatibility in the WSU sweet cherry breeding program. Acta Horticult 859:375–380
Hospital F (2009) Challenges for effective marker-assisted selection in plants. Genetica 136:303–310
Hummer KE, Janick J (2009) Rosaceae: taxonomy, economic importance, genomics. In: Folta KM, Gardiner SE (eds) Genetics and Genomics of Rosaceae. Springer, New York, pp 1–17
Iezzoni A (2010) Jewels in the genome. RosBREED Q Newsl 1(2):10
Iezzoni A, Weebadde C, Luby J, Yue C, van de Weg WE, Fazio G, Main D, Peace CP, Bassil NV, McFerson J (2010) RosBREED: Enabling marker-assisted breeding in Rosaceae. Acta Horticult 859:389–394
James CM, Clarke JB, Evans KM (2004) Identification of molecular markers linked to the mildew resistance gene Pl-d in apple. Theor Appl Genet 110:175–181
Janick J, Moore JN (1975) Advances in fruit breeding. Purdue Univ. Press, Lafayette
Jänsch M, Broggini GAL, WegerJuliane, Bus VGM, Gardiner SE,Bassett H, Patocchi A (2015) Identification of SNPs linked to eight apple disease resistance loci. Mol Breeding. In press
Jones N, Ougham H, Thomas H (1997) Markers and mapping: we are all geneticists now. New Phytol 137:165–177
Jung S, Lee T, Ru S, Main D, Iezzoni A, Peace CP, Fazio G (2013) The RosBREED Pedigree-Based Breeding Information Management System. Plant & Animal Genome XXI, San Diego, CA
Kellerhals M, Franck L, Baumgartner IO, Patocchi A, Frey JE (2011) Breeding for fire blight resistance in apple. Acta Horticult 896:385–389
Kuchel H, Ye G, Fox R, Jefferies S (2005) Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy. Mol Breed 16:67–78
Kumar LS (1999) DNA markers in plant improvement: An overview. Biotechnol Adv 17:143–182
Kumar S, Garrick DJ (2001) Genetic response to within-family selection using molecular markers in some radiata pine breeding schemes. Can J For Res 31:779–785
Kumar S, Chagné D, Bink MCAM, Volz RK, Whitworth C, Carlisle C (2012) Genomic selection for fruit quality traits in apple (Malus × domestica Borkh.). PLoS ONE 7:e36674
Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756
Luby JJ, Shaw DV (2001) Does marker-assisted selection make dollars and sense in a fruit breeding program? HortSci 36:872–879
Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, Inc, Sunderland
Moreau L, Charcosset A, Hospital F, Gallais A (1998) Marker-assisted selection efficiency in populations of finite size. Genetics 148:1353–1365
Moreau L, Lemarié S, Charcosset A, Gallais A (2000) Economic efficiency of one cycle of marker-assisted selection. Crop Sci 40:329–337
Peace CP (2013a) RosBREED by the numbers. RosBREED Q Newsl 4(2):4
Peace CP (2013b) Deliverables of the RosBREED project for U.S Rosaceae breeders: Part two. RosBREED Q Newsl 4(2):8–10
Peace CP, Jung S (2012) MAB in action: integrating DNA information into your breeding program. RosBREED Q Newsl 3(2):6–10
Peace CP, Norelli JL (2009) Genomics approaches to crop improvement in the Rosaceae. In: Folta KM, Gardiner SE (eds) Genetics and Genomics of Rosaceae. Springer, New York, pp 19–53
Peace CP, Bassil N, Coe M, Fazio G, Gallardo RK, Gasic K, Luby JJ, Main D, McFerson J, Weebadde C, van de Weg WE, Yue C, Iezzoni A (2013) Marker-assisted breeding in apple, peach, and cherry targets valuable functional alleles. Plant & Animal Genome XXI, San Diego, CA
Picañol R, Eduardo I, Aranzana MJ, Howad W, Batlle I, Iglesias I, Alonso JM, Arús P (2013) Combining linkage and association mapping to search for markers linked to the flat fruit character in peach. Euphytica 190:279–288
Pirona R, Eduardo I, Pacheco I, Da Silva Linge C, Miculan M, Verde I, Tartarini S, Dondini L, Pea G, 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 13:166
Rowland T Jr, Edge-Garza D, Oraguzie N, Peace CP (2012) Routine marker-assisted seedling selection in the Pacific Northwest sweet cherry breeding program provides resource savings. Poster presentation at 6th Rosaceous Genomics Conference, Mezzocorona, Italy
Ru S, Lee T, Edge-Garza D, Harshman J, Evans KM, Jung S, Main D, Peace CP (2014) Seedling Select: A web-based software tool to facilitate cost modeling of marker-assisted seedling selection (MASS) in Rosaceae tree fruit. Poster presentation at 7th International Rosaceae Genomics Conference, June 24–26, Seattle, WA
Salazar JA, Ruiz D, Campoy JA, Sánchez-Pérez R, Crisosto CH, Martínez-García PJ, Blenda A, Jung S, Main D, Martínez-Gómez P, Rubio M (2013) Quantitative trait loci (QTL) and Mendelian trait loci (MTL) analysis in Prunus: a breeding perspective and beyond. Plant Mol Biol Rep 32:1–18
Sandefur P, Frett T, Salgado A, Thurow L, Gasic K, Clark J, Peace CP (2014) Harnessing the power of RosBREED: development, validation, and application of DNA tests for predicting peach fruit quality, disease resistance, and other valuable traits for Rosaceae tree fruit. Oral presentation at ASHS-2014 Annual Conference, Orlando, FL
Sebolt A (2013) Breeder profile: Kate Evans. RosBREED Q Newsl 4(2):6–7
Smith C (1967) Improvement of metric traits through specific genetic loci. Anim Sci 9:349–358
Stromberg LD, Dudley JW, Rufener GK (1994) Comparing conventional early generation selection with molecular marker assisted selection in maize. Crop Sci 34:1221–1225
Tartarini S, Sansavini S (2003) The use of molecular markers in pome fruit breeding. Acta Horticult 622:129–141
Tartarini S, Gianfranceschi L, Sansavini S, Gessler C (1999) Development of reliable PCR markers for the selection of the Vf gene conferring scab resistance in apple. Plant Breed 118:183–186
Tartarini S, Sansavini S, Vinatzer B, Gennari F, Domizi C (2000) Efficiency of marker assisted selection (MAS) for the Vf scab resistance gene. Acta Horticult 538:549–552
Tehrani G, Brown SK (1992) Pollen-incompatibility and self-fertility in sweet cherry. Plant Breed Rev 9:313–338
Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822
Testolin R (2003) Marker-assisted selection in stone fruits. Acta Horticult 622:163–176
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:e90574
Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407
Yousef GG, Juvik JA (2001) Comparison of phenotypic and marker-assisted selection for quantitative traits in sweet corn. Crop Sci 41:645–655
Zhang G, Sebolt A, Sooriyapathirana S, Wang D, Bink M, Olmstead J, Iezzoni A (2009) Fruit size QTL analysis of an F1 population derived from a cross between a domesticated sweet cherry cultivar and a wild forest sweet cherry. Tree Genet Genomes 6:25–36
Acknowledgements
We thank RosBREED demonstration breeders for their responses to the MASS questionnaire and contributing their ideas. This work was funded by USDA’s National Institute of Food and Agriculture–Specialty Crop Research Initiative project, “RosBREED: Enabling Marker-Assisted Breeding in Rosaceae” (2009-51181-05808), “Tree Fruit GDR: Translating Genomics into Advances in Horticulture” (2009-51181-06036), and USDA Hatch funds provided to the Department of Horticulture, Washington State University.
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Ru, S., Main, D., Evans, K. et al. Current applications, challenges, and perspectives of marker-assisted seedling selection in Rosaceae tree fruit breeding. Tree Genetics & Genomes 11, 8 (2015). https://doi.org/10.1007/s11295-015-0834-5
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DOI: https://doi.org/10.1007/s11295-015-0834-5