[1] |
Aires A. 2017. Phenolics in foods: extraction, analysis and measurements. In Phenolic Compounds, eds. Soto-Hernandez M, Palma-Tenango M, del Rosario Garcia-Mateos M. 456 pp. IntechOpen. pp. 61−88. http://dx.doi.org/10.5772/66889 |
[2] |
Yu CHJ, Migicovsky Z, Song J, Rupasinghe HPV. 2023. (Poly) phenols of apples contribute to in vitro antidiabetic properties: assessment of Canada's Apple Biodiversity Collection. Plants, People, Planet 5:225−40 doi: 10.1002/ppp3.10315 |
[3] |
McClure KA, Gong Y, Song J, Vinqvist-Tymchuk M, Palmer LC, et al. 2019. Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols. Horticulture Research 6:107 doi: 10.1038/s41438-019-0190-y |
[4] |
Chagné D, Krieger C, Rassam M, Sullivan M, Fraser J, et al. 2012. QTL and candidate gene mapping for polyphenolic composition in apple fruit. BMC Plant Biology 12:12 doi: 10.1186/1471-2229-12-12 |
[5] |
Khan SA, Chibon P, de Vos RCH, Schipper BA, Walraven E, et al. 2012. Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16. Journal of Experimental Botany 63:2895−908 doi: 10.1093/jxb/err464 |
[6] |
Sadok IB, Tiecher A, Galvez-Lopez D, Lahaye M, Lasserre-Zuber P, et al. 2015. Apple fruit texture QTLs: year and cold storage effects on sensory and instrumental traits. Tree Genetics & Genomes 11:119 doi: 10.1007/s11295-015-0947-x |
[7] |
Laurens F, Aranzana MJ, Arus P, Bassi D, Bink M et al. 2018. An integrated approach for increasing breeding efficiency in apple and peach in Europe. Horticulture Research 5:11 doi: 10.1038/s41438-018-0016-3 |
[8] |
Lü P, Yu S, Zhu N, Chen Y, Zhou B, et al. 2018. Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nature Plants 4:784−91 doi: 10.1038/s41477-018-0249-z |
[9] |
Johnston JW, Gunaseelan K, Pidakala P, Wang M, Schaffer RJ. 2009. Co-ordination of early and late ripening events in apples is regulated through differential sensitivities to ethylene. Journal of Experimental Botany 60:2689−99 doi: 10.1093/jxb/erp122 |
[10] |
Klee HJ, Clark DG. 2010. Ethylene signal transduction in fruits and flowers. In Plant Hormones, ed. Davies PJ. Dordrecht: Springer Netherlands. pp. 377–98. https://doi.org/10.1007/978-1-4020-2686-7_18 |
[11] |
Pech JC, Latché A, Bouzayen M. 2010. Ethylene biosynthesis. In Plant Hormones, ed. Davies PJ. Dordrecht: Springer Netherlands. pp. 115–36. https://doi.org/10.1007/978-1-4020-2686-7_6 |
[12] |
Sunako T, Sakuraba W, Senda M, Akada S, Ishikawa R, et al. 1999. An allele of the ripening-specific 1-aminocyclopropane-1-carboxylic acid synthase gene (ACS1) in apple fruit with a long storage life. Plant Physiology 119:1297−304 doi: 10.1104/pp.119.4.1297 |
[13] |
Harada T, Sunako T, Wakasa Y, Soejima J, Satoh T, et al. 2000. An allele of the 1-aminocyclopropane-1-carboxylate synthase gene (Md-ACS1) accounts for the low level of ethylene production in climacteric fruits of some apple cultivars. Theoretical and Applied Genetics 101:742−46 doi: 10.1007/s001220051539 |
[14] |
Costa F, Stella S, Van de Weg WE, Guerra W, Cecchinel M, et al. 2005. Role of the Genes Md-ACO1 and Md-ACS1 in Ethylene Production and Shelf Life of Apple (Malus Domestica Borkh). Euphytica 141:181−90 doi: 10.1007/s10681-005-6805-4 |
[15] |
Baumgartner IO, Kellerhals M, Costa F, Dondini L, Pagliarani G, et al. 2016. Development of SNP-based assays for disease resistance and fruit quality traits in apple (Malus × domestica Borkh.) and validation in breeding pilot studies. Tree Genetics & Genomes 12:35 doi: 10.1007/s11295-016-0994-y |
[16] |
Costa F, Peace CP, Stella S, Serra S, Musacchi S, et al. 2010. QTL dynamics for fruit firmness and softening around an ethylene-dependent polygalacturonase gene in apple (Malus×domestica Borkh.). Journal of Experimental Botany 61:3029−39 doi: 10.1093/jxb/erq130 |
[17] |
Longhi S, Moretto M, Viola R, Velasco R, Costa F. 2012. Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus x domestica Borkh.). Journal of Experimental Botany 63:1107−21 doi: 10.1093/jxb/err326 |
[18] |
Atkinson RG, Sutherland PW, Johnston SL, Gunaseelan K, Hallett IC, et al. 2012. Down-regulation of POLYGALACTURONASE1 alters firmness, tensile strength and water loss in apple (Malus x domestica) fruit. BMC Plant Biology 12:129 doi: 10.1186/1471-2229-12-129 |
[19] |
Migicovsky Z, Yeats TH, Watts S, Song J, Forney CF, et al. 2021. Apple ripening is controlled by a nac transcription factor. Frontiers in Genetics 12:671300 doi: 10.3389/fgene.2021.671300 |
[20] |
Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, et al. 2017. Genome-wide association mapping of flowering and ripening periods in apple. Frontiers in Plant Science 8:1923 doi: 10.3389/fpls.2017.01923 |
[21] |
Larsen B, Migicovsky Z, Jeppesen AA, Gardner KM, Toldam-Andersen TB, et al. 2019. Genome-wide association studies in apple reveal loci for aroma volatiles, sugar composition, and harvest date. The Plant Genome 12:180104 doi: 10.3835/plantgenome2018.12.0104 |
[22] |
Jung M, Roth M, Aranzana MJ, Auwerkerken A, Bink M, et al. 2020. The apple REFPOP—a reference population for genomics-assisted breeding in apple. Horticulture Research 7:189 doi: 10.1038/s41438-020-00408-8 |
[23] |
Liu G, Li H, Grierson D, Fu D. 2022. NAC transcription factor family regulation of fruit ripening and quality: a review. Cells 11:525 doi: 10.3390/cells11030525 |
[24] |
Forlani S, Mizzotti C, Masiero S. 2021. The NAC side of the fruit: tuning of fruit development and maturation. BMC Plant Biology 21:238 doi: 10.1186/s12870-021-03029-y |
[25] |
Gao Y, Wei W, Zhao X, Tan X, Fan Z, et al. 2018. A NAC transcription factor, NOR-like1, is a new positive regulator of tomato fruit ripening. Horticulture Research 5:75 doi: 10.1038/s41438-018-0111-5 |
[26] |
Martín-Pizarro C, Vallarino JG, Osorio S, Meco V, Urrutia M, et al. 2021. The NAC transcription factor FaRIF controls fruit ripening in strawberry. The Plant Cell 33:1574−93 doi: 10.1093/plcell/koab070 |
[27] |
Qi X, Dong Y, Liu C, Song L, Chen L, et al. 2022. The PavNAC56 transcription factor positively regulates fruit ripening and softening in sweet cherry (Prunus avium). Physiologia Plantarum 174:e13834 doi: 10.1111/ppl.13834 |
[28] |
Pirona R, Eduardo I, Pacheco I, Da Silva Linge C, Miculan M, et al. 2013. Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach. BMC Plant Biology 13:166 doi: 10.1186/1471-2229-13-166 |
[29] |
Tan Q, Li S, Zhang Y, Chen M, Wen B, et al. 2021. Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach. Horticulture Research 8:213 doi: 10.1038/s41438-021-00648-2 |
[30] |
García-Gómez BE, Salazar JA, Dondini L, Martínez-Gómez P, Ruiz D. 2019. Identification of QTLs linked to fruit quality traits in apricot (Prunus armeniaca L.) and biological validation through gene expression analysis using qPCR. Molecular Breeding 39:28 doi: 10.1007/s11032-018-0926-7 |
[31] |
Watts S, Migicovsky Z, McClure KA, Yu CHJ, Amyotte B, et al. 2021. Quantifying apple diversity: a phenomic characterization of Canada’s Apple Biodiversity Collection. Plants, People, Planet 3:747−60 doi: 10.1002/ppp3.10211 |
[32] |
Migicovsky Z, Douglas GM, Myles S. 2022. Genotyping-by-sequencing of Canada’s apple biodiversity collection. Frontiers in Genetics 13:934712 doi: 10.3389/fgene.2022.934712 |
[33] |
Bai Y, Dougherty L, Li M, Fazio G, Cheng L, et al. 2012. A natural mutation-led truncation in one of the two aluminum-activated malate transporter-like genes at the Ma locus is associated with low fruit acidity in apple. Molecular Genetics and Genomics 287:663−78 doi: 10.1007/s00438-012-0707-7 |
[34] |
Davies T, Watts S, McClure K, Migicovsky Z, Myles S. 2022. Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii). PLoS ONE 17:e0250751 doi: 10.1371/journal.pone.0250751 |
[35] |
Migicovsky Z, Myles S. 2017. Exploiting wild relatives for genomics-assisted breeding of perennial crops. Frontiers in Plant Science 8:460 doi: 10.3389/fpls.2017.00460 |
[36] |
Migicovsky Z, Gardner KM, Money D, Sawler J, Bloom JS, et al. 2016. Genome to phenome mapping in apple using historical data. The Plant Genome 9:plantgenome2015.11.0113 doi: 10.3835/plantgenome2015.11.0113 |
[37] |
Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, et al. 2008. Genes mirror geography within Europe. Nature 456:98−101 doi: 10.1038/nature07331 |
[38] |
Li S, Zachgo S. 2013. TCP3 interacts with R2R3-MYB proteins, promotes flavonoid biosynthesis and negatively regulates the auxin response in Arabidopsis thaliana. The Plant Journal 76:901−13 doi: 10.1111/tpj.12348 |
[39] |
Xie X, Li S, Zhang R, Zhao J, Chen Y, et al. 2012. The bHLH transcription factor MdbHLH3 promotes anthocyanin accumulation and fruit colouration in response to low temperature in apples. Plant, Cell & Environment 35:1884−97 doi: 10.1111/j.1365-3040.2012.02523.x |
[40] |
An J, Liu Y, Zhang X, Bi S, Wang X, et al. 2020. Dynamic regulation of anthocyanin biosynthesis at different light intensities by the BT2-TCP46-MYB1 module in apple. Journal of Experimental Botany 71:3094−109 doi: 10.1093/jxb/eraa056 |
[41] |
Singleton VL, Orthofer R, Lamuela-Raventós RM. 1999. Analysis of total phenols and other oxidation substrates and antioxidants by means of folin-ciocalteu reagent. Methods in Enzymology 299:152−78 doi: 10.1016/S0076-6879(99)99017-1 |
[42] |
Samara M, Nasser A, Mingelgrin U. 2022. Critical examination of the suitability of the folin-ciocalteu reagent assay for quantitative analysis of polyphenols—the case of olive-mill wastewater. American Journal of Analytical Chemistry 13:476−93 doi: 10.4236/ajac.2022.1311032 |
[43] |
Brookfield P, Murphy P, Harker R, MacRae E. 1997. Starch degradation and starch pattern indices; interpretation and relationship to maturity. Postharvest Biology and Technology 11:23−30 doi: 10.1016/S0925-5214(97)01416-6 |
[44] |
Noronha H, Silva A, Dai Z, Gallusci P, Rombolà AD, et al. 2018. A molecular perspective on starch metabolism in woody tissues. Planta 248:559−68 doi: 10.1007/s00425-018-2954-2 |
[45] |
Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C. 2003. Mapping quantitative physiological traits in apple (Malus × domestica Borkh.). Plant Molecular Biology 52:511−26 doi: 10.1023/A:1024886500979 |
[46] |
Amyotte B, Bowen AJ, Banks T, Rajcan I, Somers DJ. 2017. Mapping the sensory perception of apple using descriptive sensory evaluation in a genome wide association study. PLoS ONE 12:e0171710 doi: 10.1371/journal.pone.0171710 |
[47] |
Jung M, Keller B, Roth M, Aranzana MJ, Auwerkerken A, et al. 2022. Genetic architecture and genomic predictive ability of apple quantitative traits across environments. Horticulture Research 9:uhac028 doi: 10.1093/hr/uhac028 |
[48] |
Guan Y, Peace C, Rudell D, Verma S, Evans K. 2015. QTLs detected for individual sugars and soluble solids content in apple. Molecular Breeding 35:135 doi: 10.1007/s11032-015-0334-1 |
[49] |
Kumar S, Raulier P, Chagné D, Whitworth C. 2014. Molecular-level and trait-level differentiation between the cultivated apple (Malus × domestica Borkh.) and its main progenitor Malussieversii. Plant Genetic Resources 12:330−40 doi: 10.1017/S1479262114000136 |
[50] |
Giné-Bordonaba J, Eduardo I, Arús P, Cantín CM. 2020. Biochemical and genetic implications of the slow ripening phenotype in peach fruit. Scientia Horticulturae 259:108824 doi: 10.1016/j.scienta.2019.108824 |
[51] |
Kumar S, Garrick DJ, Bink MCAM, Whitworth C, Chagné D, et al. 2013. Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics 14:393 doi: 10.1186/1471-2164-14-393 |
[52] |
Di Guardo M, Bink MCAM, Guerra W, Letschka T, Lozano L, et al. 2017. Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association. Journal of Experimental Botany 68:1451−66 doi: 10.1093/jxb/erx017 |
[53] |
Davies T, Myles S. 2023. Pool-seq of diverse apple germplasm reveals candidate loci underlying ripening time, phenolic content, and softening. Fruit Research 3:11 doi: 10.48130/FruRes-2023-0011 |
[54] |
Eduardo I, Picañol R, Rojas E, Batlle I, Howad W, et al. 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 205:627−36 doi: 10.1007/s10681-015-1445-9 |
[55] |
Zhao K, Tung C, Eizenga GC, Wright MH, Ali ML, et al. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications 2:467 doi: 10.1038/ncomms1467 |
[56] |
Chagné D, Dayatilake D, Diack R, Oliver M, Ireland H, et al. 2014. Genetic and environmental control of fruit maturation, dry matter and firmness in apple (Malus × domestica Borkh.). Horticulture Research 1:14046 doi: 10.1038/hortres.2014.46 |
[57] |
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, et al. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379 doi: 10.1371/journal.pone.0019379 |
[58] |
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81:559−75 doi: 10.1086/519795 |
[59] |
Jänsch M, Broggini GAL, Weger J, Bus VGM, Gardiner SE, et al. 2015. Identification of SNPs linked to eight apple disease resistance loci. Molecular Breeding 35:45 doi: 10.1007/s11032-015-0242-4 |
[60] |
Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, et al. 2012. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nature Genetics 44:825−30 doi: 10.1038/ng.2314 |
[61] |
Turner SD. 2018. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. The Journal of Open Source Software 3:731 doi: 10.21105/joss.00731 |
[62] |
Gao X, Starmer J, Martin ER. 2008. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genetic Epidemiology 32:361−69 doi: 10.1002/gepi.20310 |
[63] |
Gao X, Becker LC, Becker DM, Starmer JD, Province MA. 2010. Avoiding the high Bonferroni penalty in genome-wide association studies. Genetic Epidemiology 34:100−5 doi: 10.1002/gepi.20430 |
[64] |
Schloerke B, Cook D, Larmarange J, Briatte F, Marbach M, et al. 2022. GGally: Extension to 'ggplot2'. https://github.com/ggobi/ggally |