Полногеномный анализ ассоциаций с устойчивостью к грибным болезням в коллекции сои в условиях Юго-Восточного и Южного Казахстана

Соя (Glycine max (L.) Merr) – важная пищевая, кормовая и техни­ческая культура. В Казахстане площадь под соей увеличивает­ся с каждым годом, что обусловлено ее важностью в решении проблемы дефицита белка в питании людей и кормлении животных. Одной из основных проблем производства сои являются грибные болезни, вызывающие потери урожая до 30 %. Для повышения эффективности селекции, направленной на улучшение устойчивости сои к болезням, могут быть исполь­зованы современные геномные технологии. Таким образом, целью настоящего исследования был полногеномный анализ ассоциаций (GWAS) в коллекции сои, состоящей из 182 образ­цов, на устойчивость к грибным болезням в условиях Юго-Вос­точного и Южного Казахстана. В результате полевой оценки коллекции сои обнаружены растения, пораженные Fusarium spp. и Cercospora sojina в Южном регионе (НИИПББ) и Septoria glycines – в Юго-Восточном регионе (КазНИИЗиР). Исследование было нацелено на идентификацию локусов количественных признаков (ЛКП), связанных с устойчивостью к основным заболеваниям, таким как фузариоз корневой гнили (FUS), церко­спороз (FLS) и септориоз (BS). GWAS с использованием 4 442 SNP-маркеров (single nucleotide polymorphism) матрицы Illumina iSelect позволил идентифицировать 15 ассоциаций маркер – признак (MTA) на устойчивость к трем болезням на двух разных стадиях роста. Генетически картированы два ЛКП как для FUS (хромосомы 13 и 17), так и для BS (хромосомы 14 и 17), включая один предположительно новый ЛКП для BS, который был идентифицирован на хромосоме 17. Кроме того, пять предположительно новых ЛКП для FLS были идентифици­рованы на хромосомах сои 2, 7 и 15. Результаты исследования могут быть использованы для улучшения селекционных про­грамм, в том числе маркер-опосредованной селекции.

1. Abugalieva S., Didorenko S., Anuarbek S., Volkova L., Gerasimova Y., Sidorik I., Turuspekov Y. Assessment of soybean flowering and seed maturation time in different latitude regions of Kazakhstan. PLoS One. 2016;11(12):e0166894. DOI 10.1371/journal.pone.0166894.

2. Anderson J., Akond M., Kassem M., Meksem K., Kantartzi S. Quantitative trait loci underlying resistance to sudden death syndrome (SDS) in MD96-5722 by ‘Spencer’ recombinant inbred line population of soybean. 3 Biotech. 2015;5(2):203-210. DOI 10.1007/s13205-014-0211-3.

3. Bao Y., Kurle J.E., Anderson G., Young N.D. Association mapping and genomic prediction for resistance to sudden death syndrome in early maturing soybean germplasm. Mol. Breeding. 2015;35:128. DOI 10.1007/s11032-015-0324-3.

4. 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. DOI 10.1093/bioinformatics/btm308.

5. Contreras-Soto R.I., Mora F., Lazzari F., Rott de Oliveira M.A., Sca¬pium C.A., Chuster I. Genome-wide association mapping for flowering and maturity in tropical soybean: implications for breeding strategies. Breed. Sci. 2018;67:435-449. DOI 10.1270/jsbbs.17024.

6. Cook D.E., Lee T.G., Guo X., Melito S., Wang K., Bayless A.M., Wang J., Hughes T.J., Willis D.K., Clemente T.E., Diers B.W., Ji¬ang J., Hudson M.E., Bent A.F. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science. 2012;338:1206-1209. DOI 10.1126/science.1228746.

7. Copley T.R., Duceppe M.O., O’Donoughue L.S. Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines. BMC Genomics. 2018;19:167. DOI 10.1186/s12864-018-4558-4.

8. Dias M.D., Pinheiro V.F., Café-Filho A.C. Impact of anthracnose on the yield of soybean subjected to chemical control in the north region of Brazil. Summa Phytopathol. 2016;42(1):18-23. DOI 10.1590/01005405/2114.

9. Didorenko S.V., Sagitov A.O., Kudaibergenov M.S. Main diseases on crops of soybean and methods of dealing with them. AgroAlem. 2014;8(61):42-46. (in Russian)

10. Ellis M., Wang H., Paul P., St. Martin S.K., McHale L., Dorrance A. Identification of soybean genotypes resistant to Fusarium graminearum and genetic mapping of resistance quantitative trait loci in the cultivar Conrad. Crop Sci. 2012;52(5):2224-2233.

11. Evanno G., Regnaut S., Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 2005;14:2611-2620. DOI 10.1111/j.1365-294X.2005.02553.x.

12. Faske T., Kirkpatrick T., Zhou J., Tzanetakis I. Soybean diseases. Arkansas Soybean Production Handbook. 2014;11:1-18.

13. Gurung S., Mamidi S., Bonman J.M., Xiong M., Brown-Guedira G., Adhikari T.B. Genome-wide association study reveals novel quan¬titative trait loci associated with resistance to multiple leaf spot dis-eases of spring wheat. PLoS One. 2014;9(9):e108179. DOI 10.1371/journal.pone.0108179.

14. Hnetkovsky N., Chang S.J.C., Doubler T.W., Gibson P.T., Lightfoot D.A. Genetic mapping of loci underlying field resistance to soybean sudden death syndrome (SDS). Crop Sci. 1996;36:393-400. DOI 10.2135/cropsci1996.0011183X003600020030x.

15. Iquira E., Humira S., Francois B. Association mapping of QTLs for sclerotinia stem rot resistance in a collection of soybean plant introductions using a genotyping by sequencing (GBS) approach. BMC Plant Biol. 2015;15:5. DOI 10.1186/s12870-014-0408-y.

16. Kassem M.A.J., Shultz K., Meksem Y., Cho A.J., Wood M.J., Iqbal D., Lightfoot A. An updated ‘Essex’ by ‘Forrest’ linkage map and first composite interval map of QTL underlying six soybean traits. Theor. Appl. Genet. 2006;113:1015-1026. DOI 10.1007/s00122-0060361-8.

17. Klein R.J. Power analysis for genome-wide association studies. BMC Genetics. 2007;8:58. DOI 10.1186/1471-2156-8-58.

18. Kurilova D.A. The harmfulness of soybean fusarium depending on the degree of damage to the plants. Maslichnye Kultury. Nauchno-tekhnicheskiy Byulleten Vserossiyskogo NII Maslichnyh Kultur = Oil¬seeds. Scientific and Technical Bulletin of the All-Russian Research Institute of Oilseeds. 2010;2(144-145):84-89. (in Russian)

19. Leath S., Carroll R.B. Screening for resistance to Fusarium oxysporum in Soybean. Plant Dis. 1982;66(12):1140-1143.

20. Masuda T., Goldsmith P.D. World soybean production: area harvested, yield, and long-tern projections. Int. Food Agribus. Man. Rev. 2009; 12(4):143-161.

21. Mian M.A.R., Wang T., Phillips D.V., Alvernaz J., Boerma H.R. Molecular mapping of the Rcs3 gene for resistance to frogeye leaf spot in soybean. Crop Sci. 1999;39:1687-1691. DOI 10.1046/j.1439-0523. 2001.00563.x.

22. Mian R., Bond J., Joobeur T., Mengistu A., Wiebold W., Snannon G., Wrather A. Identification of soybean genotypes resistant to Cercospora sojina by field screening and molecular markers. Plant Dis. 2009;93:408-411. DOI 10.1094/PDIS-93-4-0408.

23. Mombekova G.A., Shemshurova O.N., Seitbattalova A.I., Aitkhozhina N.A., Bekmakhanova N.E. Phytopathogens of sugar beet and soybean cultivated in soil and climatic conditions of Almaty region. NAN RK. 2013;4:8-11. (in Russian)

24. Mueller D., Robertson A., Sisson A., Tylka G. Soybean Diseases. Iowa State Univ. of Sci. and Technol., 2010.

25. Oyiga B.C., Sharma R.C., Baum M., Ogbonnaya F.C., Léon J., Ballvora A. Allelic variations and differential expressions detected at quantitative trait loci for salt stress tolerance in wheat. Plant Cell Environ. 2017;41(5):919-935. DOI 10.1111/pce.12898.

26. Pataky J.K., Lim S.M. Effects of septoria brown spot on the yield components of soybeans. Plant Dis. 1981;65:588-590.

27. Peakall R., Smouse P.E. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics. 2012;28:2537-2539. DOI 10.1093/bioinformatics/bts460.

28. Pham A.T., Harris D.K., Buck J., Hoskins A., Serrano J., Abdel-Haleem H. Fine mapping and characterization of candidate genes that control resistance to Cercospora sojina K. Hara in two soybean germplasm accessions. PLoS One. 2015;10(5):e0126753. DOI 10.1371/journal.pone.0126753.

29. Polozhieva Y.V., Dubovitskaya L.K. Soybean varieties evaluation on prevalence by complex of the root rots agents. Dalnevostochnyi Agrarnyi Vestnik = Far Eastern Agrarian Herald. 2015;3(35):35-38. (in Russian)

30. Prabhu R.R., Njiti V.N., Bell-Johnson B., Johnson J.E., Schmidt M.E., Klein J.H., Lightfoot D.A. Selecting soybean cultivars for dual re¬sistance to soybean cyst nematode and sudden death syndrome using two DNA markers. Crop Sci. 1999;39(4):982-987.

31. Pritchard J.K., Stephens M., Rosenberg N.A., Donnelly P. Association mapping in structured populations. Am. J. Hum. Genet. 2000;67:170181. DOI 10.1086/302959.

32. Qin J., Song Q., Shi A., Li S., Zhang M., Zhang B. Genome-wide association mapping of resistance to Phytophthora sojae in a soybean [Glycine max (L.) Merr.] germplasm panel from maturity groups IV and V. PLoS One. 2017;12:e0184613. DOI 10.1371/journal.pone.0184613.

33. Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W., Hyten D.L., Song Q., Thelen J.J., Cheng J., Xu D., Hellsten U., May G.D., Yu Y., Sakurai T., Umezawa T., Bhattacharyya M.K., Sandhu D., Valliyodan B., Lindquist E., Peto M., Grant D., Shu S., Goodstein D., Barry K., Futrell-Griggs M., Abernathy B., Du J., Tian Z., Zhu L., Gill N., Joshi T., Libault M., Sethuraman A., Zhang X.C., Shinozaki K., Nguyen H.T., Wing R.A., Cregan P., Specht J., Grimwood J., Rokhsar D., Stacey G., Shoemaker R.C., Jackson S.A. Genome sequence of the paleopolyploid soybean. Na¬ture. 2010;463:178-183. DOI 10.1038/nature08670.

34. Schneider R., Rolling W., Song Q., Cregan R., Dorrance A.E., McHale L.K. Genome-wide association mapping of partial resis¬tance to Phytophthora sojae in soybean plant introductions from the Republic of Korea. BMC Genomics. 2016;17(1):607. DOI 10.1186/s12864-016-2918-5.

35. Semagn K., Babu R., Hearne S., Olsen M. Single nucleotide polymorphism using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol. Breeding. 2014;33(1):1-14.

36. Song Q., Hyten D.L., Jia G., Quigley C.V., Fickus E.W., Nelson R.L., Cregan P.B. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS One. 2013;8(1):e54985. DOI 10.1371/journal.pone.0054985.

37. Stacey G. (Ed.) Genetics and Genomics of Soybean. Ser.: Plant Genetics and Genomics: Crops and Models (Vol. 2). Springer, 2008.

38. Turner M.K., Kolmer J.A., Pumphrey M.O., Bulli P., Chao S., Anderson J.A. Association mapping of leaf rust resistance loci in a spring wheat core collection. Theor. Appl. Genet. 2017;130:345-361. DOI 10.1007/s00122-016-2815-y.

39. Vidic M., Dordevic V., Petrovic K., Miladinovic J. Review of soybean resistance to pathogens. Ratar. Povrt. 2013;50(2):52-61. DOI 10.5937/ratpov50-4038.

40. Wang H., Waller L., Tripathy S., St. Martin S.K., Zhou L., Krampis K., Tucker D.M., Mao Y., Hoeschele I., Maroof S.M.A., Tyler B.M., Dorrance A.E. Analysis of genes underlying soybean quantitative trait loci conferring partial resistance to Phytophthora sojae. Plant Gen. 2010;3:23-40.

41. Wang J., Liu C.,Wang J., Qi Z., Li H., Hu G., Chen Q. An integrated QTL map of fungal diseases resistance in soybean (Glycine max L. Merr.): a method of meta-analysis for mining R genes. Agric. Sci. China. 2010;9(2):223-232. DOI 10.1016/S1671-2927(09)60087-0.

42. Wimmer V., Albrecht T., Auinger H., Schoen C. Synbreed: a framework for the analysis of genomic prediction data using R. Bioinformatics. 2012;28(15):2086-2087. DOI 10.1093/bioinformatics/bts335.

43. Yang W., Weaver D.B., Nielsen B.L., Qiu J. Molecular mapping of a new gene for resistance to frogeye leaf spot of soyabean in Peking. Plant Breed. 2001;120(1):73-78. DOI 10.1046/j.1439-0523.2001.00563.x.

44. Yang X.B., Feng F. Ranges and diversity of soybean fungal diseases in North America. Phytopathology. 2001;91(8):769-775.

45. Zanke C., Ling J., Plieske J., Kollers S., Ebmeyer E., Korzun V., Argillier O., Stiewe G., Hinze M., Beier S., Ganal M.W., Roder M.S. Genetic architecture of main effect QTL for heading date in European winter wheat. Front. Plant Sci. 2014;5:217. DOI 10.3389/fpls.2014.00217.

46. Zaostrovnykh V.I. Soybean diseases. Zaschita i Karantin Rastenii = Plant Protection and Quarantine. 2005;2:49-53. (in Russian)

47. Zatybekov A., Abugalieva S., Didorenko S., Gerasimova Y., Sidorik I., Anuarbek Sh., Turuspekov Y. GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan. BMC Plant Biol. 2017;17(Suppl.4):63-70. DOI 10.1186/s12870-017-1125-0.

48. Zhang J., Singh A., Mueller D.S., Singh A.K. Genome-wide association and epistasis studies unravel the genetic architecture of sudden death syndrome resistance in soybean. Plant J. 2015;84:1124-1136. DOI 10.1111/tpj.13069.

49. Zhang J., Xia Ch., Wang X., Duan C., Sun S., Wu X., Zhu Zh. Genetic characterization and fine mapping of the novel Phytophtora resistance gene in a Chines soybean cultivar. Theor. Appl. Genet. 2013; 126:1555-1561.

50. Zhang L., Kyei-Boahen S., Zhang J., Zhang M., Freeland T., Watson C., Liu X. Modifications of optimum adaptation zones for soybean maturity groups in the USA. Crop Management. 2007;6(1). DOI 10.1094/CM-2007-0927-01-RS.

51. Zhao G., Ablett G.R., Anderson T.R., Rajcan I., Schaafsma A.W. Inheritance and genetic mapping of resistance to rhizoctonia root and hypocotyl rot in soybean. Crop Sci. 2005;45:1441-1447. DOI 10.2135/ cropsci2004.0560.

52. Zhao X., Han Y., Li Y., Liu D., Sun M., Zhao Y., Lu Ch., Li D., Yang Z., Huang L., Teng W., Qiu L., Zheng H., Li W. Loci and candidate gene identification for resistance to Sclerotinia sclerotiorum in soybean (Glycine max L. Merr.) via association and linkage maps. Plant J. 2015;82:245-255. DOI 10.1111/tpj.12810.