You are here
The use of DNA markers in raspberry (Rubus L.) research: a review
Raspberry (Rubus L.) is one of the most common berry crops in horticulture. It is a valuable food product for humans and a raw material for food processing companies. The assortment of raspberries in Ukraine includes more than 30 varieties. Modern breeding and genetic programs are aimed at expanding genetic diversity and creating new raspberries varities. Molecular genetic methods are increasingly being used in both fundamental and applied research of Rubus species. This article presents an overview of the main types of molecular markers used to study genetic polymorphism of Rubus species. Out of the whole variety of available DNA markers, such molecular methods of analysis as RAPD, RFLP, AFLP, ISSR, SSR and SNPs have proved to be the most effective in solving problems related to genotypes, population polymorphism, genetic mapping, and phylogenetic studies of raspberries. Their high efficiency is associated with increased resolution, reproducibility, high informativeness, the possibility of analysis automatization, speed, simplicity and availability. These markers are a convenient tool for genomic selection and research of genetic diversity of not only the genus Rubus representatives, but also of all living organisms. As of retrotransposon markers, which make up the main part of the eukaryotes genome, there are few scientific papers on their use for the study of representatives of the genus Rubus, unlike other crops. Significant progress in raspberry breeding is associated with the development of modern sequencing technologies. Whole-genome sequencing (WGS) allows simultaneous generation of a large number of SNP markers that are used to create genetic maps, identify pathogen resistance genes, map economically useful traits etc.
Key words: Rubus, raspberry, DNA markers, polymorphism, selection.
https://orcid.org/0000-0002-5860-5286Reference:
1. Derzhavnyj rejestr sortiv roslyn, prydatnyh dlja poshyrennja v Ukrai'ni [State register of plant varieties suitable for distribution in Ukraine]. Ministerstvo agrarnoi' polityky ta prodovol'stva Ukrai'ny [Ministry of Agrarian Policy and Food of Ukraine]. Available at: https://minagro.gov.ua/ua/file-storage/reyestr-sortiv-roslin.
2. Markovs'kyj, V.S., Bahmat, M.I. (2008). Jagidni kul'tury v Ukrai'ni [Berry crops in Ukraine]. Kamianets-Podilskyi, PP Medobory-2006, 200 p.
3. Pykalo, S.V., Demydov, O.A., Jurchenko, T.V., Homenko, S.O., Gumenjuk, O.V., Harchenko, M.V. (2020). Molekuljarni markery dlja identyfikacii' posuhostijkyh genotypiv pshenyci v umovah zmin klimatu [Molecular markers for identification of drought-resistant genotypes of wheat under conditions of climate change]. Ekologichni nauky [Environmental sciences]. no. 4(31), pp. 193‒202. DOI: 10.32846/2306- 9716/2020.eco.4-31.31
4. Polishhuk, I.M. (2020). Fitohimichne vyvchennja malyny zvychajnoi' ta stvorennja na i'i' osnovi novyh likars'kyh zasobiv: dys. na zdobuttja naukovogo stupenja doktora filosofii'. 226 – Farmacija, 22 – Ohorona zdorov’ja [Phytochemical study of common raspberry and creation of new medicinal products based on it: PhD dissertation. 226 – Pharmacy, 22 – Health care]. Kharkiv, 256 p.
5. Vos, P., Hogers, R., Bleeker, M. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. Vol. 23 (21), pp. 4407–4414.
6. Botstein, D., White, R.L., Skolnick, M., Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics. Vol. 32 (3), pp. 314–331.
7. Bushakra, J.M., Krieger, C., Deng, D., Stephens, M.J., Allan, A.C., Storey, R., Symonds, V.V., Stevenson, D., McGhie, T., Chagne, D., Buck, E.J., Gardiner, S.E. (2013). QTL involved in the modification of cyanidin compounds in black and red raspberry fruit. Theoretical and Applied Genetics. Vol. 126 (3), pp. 847–865. DOI: 10.1007/s00122-012-2022-4.
8. Bushakra, J.M., Stephens, M.J., Atmadjaja, A.N., Lewers, K.S., Symonds, V.V., Udall, J.A., Chagné, D., Buck, E.J., Gardiner, S.E. (2012). Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theor. Appl. Genet. Vol. 125(2), pp. 311‒327. DOI: 10.1007/s00122-012-1835-5.
9. Bushakra, J.M., Lewers, K.S., Staton, M.E., Zhebentyayeva, T., Saski, C.A. (2015). Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.) BMC Plant Biol. Vol. 15, pp. 258‒269. DOI: 10.1007/s00122-015-2541-x.
10. Bussemeyer, D.T., Pelikan, S., Kennedy, R.S., Rogstad, S.H. (1997). Genetic diversity of Philippine Rubus moluccanus L. (Rosaceae) populations examined with VNTR DNA probes. Trop. Biol. Vol. 14, pp. 867‒884. DOI: 10.1017/S0266467400011044.
11. Castillo, N.R.F., Bassil, N.V., Wada, S., Reed, B.M. (2010). Genetic stability of cryopreserved shoot tips of Rubus germplasm. In Vitro Cell. Dev. Biol. Plant. Vol. 46(3), pp. 246‒256. DOI: 10.1007/ s11627-009-9265-z.
12. Castillo, N.R.F., Reed, B.M., Graham, J., Fernández-Fernández, F., Bassil, N.V. (2010). Microsatellite markers for raspberry and blackberry. Am. Soc. Hortic. Sci. Vol. 135, pp. 271‒278.
13. Cekic, C., Calis, O., Ozturk, E.S. (2018). Genetic diversity of wild raspberry genotypes (Rubus idaeus L.) in North Anatolia based on ISSR markers. Appl. Ecol. Environ. Res. Vol. 16(5), pp. 6835‒6843. DOI: 10.15666/aeer/1605_68356843.
14. Dossett, M., Bassil, N., Finn, C. (2012). SSR fingerprinting of black raspberry cultivars shows discrepancies in identification. Acta Hortic. Vol. 946, pp. 49‒53. DOI: 10.17660/ActaHortic.2012.946.4.
15. Eckert, A.J. (2009). High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genetics & Genomes. Vol. 5(1), pp. 225‒234.
16. Ercisli, S., Badjakov, I., Kondakova, V., Atanassov, A., Todorovska, E. (2008). AFLP-based genetic relationships in wild and cultivated raspberry genotypes (Rubus idaeus L.). Biotechnol. Biotechnol. Equip. Vol. 22(4), pp. 907‒910.
17. FAO 2018. Statistics Raspberry Europe.
18. Garcia, A.A.F., Banchimol, L.L., Barbosa, A.M.M. (2004). Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genetics and Molecular Biology. Vol. 27 (4), no. 4, pp. 579–588.
19. Garrido, P., Morillo, E., Vásquez-Castillo, W. (2020). Genetic diversity of the Andean blackberry (Rubus glaucus Benth.) in Ecuador assessed by AFLP markers. Plant Genetic Resources. Vol. 18(4), pp. 243‒250. DOI: 10.1017/S1479262120000283
20. Glazko, V.I., Dubin, A.V., Kalendar, R.I., Glazko, G.V. (1999). Genetic relationships between soybean breeds assessed using ISSR markers. Cytology and Genetics. Vol. 33 (5), pp. 47–51.
21. Graham, J., Smith, K., MacKenzie, K., Jorgenson, L., Hackett, C., Powell, W. (2004). The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp idaeus) based on AFLPs, genomic-SSR and EST-SSR markers. Theoretical and Applied Genetics. Vol. 109, pp. 740–749. DOI: 10.1007/s00122-004-1687-8
22. Graham, J., Smith, K., Woodhead, M., Russell, J.R. (2002). Development and use of simple sequence repeat SSR markers in Rubus species. Mol. Ecol. Notes. Vol. 2, pp. 250‒252.
23. Graham, J., Squire, B., Marshall, B., Harrison, R.E. (1997). Spatially dependent genetic diversity within and between colonies of wild raspberry R. idaeus detected using RAPD markers. Mol. Ecol. Vol. 6, pp. 1001‒1008.
24. Graham, J., Woodhead, M., Smith, K., Russell, J., Marshall, B., Ramsay, G., Squire, G. (2009). New insight into wild red raspberry populations using simple sequence repeat markers. Am. Soc. Hort. Sci. Vol. 134(1), pp. 109‒119.
25. Guichoux, E., Lagache, L., Wagner, S., Chaumeil, P., Le. Ger, P., Lepais, O., Lepoittevin, C., Malausa, E., Revardel, E., Salin, F., Petit, R.J. (2011). Current trends in microsatellite genotyping. Molecular Ecology Resources. Vol. 11, pp. 591–611.
26. Hackett, C.A., Milne, L., Smith, K., Hedley, P., Morris, J., Simpson, C.J., Preedy, K., Graham, J. (2018). Enhancement of Glen Moy × Latham raspberry linkage map using GbS to further understand control of development processes leading to fruit ripening. BMC Genetics. Vol. 19, 59 p. DOI: 10.1186/s12863-018- 0666-z.
27. Hoepfner, A.S., Nybom, H., Carlsson, U., Franzen, R. (1993). DNA fingerprinting useful for monitoring cell line identity in micropropagated raspberries. Acta Agric. Scand. Sect. B. Soil Plant Sci. Vol. 43, pp. 53‒57.
28. John, J. St., Ransler, F., Quinn, T., Oyler-McCance, S. (2006). Characterization of microsatellite loci isolated in trumpeter swan (Cygnus buccinator). Mol. Ecol. Notes. Vol. 6, pp. 1083–1085.
29. Kalia, R.K., Rai, M.K., Kalia, S., Singh, R., Dhawan, A.K. (2011). Microsatellite markers: an overview of the recent progress in plants. Euphytica. Vol. 177, pp. 309–334.
30. Keane, B., Smith, M.K., Rogstad, S.H. (1998). Genetic variation in red raspberries (Rubus idaeus L., Rosaceae) from sites differing in organic pollutants compared with synthetic repeat DNA probes. Environ. Toxicol. Chem. Vol. 17, pp. 2027‒2034. DOI: 10.1002/etc.5620171019.
31. Kollmann, J., Steinger, T., Roy, B.A. (2000). Evidence of sexuality in european Rubus (Rosaceae) species based on AFLP and allozyme analysis. Am. J. Bot. Vol. 87(11), pp. 1592‒1598.
32. Lee, G.A., Song, J.Y., Choi, H.R., Chung, J.W., Jeon, Y.A., Lee, J.R., Ma, K.H., Lee, M.C. (2015). Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species. Molecules. Vol. 20, pp. 6432‒6442. DOI: 10.3390/molecules20046432.
33. Liang, Y., Lenz, R.R., Dai, W. (2016). Development of retrotransposon-based molecular markers and their application in genetic mapping in chokecherry (Prunus virginiana L.). Mol. Breed. Vol. 36, 109 p. DOI: 10.1007/s11032-016-0535-2.
34. López, A., Barrera, C., Marulanda, M. (2019). Evaluation of SSR and SNP markers in R. glaucus Benth progenitors’ selection. Rev. Bras. Frutic. Vol. 41(1), pp. 1‒14. DOI: 10.1590/0100-29452019081.
35. Marulanda, M., Lopez, A., Aguilar, S. (2007). Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers. Crop Breed. Appl. Biotechnol. Vol. 7, pp. 242‒252.
36. McGregor, C.E., Treuren, R., Hoekstra, R., Hintum, T.L. (2002). Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation. Theor. Appl. Gen. Vol. 104, pp. 146–156.
37. Miyashita, T., Kunitake, H., Yotsukura, N., Hoshino, Y. (2015). Assessment of genetic relationships among cultivated and wild Rubus accessions using AFLP-markers. Sci. Hortic. Vol. 193, pp. 165‒173.
38. Moore, P.P. (1993). Chloroplast DNA diversity in raspberry. J. Am. Soc. Hortic. Sci. Vol. 118, pp. 371‒376.
39. Nybom, H., Rogstad, S.H., Schaal, B.A. (1990). Genetic variation detected by use of the M13 ‘DNA fingerprint’ probe in Malus, Prunus and Rubus (Rosaceae). Theor. Appl. Genet. Vol. 79, pp. 153‒156.
40. Ochieng, J.A., Oyoo, M.E., Gesimba, R.M., Korir, P.C., Ojwang, P.P.O., Owuoche, J.O. (2018). Genetic diversity of blackberry (Rubus subgenus Rubus Watson) in selected counties in Kenya using simple sequence repeats (SSRs) markers. Afr. J. Biotechnol. Vol. 17(39), pp. 1247‒1264. DOI: 10.5897/ AJB2018.16613.
41. Parent, J.G., Pagé, D. (1998). Identification of raspberry cultivars by sequence characterized amplified region DNA analysis. HortScience. Vol. 33, pp. 140‒142.
42. Patamsytė, J., Kleizaitė, V., Čėsnienė, T., Rančelis, V., Žvingila, D. (2010). The genetic structure of red raspberry (Rubus idaeus L.) populations in Lithuania. Cent. Eur. J. Biol. Vol. 5(4), pp. 496–506. DOI: 10.2478/s11535-010-0034-0.
43. Ryu, J., Kim, W.J., Im, J., Kim, S.H., Lee, K.S., Jo, H.J., Kim, E.Y., Kang, S.Y., Lee, J.H., Ha, B.H. (2018). Genotyping-by-sequencing based single nucleotide polymorphisms enabled Kompetitive Allele Specific PCR marker development in mutant Rubus genotypes. Electron. J. Biotechnol. Vol. 35, pp. 57‒62. DOI: 10.1016/j.ejbt.2018.08.001.
44. Semagn, K., Bjornstad, Å., Ndjiondjop, M.N. (2006). An overview of molecular marker methods for plants. African Journal of Biotechnology. Vol. 5 (25), pp. 2540–2568.
45. Shu, Q.Y., Liu, G.S., Qi, D.M., Chu, C.C., Liu, J., Li, H.J. (2003). An effective method for axillary bud culture and RAPD analysis of cloned plants in tetraploid black locust. Plant Cell Report. Vol. 22 (3), pp. 175–180.
46. Simlat, M., Ptak, A., Kula, A., Orzel, A. (2018). Assessment of genetic variability among raspberry accessions using molecular markers. Acta Sci. Pol. Hortorum Cultus. Vol. 17(5). pp. 61‒72. DOI: 10.24326/asphc.2018.5.6.
47. USDA. 2018. Branded Food Products Database. Available at: https://ndb.nal.usda.gov/ndb/ search/list.
48. VanBuren, R., Bryant, D., Bushakra, J.M., Vining, K.J., Filichkin, S., Edger, P.P., Rowley, E.R., Priest, H.D., Michael, T.P., Dossett, M., Finn, C.E., Bassil, N.V., Mockler, T.C. (2018). Sequence and analysis of the black raspberry (Rubus occidentalis) genome. The Genomes of Rosaceous Berries and Their Wild Relatives. Springer. pp. 185‒197.
49. Varshney, R.K., Graner, A., Sorrells, M.E. (2005). Genic microsatellite markers in plants: features and applications. TRENDS in Biotechnology. Vol. 23, pp. 48‒55.
50. Ward, J.A., Bhangoo, J., Fernandez-Fernandez, F., Moore, P., Swanson, J.D., Viola, R., Velasco, R., Bassil, N., Weber, C.A., Sargent, D.J. (2013). Saturated linkage map construction in Rubus idaeususing genotyping by sequencing and genome-independent imputation. BMC genomics. Vol. 14 (2). DOI: 10.1186/1471-2164-14-2
51. Weber, C.A., Pattison, J., Samuelian, S. (2008). Marker assisted selection for resistance to root rot in red raspberry caused by Phytophthora fragariae var. rubi. Acta Hortic. Vol. 777, pp. 311‒316. DOI: 10.17660/ActaHortic.2008.777.46.
52. Wight, H., Zhou, J., Li, M., Hannenhalli, S., Mount, S., Liu, Z. (2019). Draft genome assembly and annotation of red raspberry Rubus idaeus. BioRxiv. DOI: 10.1101/546135.
53. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., Tingey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research. Vol. 18 (22), pp. 6531–6535.
54. Zane, L., Bargelloni, L., Patarnello, T. (2002). Strategies for microsatellite isolation: a review. Mol. Ecol. Vol. 11, pp. 1–16.
55. Zietkiewicz, E., Rafalski, A., Labuda, D. (1994). Genome fingerprinting by seguence repeat (SSR) -anchored polymerase chain reaction amplification. Genomics. Vol. 20, pp. 176–183.
Download this article:
| Attachment | Size |
|---|---|
 dyman_agro_2_2023.pdf | 534.51 KB |
YEAR: