Abstract：Abstract The cultivated strawberry, Fragaria×ananassa (2n=8x=56), is an octaploid perennial herb plant with complicated genetic background. Most agronomic and quality traits of strawberry are controlled by polygenes, resulting in difficulty in breeding. DNA molecular markers showed the genome variances and mutants directly, so it had been widely used in marker associated breeding, gene mapping, genetic map construction, QTL mapping, cultivar identification and genome research since 1990s. And it greatly improved the efficiency of breeding, especially for the perennial fruit trees which were highly heterozygous and had long growth period. In this paper, we reviewed the current status of the applications of molecular marker techniques in strawberry breeding and production, aiming to provide foundations for further studies and push forward strawberry breeding and the whole industry.
曹娴, 高清华, 聂京涛, 等. 2011. 草莓灰霉病抗性遗传分析和分子标记初定位[J]. 上海交通大学学报(农业科学版), 29(04): 75-78. (Cao X, Gao Q, Nie J, et al. 2011. Genetic analysis and molecular marker mapping of gray mold resistance gene in strawberry[J]. Journal of Shanghai Jiaotong University (Agricultural Science), 29(04): 75-78.) 董清华, 王西成, 赵密珍, 等. 2011. 草莓EST-SSR标记开发及在品种遗传多样性分析中的应用[J]. 中国农业科学, 44(17): 3603-3612. (Dong Q, Wang X, Zhao M, et al. 2011. Development of EST-derived SSR markers and their applicaton in strawberry genetic diversity analysis[J]. Scientia Agricultura Sinica, 44(17): 3603-3612.) 韩柏明, 赵密珍, 王静, 等. 2012. 草莓属种质资源亲缘关系的SSR标记分析[J]. 园艺学报, 39(12): 2352-2360. (Han B, Zhao M, Wang J, et al. 2012. Phylogenetic relationships among Fragaria germplasm by SSR markers[J]. Acta Horticulturae Sinica, 39(12): 2352-2360.) 刘建成, 段可, 张庆雨, 等. 2012. 草莓抗白粉病遗传图谱及其SSR标记初分析[J]. 江西农业学报, 24(11): 49-52. (Liu J, Duan K, Zhang Q, et al. 2012. Genetic mapping and preliminary analysis of ssr marker for powdery mildew resistance in strawberry[J]. Acta Agriculturae Jiangxi, 24(11): 49-52.) 赵淑清, 武维华. 2000. DNA分子标记和基因定位[J]. 生物技术通报, 6: 1-4.(Zhao S Q, Wu W H. 2000. DNA molecular markers and mapping[J]. Biotechnology Information, 6: 1-4.) Agarwal M, Shrivastava N, Padh H. 2008. Advances in molecular marker techniques and their applications in plant sciences[J]. Plant Cell Reports, 27(4): 617-631. Albani M C, Battey N H, Wilkinson M J. 2004. The development of ISSR-derived SCAR markers around the SEASONAL FLOWERING LOCUS (SFL) in Fragaria vesca[J]. Theoretical and Applied Genetics, 109: 571-579. Antanaviciute L, Surbanovski N, Harrison N, et al. 2015. Mapping QTL associated with Verticillium dahliae resistance in the cultivated strawberry (Fragaria × ananassa)[J]. Horticulture Research, 2: 15009. Ashley M V, Wilk J A, Styan S M N, et al. 2003. High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae)[J]. Theoretical and Applied Genetics, 107(7): 1201-1207. Bardakci F. 2001. Random amplified polymorphic DNA (RAPD) markers[J]. Turkish Journal of Biology, 25: 185–196. Bassil N V, Davis T M, Zhang H, et al. 2015. Development and preliminary evaluation of a 90 K Axiom? SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa[J]. BMC Genomics, 16(1): DOI 10.1186/s12864-015-1310-1. Bombarely A, Merchante C, Csukasi F, et al. 2010. Generation and analysis of ESTs from strawberry (Fragaria × ananassa) fruits and evaluation of their utility in genetic and molecular studies[J]. BMC Genomics, 11: 503. Botstein B, White R L, Skolnick M, et al. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. The American Journal of Human Genetics, 32: 314–331. Bringhurst R S. 1990. Cytogenetics and evolution in American Fragaria[J]. HortScience, 25: 879–881. Brunings A M, Moyer C, Peres N, et al. 2010. Implementation of simple sequence repeat markers to genotype Florida strawberry varieties[J]. Euphytica, 173(1): 63-75. Bushakra J M, Sargent D J, Cabrera A, et al. 2012. Rosaceae conserved orthologous set (RosCOS) markers as a tool to assess genome synteny between Malus and Fragaria[J]. Tree Genetics & Genomes, 8(4): 643-658. Castro P, Bushakra J M, Stewart P, et al. 2015. Genetic mapping of day-neutrality in cultivated strawberry[J]. Molecular Breeding, 35: 79. Castro P, Lewers K S. 2016. Identification of quantitative trait loci (QTL) for fruit-quality traits and number of weeks of flowering in the cultivated strawberry[J]. Molecular Breeding, 36: 138. Chagné D, Kirk C, How N, et al. 2016. A functional genetic marker for apple red skin coloration across different environments[J]. Tree Genetics and Genomes, 12: 1–9. Chambers A, Carle S, Njuguna W, et al. 2013. A genome-enabled, high-throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.)[J]. Molecular Breeding, 31(3): 615-629. Chelkowski J, Stepien L. 2001. Molecular markers for leaf rust resistance genes in wheat[J]. Journal of Applied Genetics, 42: 117–126. Chen C X, Zhou P, Choi Y A, et al. 2006. Mining and characterizing microsatellites from citrus ESTs[J]. Theoretical and Applied Genetics, 112: 1248-1257. Cipriani G, Pinosa F, Bonoli M, et al. 2006. A new set of microsatellite markers for Fragaria species and their application in linkage analysis[J]. Journal of Horticultural Science & Biotechnology, 81(4): 668-675. Dale A, Hancock J F, Luby J L. 2002. Breeding day-neutral strawberries for North America[J]. Acta Horticulturae, 567: 133–136. Davey J W, Hohenlohe P A, Etter P D, et al. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J]. Nature Reviews Genetics, 12: 499–510. Davik J, Sargent D J, Brurberg M B, et al. 2015. A ddRAD based linkage map of the cultivated strawberry, Fragaria × ananassa[J]. PLoS One, 10(9): e137746. Davis T M, Dimeglio L M, Yang R H, et al. 2006. Assessment of SSR transfer from the cultivated strawberry to diploid strawberry species: functionality, linkage group assignment, and use in diversity analysis[J]. Journal of the American Society for Horticultural Science, 131: 506-512. Davis T M, Yu H. 1997. A linkage map of the diploid strawberry, Fragaria vesca[J]. Journal of Heredity, 88(3): 215-221. Deng C, Davis T M. 2001. Molecular identification of the yellow fruit color (c) locus in diploid strawberry: a candidate gene approach[J]. Theoretical and Applied Genetics, 103(2-3): 316-322. FAOSTAT 2012. www.faostat3.fao.org Flavell A J, Knox M, Pearce S R, et al. 1998. Retrotransposonbased insertion polymorphisms (RBIP) for high throughput marker analysis[J]. Plant Journal, 16: 643–665. Folta K M, Staton M, Stewart P J, et al. 2005. Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)[J]. BMC Plant Biology, 5: 12. Fukuoka S, Inoue T, Miyao A, et al. 1994. Mapping of sequence-tagged sites in rice by single strand conformation polymorphism[J]. DNA Research, 1: 271–277. Gasic K, Han Y, Kertbundit S, et al. 2009. Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species[J]. Molecular Breeding, 23(3): 397-411. Govan C L, Simpson D W, Johnson A W, et al. 2008. A reliable multiplexed microsatellite set for genotyping Fragaria and its use in a survey of 60 F. × ananassa cultivars[J]. Molecular Breeding, 22(4): 649-661. Hadonou A M, Sargent D J, Wilson F, et al. 2004. Development of microsatellite markers in Fragaria, their use in genetic diversity analysis, and their potential for genetic linkage mapping[J]. Genome, 47(3): 429-438. Harrison R, Luby J, Furnier G, et al. 1997. Morphological and molecular variation among populations of octoploid Fragaria virginiana and F. chiloensis (Rosaceae) from North America[J]. American Journal of Botany, 84(5): 612-620. Haymes K M, Henken B, Davis T M, et al. 1997. Identification of RAPD markers linked to a Phytophthora fragariae resistance gene (Rpf1) in the cultivated strawberry[J]. Theoretical and Applied Genetics, 94(8): 1097-1101. Haymes K M, Weg W, Arens P, et al. 2000. Development of SCAR markers linked to a Phytophthora fragariae resistance gene and their assesment in European and North American strawberry genotypes[J]. Journal of the American Society for Horticultural Science, 125(3): 330–339. Hearne C M, Ghosh S, Todd J A. 1992. Microsatellites for linkage analysis of genetic traits[J]. Trends in Genetics, 8: 288–294. Honjo M, Nunome T, Kataoka S, et al. 2016. Simple sequence repeat markers linked to the everbearing flowering gene in long-day and day-neutral cultivars of the octoploid cultivated strawberry Fragaria × ananassa[J]. Euphytica, 209(2): 291-303. Isobe S N, Hirakawa H, Sato S, et al. 2013. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability[J]. DNA research, 20(1): 79-92. Jung H, Veerappan K, Natarajan S, et al. 2017. A system for distinguishing octoploid strawberry cultivars using high-throughput SNP genotyping[J]. Tropical Plant Biology, 10(2-3): 68-76. Kalendar R, Grob T, Regina M, et al. 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques[J]. Theoretical and Applied Genetics, 98: 704–711. Kunihisa M, Fukino N, Matsumoto S. 2005. CAPS markers improved by cluster-specific amplification for identification of octoploid strawberry (Fragaria × ananassa Duch.) cultivars, and their disomic inheritance[J]. Theoretical and Applied Genetics, 110: 1410–1418. Kunihisa M. 2011. Studies using DNA markers in Fragaria× ananassa: genetic analysis, genome structure, and cultivar identification[J]. Journal of the Japanese Society for Horticultural Science, 80(3): 231-243. Larsen B, Toldam-Andersen T B, Pedersen C, et al. 2017. Unravelling genetic diversity and cultivar parentage in the Danish apple gene bank collection[J]. Tree Genetics and Genomes, 13: 14. Lee Y R, Lee J. 2017. A genetic linkage map of allo-octoploid strawberry (Fragaria × ananassa Duch.) using SNP markers[J]. Korean Journal of Breeding Science, 49(3): 119-128. Lerceteau-K Hler E, Gu Rin G, Laigret F, et al. 2003. Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria ×ananassa) using AFLP mapping[J]. Theoretical and Applied Genetics, 107(4): 619-628. Lerceteau-K?hler E, Guérin G, Denoyes-Rothan B. 2005. Identification of SCAR markers linked to Rca2 anthracnose resistance gene and their assessment in strawberry germplasm[J]. Theoretical and Applied Genetics, 111(5): 862-870. Lerceteau-K?hler E, Moing A, Guérin G, et al. 2012. Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control[J]. Theoretical and Applied Genetics, 124(6): 1059-1077. Li G, Quiros C F. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica[J]. Theoretical and Applied Genetics, 103: 455–546. Lyamichev V, Brow M A D, Dahlberg J E. 1993. Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases[J]. Science, 260: 778–783. Mahoney L L, Sargent D J, Abebe-Akele F, et al. 2016. A high-density linkage map of the ancestral diploid strawberry, Fragaria iinumae, constructed with single nucleotide polymorphism markers from the IStraw90 Array and genotyping by sequencing[J]. Plant Genome, 9(2). Milella L, Saluzzi D, Lapelosa M, et al. 2006. Relationships between an Italian strawberry ecotype and its ancestor using RAPD markers[J]. Genetic Resources and Crop Evolution, 53(8): 1715-1720. Miller M R, Dunham J P, Amores A, et al. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers[J]. Genome Research, 17: 240–248. Mohan M, Nair S, Bhagwat A, et al. 1997. Genome mapping, molecular markers and marker-assisted selection in crop plants[J]. Molecular Breeding, 3(2): 87-103. Mullis K B, Faloona F. 1987. Specific synthesis of DNA in vitro via polymerase chain reaction[J]. Methods in Enzymology, 155: 350–355. Nagano S, Shirasawa K, Hirakawa H, et al. 2017. Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria?×?ananassa)[J]. BMC Genomics, 18: 374. Nandi S, Subudhi P K, Senadhira D, et al. 1997. Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping[J]. Molecular and General Genetics, 255: 1–8. Nier S, Simpson D W, Tobutt K R, et al. 2006. A genetic linkage map of an inter-specific diploid Fragaria BC1 mapping population and its comparison with the Fragaria reference map (FV × FN)[J]. Journal of Horticultural Science & Biotechnology, 81(4): 645-650. Orita M, Iwahana H, Kanazawa H, et al. 1989. Detection of polymorphisms of human DNA by gel electrophresis as single-strand conformation polymorphisms[J]. Proceedings of the National Academy of Sciences USA, 86: 2766–2770. Roach J A, Verma S, Peres N A, et al. 2016. FaRXf1: a locus conferring resistance to angular leaf spot caused by Xanthomonas fragariae in octoploid strawberry[J]. Theoretical and Applied Genetics, 129(6): 1191-1201. Rousseau-Gueutin M, Lerceteau-Kohler E, Barrot L, et al. 2008. Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry[J]. Genetics, 179(4): 2045-2060. Sachidanandam R, Weissman D, Schmidt S C, et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms[J]. Nature, 409: 928– 933. Samad S, Kurokura T, Koskela E, et al. 2017. Additive QTLs on three chromosomes control flowering time in woodland strawberry (Fragaria vesca L.)[J]. Horticulture Research, 4, 17020. Sánchez-Sevilla J F, Cruz-Rus E, Valpuesta V, et al. 2014. Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses[J]. BMC Genomics, 15(1): 218. Sánchez-Sevilla J F, Horvath A, Botella M A, et al. 2015. Diversity Arrays Technology (DArT) marker platforms for diversity analysis and linkage mapping in a complex crop, the octoploid cultivated strawberry (Fragaria × ananassa)[J]. PLoS One, 10(12): e144960. Sargent D J, Cipriani G, Vilanova S, et al. 2008. The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map[J]. Genome, 51(2): 120-127. Sargent D J, Clarke J, Simpson D W, et al. 2006. An enhanced microsatellite map of diploid Fragaria[J]. Theoretical and Applied Genetics, 112(7): 1349-1359. Sargent D J, Davis T M, Tobutt K R, et al. 2004. A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria[J]. Theoretical and Applied Genetics, 109(7): 1385-1391. Sargent D J, Fernandéz-Fernandéz F, Ruiz-Roja J J, et al. 2009. A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid Fragaria reference map[J]. Molecular Breeding, 24(3): 293-303. Sargent D J, Kuchta P, Girona E L, et al. 2011. Simple sequence repeat marker development and mapping targeted to previously unmapped regions of the strawberry genome sequence[J]. Plant Genome, 4(3): 165-177. Sargent D J, Passey T, ?urbanovski N, et al. 2012. A microsatellite linkage map for the cultivated strawberry (Fragaria × ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection[J]. Theoretical and Applied Genetics, 124(7): 1229-1240. Sargent D J, Rys A, Nier S, et al. 2007. The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera[J]. Theoretical and Applied Genetics, 114(2): 373-384. Senanayake Y D A, Bringhurst R S. 1967. Origin of Fragaria polyploids. I. cytological analysis[J]. American Journal of Botany, 54: 221–228. Shulaev V, Sargent D J, Crowhurst R N, et al. 2011. The genome of woodland strawberry (Fragaria vesca)[J]. Nature Genetics, 43(2): 109-116. Staudt G. 1962. Taxonomic studies in the genus Fragaria[J]. Canadian Journal of Botany, 40: 869-886. Sugimoto T, Tamaki K, Matsumoto J, et al. 2005. Detection of RAPD markers linked to the everbearing gene in Japanese cultivated strawberry[J]. Plant Breeding, 124(5): 498-501. Sun H H, Zhao Y B, Li C M, et al. 2012. Identification of markers linked to major gene loci involved in determination of fruit shape index of apples (Malus×domestica)[J]. Euphytica, 185: 185–193. Sun R, Chang Y, Yang F, et al. 2015. A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality[J]. BMC Genomics, 16: 747. Vallejo V, J Kolkman. 2002. AFLP protocol. Available at: http:// www.css.msu.edu/bean/PDF/AFLP_protocol.pdf. van Dijk T, Pagliarani G, Pikunova A, et al. 2014. Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map[J]. BMC Plant Biology, 14: 55. Verma S, Zurn J D, Salinas N, et al. 2017. Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis[J]. Horticulture Research, 4: 17062. Vining K J, Salinas N, Tennessen J A, et al. 2017. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families[J]. PEER J: 5(e3731). Vos P, Hogers R, Bleeker M, et al. 1995. AFLP: a new technique for DNA fingerprinting[J]. Nucleic Acids Research, 23: 4407–4414. Weebadde C K, Wang D, Finn C E, et al. 2008. Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry[J]. Plant Breeding, 127(1): 94-101. Welsh J, McClelland M. 1990. Fingerprinting genomes using PCR with arbitrary primers[J]. Nucleic Acids Research, 8: 7213–7218. Williams J G K, Kubelik A R, Livak K J, et al. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers[J]. Nucleic Acids Research, 18: 6531–6535. Williams M N V, Pande N, Nair S, et al. 1991. Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA[J]. Theoretical and Applied Genetics, 82: 489–498. Zietkiewicz E, Rafalski A, Labuda D. 1994. Genomic fingerprinting by simple sequence repeat (SSR) anchored polymerase chain reaction amplification[J]. Genomics, 20: 176–183. Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, et al. 2011a. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa)[J]. Theoretical and Applied Genetics, 123(5): 755-778. Zorrilla-Fontanesi Y, Cabeza A, Torres A M, et al. 2011b. Development and bin mapping of strawberry genic-SSRs in diploid Fragaria and their transferability across the Rosoideae subfamily[J]. Molecular Breeding, 27(2): 137-156.
