Molecular-genetic marking of Brassica L. species for resistance against various pathogens: achievements and prospects

Cruciferous plants  belonging to the  genus  Brassica of the  Cabbage family (Brassicaceae) are cultivated  as vegetables, oilseeds and forage crops; they occupy one of the first places in Russia in the gross yield of vegetables. The yield of cabbage crops is adversely affected  by various pathogens, including bacterial, viral and fungal infections. The diseases such as black rot of cabbage (caused by the bacterium Xanthomonas campestris pv. campestris), downy mildew (caused by Hyaloperonospora parasitica), Turnip Mosaic Virus (TuMV) are not included  in the list of quarantine diseases  in the territory of the Russian Federation and Eurasian Economic Union (EAEU), but they can affect a part of the sown area and lead to significant (up to 100 %) crop losses. The development of cultivars resistant to these  pathogens is an important trend  in Brassica crop breeding in addition  to existing methods of agrotechnical and chemical protection. The development of molecular  marker techniques and marker-assisted selection  (MAS) methods makes it possible  to significantly increase  the efficiency of breeding resistant cabbage cultivars. The review contains  information on the currently  known  genes  and quantitative trait loci (QTLs) associated with resistance to black rot, downy mildew, and TuMV. Molecular mapping data for resistance genes  of Brassica species are shown. The molecular markers (RFLP, AFLP, SSR, EST, SNP, InDel, SLAF and others) closely linked to the resistance loci and SCAR-, STS- and dCAPS-markers derived from them  for molecular screening are listed. The use of the markers reviewed  to assess  the  Brassica accessions  and  lines can help  the  researchers in finding  sources  and  donors  of pathogen resistance of cabbage crops.

1. Afrin K.S., Rahim M.A., Park J., Natarajan S., Rubel M.H., Kim H., Nou I. Screening of cabbage (Brassica oleracea L.) germplasm for resistance to black rot. Plant Breed. Biotechnol. 2018a;6(1):30-43. DOI 10.9787/PBB.2018.6.1.30.

2. Afrin K.S., Rahim M.A., Park J., Natarajan S., Kim H., Nou I. Identification of NBS-encoding genes linked to black rot resistance in cabbage (Brassica oleracea var. capitata). Mol. Biol. Rep. 2018b;45(5): 773-785. DOI 10.1007/s11033-018-4217-5.

3. Artemyeva A.M., Ignatov A.N., Volkova A.I., Kocherina N.V., Konopleva M.N., Chesnokov Yu.V. Physiological and genetic components of black rot resistance in double haploid lines of B. rapa L. Agricultural Biology (Sel’skokhozyaistvennaya Biologiya). 2018; 53(1):157-169. DOI 10.15389/agrobiology.2018.1.157eng.

4. Artemyeva A.M., Solovjova A.E., Kocherina N.V., Berensen F.A., Rudneva E.N., Chesnokov Yu.V. Mapping of chromosome loci determined manifestation of morphological and biochemical traits of quality in Brassica rapa L. crops. Russ. J. Plant Physiol. 2016; 63(2):259-272. DOI 10.1134/S1021443716020047.

5. Carlier J.D., Alabaça C.A., Coelho P.S., Monteiro A.A., Leitão J.M. The downy mildew resistance locus Pp523 is located on chromosome C8 of Brassica oleracea L. Plant Breed. 2012;2131(1): 170-175. DOI 10.1111/j.1439-0523.2011.01904.x.

6. Carlier J.D., Alabaça C.A., Sousa N.H., Coelho P.S., Monteiro A.A., Paterson A.H., Leitão J.M. Physical mapping in a triplicated genome: mapping the downy mildew resistance locus Pp523 in Brassica oleracea L. G3: Genes Genomes Genetics. 2011;1(7):593-601. DOI 10.1534/g3.111.001099.

7. Cruz J., Tenreiro R., Cruz L. Assessment of diversity of Xanthomonas campestris pathovars affecting cruciferous plants in Portugal and disclosure of two novel Xanthomonas campestris pv. campestris races. J. Plant Pathol. 2017;99:403-414. DOI 10.4454/jpp.v99i2.3890.

8. Dyakova Yu.T. Basics of Plant Pathology. Moscow, 2017. (in Russian) Fadina O.A., Structural features of the FRIGIDA gene in Brassica species: PhD Thesis. Moscow: All-Russia Research Institute of Agricultural Biotechnology Publ., 2014. http://vniisb.metacontent.ru/documents/2014/fadina.pdf (in Russian)

9. Farinhó M., Coelho P., Carlier J., Svetleva D., Monteiro A., Leitao J. Mapping of a locus for adult plant resistance to downy mildew in broccoli (Brassica oleracea convar. italica). Theor. Appl. Genet. 2004;109:1392-1398. DOI 10.1007/s00122-004-1747-0.

10. Farinhó M., Coelho P., Monteiro A., Leitão J. SCAR and CAPS markers flanking the Brassica oleracea L. Pp523 downy mildew resistance locus demarcate a genomic region syntenic to the toparm end of Arabidopsis thaliana L. chromosome 1. Euphytica. 2007;157:211-215. DOI 10.1007/s10681-007-9414-6.

11. Farnham M.W., Wang M., Thomas C.E. A single dominant gene for downy mildew resistance in broccoli. Euphytica. 2002;128: 405-407.

12. Flor H.H. Current status of the gene-for-gene concept. Annu. Rev. Phytopathol. 1971;9:275-296.

13. Fraser R.S.S. The genetics of plant-virus interactions: implications for plant breeding. Euphytica. 1992;63:175. DOI 10.1007/BF00023922.

14. Gibbs A.J., Nguyen H.D., Ohshima K. The ‘emergence’ of turnip mosaic virus was probably a ‘gene-for-quasi-gene’ event. Curr. Opin. Virol. 2015;10:20-26. DOI 10.1016/j.coviro.2014.12.004.

15. Giovannelli J.L., Farnham M.W., Wang M. Development of sequence characterized amplified region markers linked to downy mildew resistance in broccoli. J. Amer. Soc. Hort. Sci. 2002;127(4):597-601.

16. Goker M., Garcia-Blazquez G., Voglmayr H., Telleria M.T., Martin M.P. Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS One. 2009;4(7):e6319. DOI 10.1371/journal.pone.0006319.

17. Hughes S.L., Hunter P.J., Sharpe A.G., Kearsey M.J., Lydiate D.J., Walsh J.A. Genetic mapping of the novel Turnip mosaic virus resistance gene TuRB03 in Brassica napus. Theor. Appl. Genet. 2003; 99:1149-1154. DOI 10.1007/s00122-003-1363-4.

18. Iglesias-Bernabé L., Madloo P., Rodríguez V.M., Francisco M., Soengas P. Dissecting quantitative resistance to Xanthomonas campestris pv. campestris in leaves of Brassica oleracea by QTL analysis. Sci. Rep. 2019;9:2015. DOI 10.1038/s41598-019-38527-5.

19. Ignatov A.N. Occurrence of bacterial agents of dangerous plant diseases in Russia. Zashchita Kartofelya = Potato Protection. 2014;2:53-57. (in Russian)

20. Ignatov A.N., Kuginuki Y., Suprunova T.P., Pozmogova G.E., Seitova A.M., Dorokhov D.B., Hirai M. RAPD markers linked to locus controlling resistance for race 4 of the black rot causative agent, Xanthmonas campestris pv. campestris (Pamm.) Dow. in Brassica rapa L. Russ. J. Genet. 2000;36:281-283.

21. Jenner C.E., Tomimura K., Ohshima K., Hughes S.L., Walsh J.A. Mutations in Turnip mosaic virus P3 and cylindrical inclusion proteins are separately required to overcome two B. napus resistance genes. Virology. 2002;300:50-59. DOI 10.1006/viro.2002.1519.

22. Jin M., Lee S., Ke L., Kim J.S., Seo M., Sohn S., Park B., Bonnema G. Identification and mapping of a novel dominant resistance gene, TuRB07 to Turnip mosaic virus in Brassica rapa. Theor. Appl. Genet. 2014;127:509-519. DOI 10.1007/s00122-013-2237-z.

23. Kaur R., Shivani S.B., Kanwar H.S., Dohroo N.P., Majeed S., Sharma D.R. Detecting RAPD markers associated with black rot resistance in cabbage (Brassica oleracea var. capitata). Fruit Veget. Cereal Sci. Biotechnol. 2009;3:12-15.

24. Kifuji Y., Hanzaea H., Terasawa Y., Nishio T. QTL analysis of black rot resistance in cabbage using newly developed EST-SNP markers. Euphytica. 2013;190:289-295. DOI 10.1007/s10681-012-0847-1.

25. Kim S., Song Y.H., Lee J.Y., Choi S.R., Dhandapani V., Jang C.S., Lim Y.P., Han T. Identification of the BrRHP1 locus that confers resistance to downy mildew in Chinese cabbage (Brassica rapa ssp. pekinensis) and development of linked molecular markers. Theor. Appl. Genet. 2011;123:1183. DOI 10.1007/s00122-011-1658-9.

26. Lazarev A.M., Mysnik E.N., Ignatov A.N. Area and harmfulness zones of Black Rot of cabbage. Vestnik Zashchity Rasteniy = Plant Protection Bulletin. 2017;1(91):52-55. (in Russian)

27. Lee J., Izzah N.K., Jayakodi V., Perumal S., Joh H.J., Lee H.J., Lee S., Park J.Y., Yang K., Nou I., Seo J., Yoo J., Suh Y., Ahn K., Lee J.H., Choi G.J., Yu Y., Kim H., Yang T. Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage. BMC Plant Biol. 2015;15:32. DOI 10.1186/s12870-015-0424-6.

28. Li G., Qian W., Zhang S., Zhang S., Li F., Zhang H., Wu J., Wang X., Sun R. Development of gene-based markers for the Turnip mosaic virus resistance gene retr02 in Brassica rapa. Plant Breed. 2016; 135:466-470. DOI 10.1111/pbr.12372.

29. Li H., Yu S., Zhang F., Yu Y., Zhao X., Zhang D., Zhao X. Development of molecular markers linked to the resistant QTL for downy mildew in Brassica rapa L. ssp. pekinensis. Hereditas (Beijing). 2011:33(11):1271-1278. DOI 10.3724/SP.J.1005.2011.01271. (in Chinese)

30. Li Q., Zhang X., Zeng Q., Zhang Z., Liu S., Pei Y., Wang S., Liu X., Xu W., Fu W., Zhao Z., Song X. Identification and mapping of a novel Turnip mosaic virus resistance gene TuRBCS01 in Chinese cabbage (Brassica rapa L.). Plant Breed. 2014;134(2):221-225. DOI 10.1111/pbr.12239.

31. Lydiate D.J., Rusholme R.L., Higgins E.E., Walsh J.A. Genetic control of immunity to Turnip mosaic virus (TuMV) pathotype 1 in Brassica rapa (Chinese cabbage). Genome. 2014;57:419-425. DOI 10.1139/gen-2014-0070.

32. Mahajan V., Gill H.S., More T.A. Inheritance of downy mildew resistance in Indian cauliflower (group III). Euphytica. 1995;86:1-3. DOI 10.1007/BF00035932.

33. McDowell J.M., Simon S.A. Recent insights into R gene evolution. Mol. Plant Pathol. 2006;7(5):437-448. DOI 10.1111/J.1364-3703.2006.00342.x.

34. Nagaharu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jap. J. Bot. 1935;7:389-452.

35. Neik T.X., Barbetti M.J., Batley J. Current status and challenges in identifying disease resistance genes in Brassica napus. Front. Plant Sci. 2017;8:1788. DOI 10.3389/fpls.2017.01788.

36. Qian W., Zhang S.J., Zhang S.F., Li F., Zhang H., Wu J., Wang X.W., Walsh J.A., Sun R.F. Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.). Theor. Appl. Genet. 2013;126:179-188. DOI 10.1007/s00122-012-1972-x.

37. Rusholme R.L., Higgins E.E., Walsh J.A., Lydiate D.J. Genetic control of broad-spectrum resistance to Turnip mosaic virus in Brassica rapa (Chinese cabbage). Theor. Appl. Genet. 2007;107:1169-1173. DOI 10.1007/s00122-003-1363-4.

38. Saha P., Kalia P., Sharma M., Singh D. New source of black rot disease resistance in Brassica oleracea and genetic analysis of resistance. Euphytica. 2016;207:35-48. DOI 10.1007/s10681-015-1524-y.

39. Saharan G.S., Mehta N., Meena P.D. Downy Mildew Disease of Crucifers: Biology, Ecology and Disease Management. Springer Nature Singapore Pte Ltd., 2017. DOI 10.1007/978-981-10-7500-1.

40. Sharma B.B., Kalia P., Yadava D.K., Singh D., Sharma T.R. Genetics and molecular mapping of black rot resistance locus Xca1bc on chromosome B-7 in Ethiopian mustard. PLoS One. 2016;11(3):e0152290. DOI 10.1371/journal.pone.0152290.

41. Singh S., Sharma S.R., Kalia P., Deshmukh R., Kumar V., Sharma P., Sharma T.R. Molecular mapping of the downy mildew resistance gene Ppa3 in cauliflower (Brassica oleracea var. botrytis L.). J. Hortic. Sci. Biotechnol. 2012;87(2):137-143. DOI 10.1080/14620316.2012.11512844.

42. Soengas P., Hand P., Vicente J.G., Pole J.M., Pink D.A.C. Identification of quantitative trait loci for resistance to Xanthomonas campestris pv. campestris in Brassica rapa. Theor. Appl. Genet. 2007;114:637-645. DOI 10.1007/s00122-006-0464-2.

43. Taylor J.D., Conway J., Roberts S.J., Astley D., Vicente J.G. Sources and origin of resistance to Xanthomonas campestris pv. campestris in Brassica genomes. Phytopathology. 2002;92:105-111. DOI 10.1094/PHYTO.2002.92.1.105.

44. Tonu N., Doullah M., Shimizu M., Karim M., Kawanabe T., Fujimoto R., Okazaki K. Comparison of cositions of QTLs conferring resistance to X. campestris pv. campestris in B. oleracea. Am. J. Plant Sci. 2013;4(8):11-20. DOI 10.4236/ajps.2013.48A002.

45. Vicente J.G., Holub E.B. Pathogen profile: Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops. Mol. Plant Pathol. 2013;14(1):2-18. DOI 10.1111/j.1364-3703.2012.00833.x.

46. Walsh J.A., Jenner C.E. Turnip mosaic virus and the quest for durable resistance. Mol. Plant Pathol. 2002;3(5):289-300. DOI 10.1046/j.1364-3703.2002.00132.x.

47. Walsh J.A., Sharpe A.G., Jenner C.E., Lydiate D.J. Characterisation of resistance to turnip mosaic virus in oilseed rape (Brassica napus) and genetic mapping of TuRB01. Theor. Appl. Genet. 1999;99:1149-1154.

48. Xinhua W., Huoying C., Yuying Z., Ruixian H. An AFLP marker linked to turnip mosaic virus resistance gene in pak-choi. Afr. J. Biotechnol. 2009;8(11):2508-2512.

49. Xinhua W., Yang L., Huoying C.A. Linkage map of pak-choi (B. rapa ssp. chinensis) based on AFLP and SSR markers and identification of AFLP markers for resistance to TuMV. Plant Breed. 2011;130:275-277. DOI 10.1111/j.14390523.2010.01811.x.

50. Yu S., Su T., Zhi S., Zhang F., Wang W., Zhang D., Zhao X., Yu Y. Construction of a sequence-based bin map and mapping of QTLs for downy mildew resistance at four developmental stages in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Mol. Breed. 2016;36:44. DOI 10.1007/s11032-016-0467-x.

51. Yu S., Zhang F., Yu R., Zou Y., Qi J., Zhao X., Yu Y., Zhang D., Li L. Genetic mapping and localization of a major QTL for seedling resistance to downy mildew in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol. Breed. 2009;23:573-590. DOI 10.1007/s11032-009-9257-z.

52. Yu S., Zhang F., Zhao X., Yu Y., Zhang D. Sequence-characterized amplified region and simple sequence repeat markers for identifying the major trait locus responsible for seedling resistance to downy mildew in Chinese cabbage (Brassica rapa ssp. pekinensis). Plant Breed. 2011;130:580-583. DOI 10.1111/j.1439-0523.2011.01874.x.

53. Zhang F.L., Wang M., Liu X.C., Zhao X.Y., Yang J.P. Quantitative trait loci analysis for resistance against Turnip mosaic virus based on a double-haploid population in Chinese cabbage. Plant Breed. 2008;127(1):82-86. DOI 10.1111/j.1439-0523.2007.01431.x.

54. Zhi S., Su T., Yu S., Zhang F., Yu Y., Zhang D., Zhao X., Wang W., Lu G., Zhu Y. Genetic characteristics of A01-located resistant loci to downy mildew in Chinese cabbage by genome-wide association studies. Plant Ph. J. 2016;52:693-702. DOI 10.13592/j.cnki.ppj.2016.0026. (in Chinese)