1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
Mega, K.; Tomita, E.; Kitamura, S.; Saito, S.; Mizukami, S. The Grand Dictionary of Horticulture; Aoba, T., Ed.; Shogakukan: Tokyo,
Japan, 1988; ISBN 978-4-09-305111-8.
Horiuchi, S.; Yoshida, M.; Kariya, H.; Nakamura, T.; Hasebe, H.; Suzaki, T.; Sakitani, T. Nihonnoume Sekainoume; Yokendo: Tokyo,
Japan, 1996.
Chen, J. China Mei Flower (Prunus Mume) Cultivars in Colour; China Forestry Publishing House: Beijing, China, 2017.
Ministry of Agriculture, Forestry and Fisheries Japan the 96th Statistical Yearbook of Ministry of Agriculture, Forestry and
Fisheries: MAFF. Available online: https://www.maff.go.jp/e/data/stat/96th/index.html (accessed on 5 May 2023).
Ministry of Agriculture, Forestry and Fisheries Japan Survey on Production Dynamics of Specialty Fruit Trees (in Japanese).
Available online: https://www.e-stat.go.jp/stat-search/file-download?statInfId=000040042773&fileKind=0 (accessed on 5
May 2023).
Ikeda, K.; Nishide, M.; Tsujimoto, K.; Nagashima, S.; Kuwahara, T.; Mitani, T.; Koyama, A.H. Antiviral and Virucidal Activities of
Umesu Phenolics on Influenza Viruses. Jpn. J. Infect. Dis. 2020, 73, 8–13. [CrossRef] [PubMed]
Enomoto, S.; Yanaoka, K.; Utsunomiya, H.; Niwa, T.; Inada, K.; Deguchi, H.; Ueda, K.; Mukoubayashi, C.; Inoue, I.; Maekita,
T.; et al. Inhibitory Effects of Japanese Apricot (Prunus Mume Siebold et Zucc.; Ume) on Helicobacter Pylori-Related Chronic
Gastritis. Eur. J. Clin. Nutr. 2010, 64, 714–719. [CrossRef] [PubMed]
Kono, R.; Nakamura, M.; Nomura, S.; Kitano, N.; Kagiya, T.; Okuno, Y.; Inada, K.; Tokuda, A.; Utsunomiya, H.; Ueno, M.
Biological and Epidemiological Evidence of Anti-Allergic Effects of Traditional Japanese Food Ume (Prunus Mume). Sci. Rep.
2018, 8, 11638. [CrossRef] [PubMed]
Bailly, C. Anticancer Properties of Prunus Mume Extracts (Chinese Plum, Japanese Apricot). J. Ethnopharmacol. 2020, 246, 112215.
[CrossRef]
Fisher, E.E. Venturia Carpophila Sp.Nov., the Ascigerous State of the Apricot Freckle Fungus. Trans. Br. Mycol. Soc. 1961, 44,
337-IN4. [CrossRef]
Chen, C.; Bock, C.H.; Wood, B.W. Draft Genome Sequence of Venturia Carpophila, the Causal Agent of Peach Scab. Stand. Genom.
Sci. 2017, 12, 68. [CrossRef]
Takeda, T.; Hishiike, M.; Numaguchi, K. Occurrence of QoI-Resistant Strains of Cladosporium Carpophilum Causing Japanese
Apricot Scab in Wakayama Prefecture. Ann. Rept. Kansai Pl. Prot. 2022, 64, 75–80. [CrossRef]
Mori, M.; Yamana, T. Occurrence of DMI-Resistant Strains of Venturia Inaequalis Causing Apple Scab in Hokkaido. Ann. Rept. Soc.
Pl. Prot. Nort. Jap. 2022, 76–80. [CrossRef]
Shimada, T.; Haji, T.; Yamaguchi, M.; Takeda, T.; Nomura, K.; Yoshida, M. Classification of Mume (Prunus mume Sieb. et Zucc.) by
RAPD Assay. J. Jpn. Soc. Hort. Sci. 1994, 63, 543–551. [CrossRef]
Numaguchi, K.; Ishio, S.; Kitamura, Y.; Nakamura, K.; Ishikawa, R.; Ishii, T. Microsatellite Marker Development and Population
Structure Analysis in Japanese Apricot (Prunus mume Sieb. et Zucc.). Hort. J. 2019, 88, 222–231. [CrossRef]
Hayashi, K.; Shimazu, K.; Yaegaki, H.; Yamaguchi, M.; Iketani, H.; Yamamoto, T. Genetic Diversity in Fruiting and FlowerOrnamental Japanese Apricot (Prunus mume) Germplasms Assessed by SSR Markers. Breed Sci. 2008, 58, 401–410. [CrossRef]
Ohta, S.; Hayashi, K.; Yaegaki, H.; Mitsui, N.; Omura, M.; Nishitani, C.; Yamamoto, T. Genetic Relationship among Fruiting and
Flower-Japanese Apricot Characterized by Chloroplast DNA Markers. DNA Polymorph. 2006, 14, 138–140.
Numaguchi, K.; Akagi, T.; Kitamura, Y.; Ishikawa, R.; Ishii, T. Interspecific Introgression and Natural Selection in the Evolution of
Japanese Apricot (Prunus mume). Plant J. 2020, 104, 1551–1567. [CrossRef] [PubMed]
Zhang, Q.; Zhang, H.; Sun, L.; Fan, G.; Ye, M.; Jiang, L.; Liu, X.; Ma, K.; Shi, C.; Bao, F.; et al. The Genetic Architecture of Floral
Traits in the Woody Plant Prunus Mume. Nat. Commun. 2018, 9, 1702. [CrossRef]
Tao, R.; Habu, T.; Yamane, H.; Sugiura, A.; Iwamoto, K. Molecular Markers for Self-Compatibility in Japanese Apricot (Prunus
mume). HortScience 2000, 35, 1121–1123. [CrossRef]
Horticulturae 2023, 9, 872
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.
45.
46.
13 of 14
McClure, K.A.; Sawler, J.; Gardner, K.M.; Money, D.; Myles, S. Genomics: A Potential Panacea for the Perennial Problem. Am. J.
Bot. 2014, 101, 1780–1790. [CrossRef]
Groth, J.V.; Ozmon, E.A.; Busch, R.H. Repeatability and Relationship of Incidence and Severity Measures of Scab of Wheat Caused
by Fusarium Graminearum in Inoculated Nurseries. Plant Dis. 1999, 83, 1033–1038. [CrossRef]
Cardoso, J.E.; Santos, A.A.; Rossetti, A.G.; Vidal, J.C. Relationship between Incidence and Severity of Cashew Gummosis in
Semiarid North-Eastern Brazil. Plant Pathol. 2004, 53, 363–367. [CrossRef]
Verde, I.; Jenkins, J.; Dondini, L.; Micali, S.; Pagliarani, G.; Vendramin, E.; Paris, R.; Aramini, V.; Gazza, L.; Rossini, L.; et al. The
Peach v2.0 Release: High-Resolution Linkage Mapping and Deep Resequencing Improve Chromosome-Scale Assembly and
Contiguity. BMC Genom. 2017, 18, 225. [CrossRef]
Alexander, D.H.; Novembre, J.; Lange, K. Fast Model-Based Estimation of Ancestry in Unrelated Individuals. Genome Res. 2009,
19, 1655–1664. [CrossRef]
Browning, B.L.; Zhou, Y.; Browning, S.R. A One-Penny Imputed Genome from Next-Generation Reference Panels. Am. J. Hum.
Genet. 2018, 103, 338–348. [CrossRef]
Bradbury, P.J.; Zhang, Z.; Kroon, D.E.; Casstevens, T.M.; Ramdoss, Y.; Buckler, E.S. TASSEL: Software for Association Mapping of
Complex Traits in Diverse Samples. Bioinformatics 2007, 23, 2633–2635. [CrossRef] [PubMed]
Barrett, J.C.; Fry, B.; Maller, J.; Daly, M.J. Haploview: Analysis and Visualization of LD and Haplotype Maps. Bioinformatics 2005,
21, 263–265. [CrossRef]
McDonald, B.A.; Stukenbrock, E.H. Rapid Emergence of Pathogens in Agro-Ecosystems: Global Threats to Agricultural Sustainability and Food Security. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2016, 371, 20160026. [CrossRef]
Papp, D.; Gao, L.; Thapa, R.; Olmstead, D.; Khan, A. Field Apple Scab Susceptibility of a Diverse Malus Germplasm Collection
Identifies Potential Sources of Resistance for Apple Breeding. CABI Agric. Biosci. 2020, 1, 16. [CrossRef]
Kitamura, Y.; Takeda, T.; Numaguchi, K.; Tsuchida, Y.; Negoro, K.; Hayashi, K.; Iwamoto, K.; Hishiike, M.; Naka, K.; Shimazu, K.
Breeding of scab-resistant Japanese apricot (Prunus mume Sieb. et Zucc.) “Seiko” and evaluation of possibility for fungicide-saving
cultivation. Bull. Wakayama Prefect. Exp. Station. Agric. Forest. Fish. 2018, 6, 27–35.
Numaguchi, K.; Kitamura, Y.; Takeda, T.; Shimomura, Y.; Tsunaki, K.; Kashiwamoto, T.; Shimazu, K.; Hishiike, M.; Iwamoto, K.;
Negoro, K.; et al. Breeding of Japanese apricot (Prunus mume Sieb. et Zucc.) ‘Seishu’. Bull. Wakayama Prefect. Exp. Station. Agric.
Forest. Fish. 2021, 9, 73–85.
Korte, A.; Farlow, A. The Advantages and Limitations of Trait Analysis with GWAS: A Review. Plant Methods 2013, 9, 29.
[CrossRef]
Jones, D.A.; Jones, J.D.G. The Role of Leucine-Rich Repeat Proteins in Plant Defences. In Advances in Botanical Research; Andrews,
J.H., Tommerup, I.C., Callow, J.A., Eds.; Academic Press: Cambridge, MA, USA, 1997; Volume 24, pp. 89–167.
Weis, C.; Pfeilmeier, S.; Glawischnig, E.; Isono, E.; Pachl, F.; Hahne, H.; Kuster, B.; Eichmann, R.; Hückelhoven, R. CoImmunoprecipitation-Based Identification of Putative BAX INHIBITOR-1-Interacting Proteins Involved in Cell Death Regulation
and Plant–Powdery Mildew Interactions. Mol. Plant Pathol. 2013, 14, 791–802. [CrossRef]
Van Damme, M.; Huibers, R.P.; Elberse, J.; Van den Ackerveken, G. Arabidopsis DMR6 Encodes a Putative 2OG-Fe(II) Oxygenase
That Is Defense-Associated but Required for Susceptibility to Downy Mildew. Plant J. 2008, 54, 785–793. [CrossRef]
Thatcher, L.F.; Powell, J.J.; Aitken, E.A.B.; Kazan, K.; Manners, J.M. The Lateral Organ Boundaries Domain Transcription Factor
LBD20 Functions in Fusarium Wilt Susceptibility and Jasmonate Signaling in Arabidopsis. Plant Physiol. 2012, 160, 407–418.
[CrossRef]
Hu, Y.; Zhang, J.; Jia, H.; Sosso, D.; Li, T.; Frommer, W.B.; Yang, B.; White, F.F.; Wang, N.; Jones, J.B. Lateral Organ Boundaries 1 Is
a Disease Susceptibility Gene for Citrus Bacterial Canker Disease. Proc. Natl. Acad. Sci. USA 2014, 111, E521–E529. [CrossRef]
[PubMed]
Rissel, D.; Peiter, E. Poly(ADP-Ribose) Polymerases in Plants and Their Human Counterparts: Parallels and Peculiarities. Int. J.
Mol. Sci. 2019, 20, 1638. [CrossRef]
Minamikawa, M.F.; Takada, N.; Terakami, S.; Saito, T.; Onogi, A.; Kajiya-Kanegae, H.; Hayashi, T.; Yamamoto, T.; Iwata, H.
Genome-Wide Association Study and Genomic Prediction Using Parental and Breeding Populations of Japanese Pear (Pyrus
Pyrifolia Nakai). Sci. Rep. 2018, 8, 11994. [CrossRef]
Minamikawa, M.F.; Nonaka, K.; Kaminuma, E.; Kajiya-Kanegae, H.; Onogi, A.; Goto, S.; Yoshioka, T.; Imai, A.; Hamada, H.;
Hayashi, T.; et al. Genome-Wide Association Study and Genomic Prediction in Citrus: Potential of Genomics-Assisted Breeding
for Fruit Quality Traits. Sci. Rep. 2017, 7, 4721. [CrossRef] [PubMed]
Roth, M.; Muranty, H.; Di Guardo, M.; Guerra, W.; Patocchi, A.; Costa, F. Genomic Prediction of Fruit Texture and Training
Population Optimization towards the Application of Genomic Selection in Apple. Hortic. Res. 2020, 7, 148. [CrossRef]
Li, Y.-L.; Weng, J.-C.; Hsiao, C.-C.; Chou, M.-T.; Tseng, C.-W.; Hung, J.-H. PEAT: An Intelligent and Efficient Paired-End
Sequencing Adapter Trimming Algorithm. BMC Bioinform. 2015, 16, S2. [CrossRef] [PubMed]
Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics 2014, 30,
2114–2120. [CrossRef]
Li, H. Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM. arXiv 2013, arXiv:1303.3997.
Li, H.; Handsaker, B.; Wysoker, A.; Fennell, T.; Ruan, J.; Homer, N.; Marth, G.; Abecasis, G.; Durbin, R. The Sequence Alignment/Map Format and SAMtools. Bioinformatics 2009, 25, 2078–2079. [CrossRef]
Horticulturae 2023, 9, 872
47.
48.
49.
50.
51.
52.
14 of 14
Auwera, G.A.; O’Connor, B.D. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra; O’Reilly Media: Sebastopol, CA,
USA, 2020.
Danecek, P.; Auton, A.; Abecasis, G.; Albers, C.A.; Banks, E.; DePristo, M.A.; Handsaker, R.E.; Lunter, G.; Marth, G.T.; Sherry, S.T.;
et al. The Variant Call Format and VCFtools. Bioinformatics 2011, 27, 2156–2158. [CrossRef]
Purcell, S.; Neale, B.; Todd-Brown, K.; Thomas, L.; Ferreira, M.A.R.; Bender, D.; Maller, J.; Sklar, P.; de Bakker, P.I.W.; Daly, M.J.;
et al. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am. J. Hum. Genet. 2007, 81,
559–575. [CrossRef]
Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New Models
and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 2020, 37, 1530–1534. [CrossRef]
Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast Model Selection for Accurate
Phylogenetic Estimates. Nat. Methods 2017, 14, 587–589. [CrossRef]
Minh, B.Q.; Nguyen, M.A.T.; von Haeseler, A. Ultrafast Approximation for Phylogenetic Bootstrap. Mol. Biol. Evol. 2013, 30,
1188–1195. [CrossRef]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content.
...