Genomics-assisted breeding in fruit trees

Hiroyoshi Iwata; Mai F. Minamikawa; Hiromi Kajiya-Kanegae; Motoyuki Ishimori; Takeshi Hayashi

doi:10.1270/jsbbs.66.100

journal article Jan 01, 2016

Genomics-assisted breeding in fruit trees

Hiroyoshi Iwata

Mai F. Minamikawa Hiromi Kajiya-Kanegae Motoyuki Ishimori Takeshi Hayashi

Breeding Science Vol. 66 No. 1 pp. 100-115 · Japanese Society of Breeding

View at Publisher Save 10.1270/jsbbs.66.100

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References

150

[1]

Abe, M., Y. Kobayashi, S. Yamamoto, Y. Daimon, A. Yamaguchi, Y. Ikeda, H. Ichinoki, M. Notaguchi, K. Goto and T. Araki (2005) FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science 309: 1052–1056. 10.1126/science.1115983

[2]

Albrechtsen, A., F.C. Nielsen and R. Nielsen (2010) Ascertainment biases in SNP chips affect measures of population divergence. Mol. Biol. Evol. 27: 2534–2547. 10.1093/molbev/msq148

[3]

Amasino, R. (2010) Seasonal and developmental timing of flowering. Plant J. 61: 1001–1013. 10.1111/j.1365-313x.2010.04148.x

[4]

Antanaviciute, L., F. Fernández-Fernández, J. Jansen, E. Banchi, K.M. Evans, R. Viola, R. Velasco, J.M. Dunwell, M. Troggio and D.J. Sargent (2012) Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genomics 13: 203. 10.1186/1471-2164-13-203

[5]

Araus, J.L. and J.E. Cairns (2014) Field high-throughput phenotyping: the new crop breeding frontier. Trends Plant Sci. 19: 52–61. 10.1016/j.tplants.2013.09.008

[6]

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

Nathan A. Baird, Paul D. Etter, Tressa S. Atwood et al.

PLoS ONE 10.1371/journal.pone.0003376

[7]

Ban, Y., N. Mitani, T. Hayashi, A. Sato, A. Azuma, A. Kono and S. Kobayashi (2014) Exploring quantitative trait loci for anthocyanin content in interspecific hybrid grape (Vitis labruscana × Vitis vinifera). Euphytica 198: 101–114. 10.1007/s10681-014-1087-3

[8]

Beaulieu, J., T. Doerksen, S. Clément, J. MacKay and J. Bousquet (2014a) Accuracy of genomic selection models in a large population of open-pollinated families in white spruce. Heredity 113: 343–352. 10.1038/hdy.2014.36

[9]

Genomic selection accuracies within and between environments and small breeding groups in white spruce

Jean Beaulieu, Trevor K Doerksen, John MacKay et al.

BMC Genomics 2014 10.1186/1471-2164-15-1048

[10]

Bink, M.C., J. Jansen, M. Madduri, R.E. Voorrips, C.E. Durel, A.B. Kouassi, F. Laurens, F. Mathis, C. Gessler, D. Gobbin et al. (2014) Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor. Appl. Genet. 127: 1073–1090. 10.1007/s00122-014-2281-3

[11]

Brachi, B., G.P. Morris and J.O. Borevitz (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol. 12: 232. 10.1186/gb-2011-12-10-232

[12]

TASSEL: software for association mapping of complex traits in diverse samples

Peter J Bradbury, Zhichao Zhang, Dallas E. Kroon et al.

Bioinformatics 10.1093/bioinformatics/btm308

[13]

Breseghello, F. and M.E. Sorrells (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165–1177. 10.1534/genetics.105.044586

[14]

Broman, K.W., H. Wu, Ś. Sen and G.A. Churchill (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890. 10.1093/bioinformatics/btg112

[15]

Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

Sharon R. Browning, Brian L. Browning

The American Journal of Human Genetics 10.1086/521987

[16]

Bus, V., H. Bassett, D. Bowatte, D. Chagné, C. Ranatunga, D. Ulluwishewa, C. Wiedow and S. Gardiner (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. 10.1007/s11295-009-0265-2

[17]

Calus, M.P.L. (2010) Genomic breeding value prediction: methods and procedures. Animal 4: 157–164. 10.1017/s1751731109991352

[18]

Cao, K., L. Wang, G. Zhu, W. Fang, C. Chen and J. Luo (2012). Genetic diversity, linkage disequilibrium, and association mapping analyses of peach (Prunus persica) landraces in China. Tree Genet. Genomes 8: 975–990. 10.1007/s11295-012-0477-8

[19]

Catchen, J.M., A. Amores, P. Hohenlohe, W. Cresko and J.H. Postlethwait (2011) Stacks: Building and genotyping loci de novo from short-read sequences. G3 (Bethesda) 1: 171–182. 10.1534/g3.111.000240

[20]

Cevik, V., C.D. Ryder, A. Popovich, K. Manning, G.J. King and G.B. Seymour (2010) A FRUITFULL-like gene is associated with genetic variation for fruit flesh firmness in apple (Malus domestica Borkh.). Tree Genet. Genomes 6: 271–279. 10.1007/s11295-009-0247-4

[21]

Chagné, D., R.N. Crowhurst, M. Troggio, M.W. Davey, B. Gilmore, C. Lawley, S. Vanderzande, R.P. Hellens, S. Kumar, A. Cestaro et al. (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7: e31745. 10.1371/journal.pone.0031745

[22]

Chagné, D., D. Dayatilake, R. Diack, M. Oliver, H. Ireland, A. Watson, S.E. Gardiner, J.W. Johnston, R.J. Schaffer and S. Tustin (2014) Genetic and environmental control of fruit maturation, dry matter and firmness in apple (Malus × domestica Borkh.). Hortic. Res. 1: 14046. 10.1038/hortres.2014.46

[23]

Chia, J.-M. and D. Ware (2011) Sequencing for the cream of the crop. Nat. Biotechnol. 29: 138–139. 10.1038/nbt.1756

[24]

Corbesier, L., C. Vincent, S. Jang, F. Fornara, Q. Fan, I. Searle, A. Giakountis, S. Farrona, L. Gissot, C. Turnbull et al. (2007) FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316: 1030–1033. 10.1126/science.1141752

[25]

Correa, J., M. Mamani, C. Muñoz-Espinoza, D. Laborie, C. Muñoz, M. Pinto and P. Hinrichsen (2014). Heritability and identification of QTLs and underlying candidate genes associated with the architecture of the grapevine cluster (Vitis vinifera L.). Theor. Appl. Genet. 127: 1143–1162. 10.1007/s00122-014-2286-y

[26]

Costa, F. (2015) MetaQTL analysis provides a compendium of genomic loci controlling fruit quality traits in apple. Tree Genet. Genomes 11: 819. 10.1007/s11295-014-0819-9

[27]

Cristofani, M., M.A. Machado and D. Grattapaglia (1999) Genetic linkage maps of Citrus sunki Hort. ex. Tan. and Poncirus trifoliata (L.) Raf. and mapping of citrus tristeza virus resistance gene. Euphytica 109: 25–32. 10.1023/a:1003637116745

[28]

Cros, D., M. Denis, L. Sánchez, B. Cochard, A. Flori, T. Durand-Gasselin, B. Nouy, A. Omoré, V. Pomiès, V. Riou et al. (2015) Genomic selection prediction accuracy in a perennial crop: case study of oil palm (Elaeis guineensis Jacq.). Theor. Appl. Genet. 128: 397–410. 10.1007/s00122-014-2439-z

[29]

Davey, J.W., P.A. Hohenlohe, P.D. Etter, J.Q. Boone, J.M. Catchen and M.L. Blaxter (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12: 499–510. 10.1038/nrg3012

[30]

Deery, D., J. Jimenez-Berni, H. Jones, X. Sirault and R. Furbank (2014) Proximal remote sensing buggies and potential applications for field-based phenotyping. Agronomy 5: 349–379. 10.3390/agronomy4030349

[31]

De Givry, S., M. Bouchez, P. Chabrier, D. Milan and T. Schiex (2005) CARTHAGENE: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 21: 1703–1704. 10.1093/bioinformatics/bti222

[32]

Denis, M. and J.-M. Bouvet (2013) Efficiency of genomic selection with models including dominance effect in the context of Eucalyptus breeding. Tree Genet. Genomes 9: 37–51. 10.1007/s11295-012-0528-1

[33]

Dirlewanger, E., E. Graziano, T. Joobeur, F. Garriga-Calderé, P. Cosson, W. Howad and P. Arús (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc. Natl. Acad. Sci. USA 101: 9891–9896. 10.1073/pnas.0307937101

[34]

Doucleff, M., Y. Jin, F. Gao, S. Riaz, A.F. Krivanek and M.A. Walker (2004) A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica. Theor. Appl. Genet. 109: 1178–1187. 10.1007/s00122-004-1728-3

[35]

Eccel, E., R. Rea, A. Caffarra and A. Crisci (2009) Risk of spring frost to apple production under future climate scenarios: the role of phonological acclimation. Int. J. Biometeorol. 53: 273–286. 10.1007/s00484-009-0213-8

[36]

Edge-Garza, D.A., C.P. Peace and Y. Zhu (2010) Enabling marker-assisted seedling selection in the Washington apple breeding program. Acta Hortic. 859: 369–373. 10.17660/actahortic.2010.859.44

[37]

Eduardo, I., I. Pacheco, G. Chietera, D. Bassi, C. Pozzi, A. Vecchietti and L. Rossini (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. 10.1007/s11295-010-0334-6

[38]

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

Robert J. Elshire, Jeffrey C. Glaubitz, Qi Sun et al.

PLoS ONE 10.1371/journal.pone.0019379

[39]

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

Jeffrey B. Endelman

The Plant Genome 10.3835/plantgenome2011.08.0024

[40]

Endo, T., T. Shimada, H. Fujii, Y. Kobayashi, T. Araki and M. Omura (2005) Ectopic expression of an FT homolog from Citrus confers an early flowering phenotype on trifoliate orange (Poncirus trifoliata L. Raf.). Transgenic Res. 14: 703–712. 10.1007/s11248-005-6632-3

[41]

Fan, L., M.-Y. Zhang, Q.-Z. Liu, L.-T. Li, Y. Song, L.-F. Wang, S.-L. Zhang and J. Wu (2013) Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Mol. Biol. Rep. 31: 1271–1282. 10.1007/s11105-013-0586-z

[42]

Fernández-Fernández, F., L. Antanaviciute, M.M. van Dyk, K.R. Tobutt, K.M. Evans, D.J.G. Rees, J.M. Dunwell and D.J. Sargent (2012) A genetic linkage map of an apple rootstock progeny anchored to the Malus genome sequence. Tree Genet. Genomes 8: 991–1002. 10.1007/s11295-012-0478-7

[43]

Ferrándiz, C., Q. Gu, R. Martienssen and M.F. Yanofsky (2000) Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development 127: 725–734. 10.1242/dev.127.4.725

[44]

Future Scenarios for Plant Phenotyping

Fabio Fiorani, Ulrich Schurr

Annual Review of Plant Biology 10.1146/annurev-arplant-050312-120137

[45]

Flachowsky, H., A. Peil, T. Sopanen, A. Elo and V. Hanke (2007) Overexpression of BpMADS4 from silver birch (Betula pendula Roth.) induces early-flowering in apple (Malus × domestica Borkh.). Plant Breed. 126: 137–145. 10.1111/j.1439-0523.2007.01344.x

[46]

Flachowsky, H., P.-M. Le Roux, A. Peil, A. Patocchi, K. Richter and M.-V. Hanke (2011) Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker-assisted selection. New Phytol. 192: 364–377. 10.1111/j.1469-8137.2011.03813.x

[47]

Flachowsky, H., I. Szankowski, S. Waidmann, A. Peil, C. Tränkner and M.-V. Hanke (2012) The MdTFL1 gene of apple (Malus × domestica Borkh.) reduces vegetative growth and generation time. Tree Physiol. 32: 1288–1301. 10.1093/treephys/tps080

[48]

Fodor, A., V. Segura, M. Denis, S. Neuenschwander, A. Fournier-Level, P. Chatelet, F.A.A. Homa, T. Lacombe, P. This and L.L. Cunff (2014) Genome-wide prediction methods in highly diverse and heterozygous species: Proof-of-concept through simulation in grapevine. PLoS ONE 9: e110436. 10.1371/journal.pone.0110436

[49]

Folta, K.M. and S.E. Gardiner (2009) Genetics and genomics of Rosaceae. New York, Springer. 10.1007/978-0-387-77491-6

[50]

Freiman, A., L. Shlizerman, S. Golobovitch, Z. Yablovitz, R. Korchinsky, Y. Cohen, A. Samach, E. Chevreau, P.-M. Le Roux, A. Patocchi et al. (2012) Development of a transgenic early flowering pear (Pyrus communis L.) genotype by RNAi silencing of PcTFL1-1 and PcTFL1-2. Planta 235: 1239–1251. 10.1007/s00425-011-1571-0

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Details

Published: Jan 01, 2016
Vol/Issue: 66(1)
Pages: 100-115

Authors

H

Hiroyoshi Iwata

Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo

M

Mai F. Minamikawa

Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo

H

Hiromi Kajiya-Kanegae

Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo

M

Motoyuki Ishimori

Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo

T

Takeshi Hayashi

Agroinfomatics Division, NARO Agricultural Research Center (NARC)

Cite This Article

Hiroyoshi Iwata, Mai F. Minamikawa, Hiromi Kajiya-Kanegae, et al. (2016). Genomics-assisted breeding in fruit trees. Breeding Science, 66(1), 100-115. https://doi.org/10.1270/jsbbs.66.100

Genomics-assisted breeding in fruit trees

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