Akagi, T., Hanada, T., Yaegaki, H., Gradziel, T. M., and Tao, R. (2016). Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication. DNA Research 23, 271–282.
Alexander, D. H., Novembre, J., and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19, 1655–1664.
Allaby, R. G., Ware, R. L., and Kistler, L. (2019). A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evolutionary Applications 12, 29–37.
Anderson, E. C., and Thompson, E. A. (2002). A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160, 1217–1229.
Baack, E. J., and Rieseberg, L. H. (2007). A genomic view of introgression and hybrid speciation. Current Opinion in Genetics & Development 17, 513–518.
Bamshad, M. J., Ng, S. B., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A., et al. (2011). Exome sequencing as a tool for Mendelian disease gene discovery. Nature Reviews Genetics 12, 745–755.
Beaumont, M. A., Zhang, W., and Balding, D. J. (2002). Approximate Bayesian computation in population genetics. Genetics 162, 2025–2035.
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27, 573–580.
Bortiri, E., Oh, S.-H., Jiang, J., Baggett, S., Granger, A., Weeks, C., et al. (2001). Phylogeny and systematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA. Systematic Botany 26, 797–807.
Boutanaev, A. M., Moses, T., Zi, J., Nelson, D. R., Mugford, S. T., Peters, R. J., et al. (2015). Investigation of terpene diversification across multiple sequenced plant genomes. Proceedings of the National Academy of Sciences, U. S. A. 112, E81–E88.
Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., and Buckler, E. S. (2007). TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635.
Brandenburg, J.-T., Mary-Huard, T., Rigaill, G., Hearne, S. J., Corti, H., Joets, J., et al. (2017). Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLOS Genetics 13, e1006666.
Brantley, W. (2004). About Pluots. Gastronomica 4, 84–89.
Browning, B. L., Zhou, Y., and Browning, S. R. (2018). A one-penny imputed genome from next-generation reference panels. The American Journal of Human Genetics 103, 338–348.
Chen, E., Huang, X., Tian, Z., Wing, R. A., and Han, B. (2019). The genomics of Oryza species provides insights into rice domestication and heterosis. Annual Review of Plant Biology 70, 639–665.
Chen, J. (2017). China mei flower (Prunus mume) cultivars in colour. Beijing: China Forestry Publishing House.
Cheng, Y., Zhou, W., El Sheery, N. I., Peters, C., Li, M., Wang, X., et al. (2011). Characterization of the Arabidopsis glycerophosphodiester phosphodiesterase (GDPD) family reveals a role of the plastid-localized AtGDPD1 in maintaining cellular phosphate homeostasis under phosphate starvation. The Plant Journal 66, 781–795.
Choi, J. Y., and Purugganan, M. D. (2018). Multiple Origin but single domestication led to Oryza sativa. G3: Genes, Genomes, Genetics 8, 797–803.
Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., et al. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92.
Clark, L. V., and Jasieniuk, M. (2011). POLYSAT: an R package for polyploid microsatellite analysis. Molecular Ecology Resources 11, 562–566.
Clark, R. M., Linton, E., Messing, J., and Doebley, J. F. (2004). Pattern of diversity in the genomic region near the maize domestication gene tb1. Proceedings of the National Academy of Sciences, U. S. A. 101, 700–707.
Cornille, A., Gladieux, P., Smulders, M. J. M., Roldán-Ruiz, I., Laurens, F., Le Cam, B., et al. (2012). New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genetics 8, e1002703.
Cornuet, J.-M., Pudlo, P., Veyssier, J., Dehne-Garcia, A., Gautier, M., Leblois, R., et al. (2014). DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 30, 1187–1189.
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., et al. (2011). The variant call format and VCFtools. Bioinformatics 27, 2156–2158.
Dardick, C., and Ronald, P. (2006). Plant and Animal Pathogen Recognition Receptors Signal through Non- RD Kinases. PLoS Pathogens 2, e2.
Diamond, J. (2002). Evolution, consequences and future of plant and animal domestication. Nature 418, 700–707.
Diez, C. M., Trujillo, I., Martinez-Urdiroz, N., Barranco, D., Rallo, L., Marfil, P., et al. (2015). Olive domestication and diversification in the Mediterranean Basin. New Phytologist. 206, 436–447.
Doebley, J. F., Gaut, B. S., and Smith, B. D. (2006). The molecular genetics of crop domestication. Cell 127, 1309–1321.
Doebley, J., Stec, A., and Hubbard, L. (1997). The evolution of apical dominance in maize. Nature 386, 485–488.
Dvorak, J., Deal, K. R., Luo, M.-C., You, F. M., von Borstel, K., and Dehghani, H. (2012). The Origin of Spelt and Free-Threshing Hexaploid Wheat. Journal of Heredity 103, 426–441.
Earl, D. A., and vonHoldt, B. M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359–361.
Ebana, K., Kojima, Y., Fukuoka, S., Nagamine, T., and Kawase, M. (2008). Development of mini core collection of Japanese rice landrace. Breeding Science 58, 281–291.
Ellis, J., Dodds, P., and Pryor, T. (2000). Structure, function and evolution of plant disease resistance genes. Current Opinion in Plant Biology 3, 278–284.
Evanno, G., Regnaut, S., and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 2611–2620.
Excoffier, L., Estoup, A., and Cornuet, J.-M. (2005). Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics 169, 1727–1738.
Faust, M., Timon, B., Surányi, D., Nyujtó, F., and Gradziel, T. M. (2011). Origin and dissemination of Prunus crops: peach, cherry, apricot, plum and almond. , ed. J. Jules Belgium: ISHS.
Ferrer-Admetlla, A., Liang, M., Korneliussen, T., and Nielsen, R. (2014). On detecting incomplete soft or hard selective sweeps using haplotype structure. Molecular Biology and Evolution 31, 1275–1291.
Frantz, L. A. F., Mullin, V. E., Pionnier-Capitan, M., Lebrasseur, O., Ollivier, M., Perri, A., et al. (2016). Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 352, 1228– 1231.
Gao, Z. H., Shen, Z. J., Han, Z. H., Fang, J. G., Zhang, Y. M., and Zhang, Z. (2004). Microsatellite markers and genetic diversity in Japanese apricot (Prunus mume). HortScience 39, 1571–1574.
Gaunt, T. R., Rodriguez, S., Zapata, C., and Day, I. N. (2006). MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers. BMC Bioinformatics 7, 227.
Gaut, B. S., Díez, C. M., and Morrell, P. L. (2015). Genomics and the contrasting dynamics of annual and perennial domestication. Trends in Genetics 31, 709–719.
Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., et al. (2009). Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology 27, 182–189.
Gros-Balthazard, M., Besnard, G., Sarah, G., Holtz, Y., Leclercq, J., Santoni, S., et al. (2019). Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. The Plant Journal 100, 143–157.
Haas, M., Schreiber, M., and Mascher, M. (2019). Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. Journal of Integrative Plant Biology 61, 204–225.
Haasl, R. J., and Payseur, B. A. (2011). Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity 106, 158–171.
Harrison, R. G., and Larson, E. L. (2014). Hybridization, introgression, and the nature of species boundaries. Journal of Heredity 105, 795–809.
Hayashi, K. (2009). Genetic diversity analysis in Japanese apricot using DNA markers (In Japanese). Ph.D. Thesis, University of Tsukuba, Tsukuba.
Hayashi, K., Shimazu, K., Yaegaki, H., Yamaguchi, M., Iketani, H., and Yamamoto, T. (2008). Genetic diversity in fruiting and flower-ornamental Japanese apricot (Prunus mume) germplasms assessed by SSR markers. Breeding science 58, 401–410.
He, F., Pasam, R., Shi, F., Kant, S., Keeble-Gagnere, G., Kay, P., et al. (2019). Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics 51, 896–904.
Hedrick, P. W. (2005). A standardized genetic differentiation measure. Evolution 59, 1633–1638.
Hijikata, S. (1984). “Ume. Hinsyu seitai to saibai,” in Nougyou gijyutsu taikei, Kaju-hen 6 (Tokyo: Nosan Gyoson Bunka Kyokai), 27–46 (In Japanese).
Horiuchi, S., Yoshida, M., Kariya, H., Nakamura, T., Hasebe, H., Suzaki, T., et al. (1996). Nihonnoume Sekainoume. Tokyo: Yokendo (In Japanese).
Htun, T. M., Inoue, C., Chhourn, O., Ishii, T., and Ishikawa, R. (2014). Effect of quantitative trait loci for seed shattering on abscission layer formation in Asian wild rice Oryza rufipogon. Breeding Science 64, 199–205.
Hudson, R. R. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337–338.
Hufford, M. B., Lubinksy, P., Pyhäjärvi, T., Devengenzo, M. T., Ellstrand, N. C., and Ross-Ibarra, J. (2013). The genomic signature of crop-wild introgression in maize. PLoS Genetics. 9, e1003477.
Iemura, H., Shimazu, K., and Natsumi, K. (1995). Occurrence of a graft-transmissible disease of mume (Abstract in Japanese). Annals of the Phytopathological Society of Japan 61, 631.
Ishii, T., Numaguchi, K., Miura, K., Yoshida, K., Thanh, P. T., Htun, T. M., et al. (2013). OsLG1 regulates a closed panicle trait in domesticated rice. Nature Genetics 45, 462–465.
Iwata, H., Hayashi, T., Terakami, S., Takada, N., Sawamura, Y., and Yamamoto, T. (2013). Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breeding Science 63, 125–140.
Jakobsson, M., and Rosenberg, N. A. (2007). CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806.
Jebanathirajah, J. A., Peri, S., and Pandey, A. (2002). Toll and interleukin-1 receptor (TIR) domain- containing proteins in plants: a genomic perspective. Trends in Plant Science 7, 388–391.
Jin, J., Huang, W., Gao, J.-P., Yang, J., Shi, M., Zhu, M.-Z., et al. (2008). Genetic control of rice plant architecture under domestication. Nature Genetics 40, 1365–1369.
Jost, L. (2008). GST and its relatives do not measure differentiation. Molecular Ecology 17, 4015–4026.
Kaga, A., Shimizu, T., Watanabe, S., Tsubokura, Y., Katayose, Y., Harada, K., et al. (2012). Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections. Breeding Science 61, 566–592.
Kansako, M., Iemura, H., Natsumi, K., and Shimazu, K. (2000). Studies on Japanese apricot [Prunus mume] leaf-edge necrosis disease (In Japanese). Bulletin of the Wakayama Research Center of Agriculture, Forestry and Fisheries 1, 67–78.
Kaur, P., and Gaikwad, K. (2017). From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement. Frontiers in Plant Science 8, 2164.
Kistler, L., Maezumi, S. Y., Souza, J. G. de, Przelomska, N. A. S., Costa, F. M., Smith, O., et al. (2018). Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 362, 1309–1313.
Kitamura, Y., Habu, T., Yamane, H., Nishiyama, S., Kajita, K., Sobue, T., et al. (2018). Identification of QTLs controlling chilling and heat requirements for dormancy release and bud break in Japanese apricot (Prunus mume). Tree Genetics & Genomes 14, 33.
Kloosterman, A. D., Budowle, B., and Daselaar, P. (1993). PCR-amplification and detection of the human D1S80 VNTR locus. Amplification conditions, population genetics and application in forensic analysis. International Journal of Legal Medicine 105, 257–264.
Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., et al. (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25, 2283–2285
Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., et al. (2012). VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research. 22, 568–576.
Konishi, S., Izawa, T., Lin, S. Y., Ebana, K., Fukuta, Y., Sasaki, T., et al. (2006). An SNP caused loss of seed shattering during rice domestication. Science 312, 1392–1396.
Kosova, G., Pickrell, J. K., Kelley, J. L., McArdle, P. F., Shuldiner, A. R., Abney, M., et al. (2010). The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate.
Kurihara, J., Tomaru, K., Otsubo, T., T. Natsuaki, K. T., and Arimoto, Y. (2006). Mume leaf margin necrosis, a new disease of Japanese apricot [Prunus mume] caused by multiple infection with Cucumber mosaic virus and prunus necrotic ringspot related Ilarvirus. Journal of agriculture science, Tokyo University of Agriculture 50, 95–105
Kyotani, H., Yoshida, M., Yamaguchi, M., Ishizawa, Y., Kozono, T., Nshida, T., et al. (1988). Breeding of plum-mume parental lines “PM-1-1” and “PM-1-4”, interspecific hybrids of Japanese plum (Prunus salicina Lindl.) and mume (P. mume Sieb. et Zucc.). Bulletin of the Fruit Tree Research Station 15, 1–10.
Lee, T.-H., Guo, H., Wang, X., Kim, C., and Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics 15, 162.
Lee, W., Ahn, S., Taye, M., Sung, S., Lee, H.-J., Cho, S., et al. (2016). Detecting positive selection of Korean native goat populations using next-generation sequencing. Moleucles and Cells 39, 862– 868.
Li, C., Zhou, A., and Sang, T. (2006). Rice domestication by reducing shattering. Science 311, 1936–1939.
Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio].
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079.
MAFF (2017). Statistics on production of fruit classified by cultivar. Available at: https://www.maff.go.jp/j/tokei/kouhyou/tokusan_kazyu/ [Accessed May 5, 2020] (In Japanese).
MAFF (2019). The 93re statistical yearbook of Ministry of Agriculture, Forestry and Fisheries. Available at: https://www.maff.go.jp/e/data/stat/93th/index.html [Accessed May 5, 2020].
Mariette, S., Wong Jun Tai, F., Roch, G., Barre, A., Chague, A., Decroocq, S., et al. (2016). Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca). New Phytologist. 209, 773–784.
Mascher, M., Schuenemann, V. J., Davidovich, U., Marom, N., Himmelbach, A., Hübner, S., et al. (2016). Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication
McClure, K. A., Sawler, J., Gardner, K. M., Money, D., and Myles, S. (2014). Genomics: a potential panacea for the perennial problem. American Journal of Botany 101, 1780–1790.
Mega, K., Tomita, E., Kitamura, S., Saito, S., and Mizukami, S. (1988). The grand dictionary of horticulture. , ed. T. Aoba Tokyo: Shogakukan (In Japanese).
Mehlenbacher, S., Cocin, V., and Hough, L. (1991). “Apricots (Prunus),” in Genetic resources of temperate fruit and nut crops (Wagenengen: ISHS), 65–107.
Miller, A. J., and Gross, B. L. (2011). From forest to field: perennial fruit crop domestication. American Journal of Botany 98, 1389–1414.
Molnár-Láng, M., Ceoloni, C., and Doležel, J. (2015). Alien Introgression in Wheat: Cytogenetics, Molecular Biology, and Genomics. New York: Springer.
Morimoto, T., Kitamura, Y., Numaguchi, K., Akagi, T., and Tao, R. (2019). Characterization of post-mating interspecific cross-compatibility in Prunus (Rosaceae). Scientia Horticulturae 246, 693–699.
Nadachowska-Brzyska, K., Burri, R., and Ellegren, H. (2019). Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers. Molecular Ecology. 28, 2290–2304.
Nakaune, R., Takeda, T., Numaguchi, K., Nakazono-Nagaoka, E., and Fujikawa, T. (2018). Ampeloviruses associated with incomplete flower syndrome and leaf-edge necrosis in Japanese apricot. Journal of General Plant Pathology 84, 202–207.
Narasimhan, V. M., Patterson, N., Moorjani, P., Rohland, N., Bernardos, R., Mallick, S., et al. (2019). The formation of human populations in South and Central Asia. Science 365, eaat7487.
Nei, M. (1972). Genetic distance between populations. The American Naturalist 106, 283–292. Nei, M. (1987). Molecular evolutionary genetics. New York: Columbia University Press.
Nei, M., Tajima, F., and Tateno, Y. (1983). Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. Journal of Molecular Evolution 19, 153–170.
Nielsen, R., Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G., and Bustamante, C. (2005). Genomic scans for selective sweeps using SNP data. Genome Research 15, 1566–1575.
Numaguchi, K., Takeda, T., Tsuchida, Y., and Nakaune, R. (2019). Large-scale field survey reveals overall yield loss in Japanese apricot possibly caused by two ampeloviruses. Journal of General Plant Pathology 85, 116–121.
Ohnishi, T., Szatmari, A.-M., Watanabe, B., Fujita, S., Bancos, S., Koncz, C., et al. (2006). C-23 hydroxylation by Arabidopsis CYP90C1 and CYP90D1 reveals a novel shortcut in brassinosteroid biosynthesis. Plant Cell 18, 3275–3288.
Ohta, S., Hayashi, K., Yaegaki, H., Mitsui, N., Omura, M., Nishitani, C., et al. (2006). Genetic relationship among fruiting and flower-Japanese apricot characterized by chloroplast DNA markers. DNA Polymorphism 14, 138–140.
Ohtubo, T., Kurihara, J., Sakakibara, M., and Tomaru, K. (2002). Confirmation of symptom reproduction in mume leaf margin necrosis disease on Prunus mume (c.v. Nankou) by sap inoculation with causal two viruses, Cucumber mosaic and Prunus necrotic ringspot-like viruses. Journal of agriculture science, Tokyo University of Agriculture 47, 11–16.
Otsubo, T., Harano, H., Natuaki, K., and Tomaru, K. (1991). Chakasu disorder of Japanese apricot. Journal of the Japanese Society for Horticultural Science 60, 164–165.
Panaud, O., Chen, X., and McCouch, S. R. (1996). Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Molecular Genetics and Genomics 252, 597–607.
Pankin, A., Altmüller, J., Becker, C., and von Korff, M. (2018). Targeted resequencing reveals genomic signatures of barley domestication. New Phytologist. 218, 1247–1259.
Patterson, N., Price, A. L., and Reich, D. (2006). Population structure and eigenanalysis. PLoS Genetics. 2, e190.
Pavlidis, P., Živković, D., Stamatakis, A., and Alachiotis, N. (2013). SweeD: Likelihood-based detection of selective sweeps in thousands of genomes. Molecular Biology and Evolution 30, 2224–2234.
Peakall, R., and Smouse, P. E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28, 2537–2539.
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., et al. (2011). Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research 12, 2825−2830.
Pritchard, J. K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945–959.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81, 559–575.
Purugganan, M. D., and Fuller, D. Q. (2009). The nature of selection during plant domestication. Nature 457, 843–848.
Quesada, V. (2016). The roles of mitochondrial transcription termination factors (MTERFs) in plants. Physiologia Plantarum 157, 389–399.
R Development Core Team (2008). A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Ramasamy, R. K., Ramasamy, S., Bindroo, B. B., and Naik, V. G. (2014). STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. Springerplus 3, 431.
Raymond, M., and Rousset, F. (1995). GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248–249.
Ricci, W. A., Lu, Z., Ji, L., Marand, A. P., Ethridge, C. L., Murphy, N. G., et al. (2019). Widespread long- range cis-regulatory elements in the maize genome. Nature Plants 5, 1237–1249.
Rousset, F. (2008). genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources 8, 103–106.
Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., et al. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913–918.
Schuelke, M. (2000). An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18, 233–234.
Shi, T., Luo, W., Li, H., Huang, X., Ni, Z., Gao, H., et al. (2020). Association between blooming time and climatic adaptation in Prunus mume. Ecology and Evolution 10, 292–306.
Shimada, T. (Kobe U. (Japan) F. of A., Haji, T., Yamaguchi, M., Takeda, T., Nomura, K., and Yoshida, M. (1994). Classification of mume (Prunus mume Sieb. et Zucc.) by RAPD assay. Journal of the Japanese Society for Horticultural Science 63, 543–551.
Smith, O., Nicholson, W. V., Kistler, L., Mace, E., Clapham, A., Rose, P., et al. (2019). A domestication history of dynamic adaptation and genomic deterioration in Sorghum. Nature Plants 5, 369–379.
Stephan, W. (2019). Selective Sweeps. Genetics 211, 5–13.
Stitzer, M. C., and Ross-Ibarra, J. (2018). Maize domestication and gene interaction. New Phytologist 220, 395–408.
Suarez-Gonzalez, A., Hefer, C. A., Lexer, C., Douglas, C. J., and Cronk, Q. C. B. (2018). Introgression from Populus balsamifera underlies adaptively significant variation and range boundaries in P. trichocarpa. New Phytologist 217, 416–427.
Szpiech, Z. A., and Hernandez, R. D. (2014). selscan: an efficient multithreaded program to perform EHH- based scans for positive selection. Molecular Biology and Evolution 31, 2824–2827.
Takezaki, N., Nei, M., and Tamura, K. (2010). POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Molecular Biology and Evolution 27, 747–752.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30, 2725–2729.
Tsuda, Y., Nakao, K., Ide, Y., and Tsumura, Y. (2015). The population demography of Betula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing. Molecular Ecology 24, 1403–1418.
Tzonev, R., and Yamaguchi, M. (1999). Investigation on same far-east Prunus species: Phenology. Acta Horticulturae 488, 239–241.
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., et al. (2012). Primer3— new capabilities and interfaces. Nucleic Acids Research 40, e115–e115.
Verde, I., Jenkins, J., Dondini, L., Micali, S., Pagliarani, G., Vendramin, E., et al. (2017). The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics 18, 225.
Vij, S., and Tyagi, A. K. (2008). A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response. Functional & Integrative Genomics 8, 301–307.
Voight, B. F., Kudaravalli, S., Wen, X., and Pritchard, J. K. (2006). A map of recent positive selection in the human genome. PLOS Biology 4, e72.
Wada, T., Noguchi, Y., Isobe, S., Kunihisa, M., Sueyoshi, T., and Shimomura, K. (2017). Development of a core collection of strawberry cultivars based on SSR and CAPS marker polymorphisms. The Horticulture Journal 86, 365–378.
Wang, H., Nussbaum-Wagler, T., Li, B., Zhao, Q., Vigouroux, Y., Faller, M., et al. (2005). The origin of the naked grains of maize. Nature 436, 714–719.
Watanabe, N., Sugiyama, K., Yamagishi, Y., and Sakata, Y. (2002). Comparative telosomic mapping of homoeologous genes for brittle rachis in tetraploid and hexaploid wheats. Hereditas 137, 180–185.
Weitzel, C., and Simonsen, H. T. (2015). Cytochrome P450-enzymes involved in the biosynthesis of mono- and sesquiterpenes. Phytochemistry Reviews 14, 7–24.
Wu, G. A., Prochnik, S., Jenkins, J., Salse, J., Hellsten, U., Murat, F., et al. (2014). Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology 32, 656–662.
Wu, G. A., Terol, J., Ibanez, V., López-García, A., Pérez-Román, E., Borredá, C., et al. (2018). Genomics of the origin and evolution of Citrus. Nature 554, 311–316.
Yaegaki, H., Haji, T., Nakamura, Y., Miyake, M., Nishimura, K., Kyotani, H., et al. (2003). Varietal and yearly variations in fruit and endocarp weights and their ratio in Japanese apricot (Prunus mume Sieb. et Zucc.) cultivars (In Japanese with English abstract). Journal of the Japanese Society for Horticultural Science 72, 546–550.
Yaegaki, H., Yamaguchi, M., Haji, T., Suesada, Y., Miyake, M., Kihara, T., et al. (2012). New Japanese apricot cultivar “Tsuyuakane” (In Japanese with English abstract). Bulletin of the NARO Institute of Fruit Tree Science, 1–6.
Yamaguchi, M., Yaegaki, H., Suesada, Y., Haji, T., and Miyake, M. (2018). Study on interspecific hybridization among the subgenera Amygdalus, Prunophora, and Cerasus (In Japanese). Horticultural Research (Japan) 17, 147–159.
Yamane, H. (2014). Regulation of Bud Dormancy and Bud Break in Japanese Apricot (Prunus mume Siebold & Zucc.) and Peach [Prunus persica (L.) Batsch]: A summary of recent studies. Journal of the Japanese Society for Horticultural Science 83, 187–202.
Yoshida, M. (1984). “Ume. Gensanchi to raireki,” in Nougyou gijyutsu taikei, Kaju-hen 6 (Tokyo: Nosan Gyoson Bunka Kyokai), 3–6 (In Japanese).
Yoshida, M., and Yamanishi, H. (1988). Apricot cultivars in Japan. Acta Horticulturae 209, 69–81.
Yu, Y., Fu, J., Xu, Y., Zhang, J., Ren, F., Zhao, H., et al. (2018). Genome re-sequencing reveals the evolutionary history of peach fruit edibility. Nature Communications 9, 5404.
Yuying, S., Xiajun, D., Fei, W., Binhua, C., Zhihong, G., and Zhen, Z. (2011). Analysis of genetic diversity in Japanese apricot (Prunus mume Sieb. et Zucc.) based on REMAP and IRAP molecular markers. Scientia Horticulturae 132, 50–58.
Zeder, M. A. (2015). Core questions in domestication research. Proceedings of the National Academy of Sciences, U. S. A. 112, 3191–3198.
Zeder, M. A., Emshwiller, E., Smith, B. D., and Bradley, D. G. (2006). Documenting domestication: the intersection of genetics and archaeology. Trends in Genetics. 22, 139–155.
Zhang, C., Dong, S.-S., Xu, J.-Y., He, W.-M., and Yang, T.-L. (2019). PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786–1788.
Zhang, J., Zhang, Q., Cheng, T., Yang, W., Pan, H., Zhong, J., et al. (2015). High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc). DNA Research 22, 183–191.
Zhang, Q., Chen, W., Sun, L., Zhao, F., Huang, B., Yang, W., et al. (2012). The genome of Prunus mume. Nature Communications 3, 1318.
Zhang, Q., Zhang, H., Sun, L., Fan, G., Ye, M., Jiang, L., et al. (2018). The genetic architecture of floral traits in the woody plant Prunus mume. Nature Communications 9, 1702.
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