Allelic and epigenetic DNA variation in relation to F1 heterosis manifestation in F1 hybrids of Capsicum annuum L.

Managing F₁ heterosis is one of the major objectives in hybrid crop breeding programs. The classical theory considers the heterozygosity in F₁ hybrids to be the main factor contributing to heterosis and therefore presumes a linear relationship between the value of genetic polymorphisms in parental lines and the heterotic response of their F₁ offspring. Therefore, the genetic diversity information is viewed as a tool for selection of promising cross-combinations, but results published by different researchers are inconsistent. In this work, we studied the contributions of structural and nonstructural DNA polymorphisms to F₁ heterosis manifestation. We used SSR and methyl-sensitive AFLP (MSAP with HpaII and MspI izoshisomers) protocols for obtaining specific patterns for heterotic and nonheterotic F₁ hybrids of sweet pepper (Capsicum annuum L.) from a Belarusian breeding program. We found out that a certain portion of heterosis for yield-related traits might be explained by the polymorphism revealed by SSR analysis. According to our data, the total number of polymorphic SSR loci and the ratio of polymorphic and nonpolymorphic loci demonstrate a significant predictive value and can serve as additional prognostic criteria for the selection of promising cross-combinations. From the MSAP assay, we found a relationship between heterosis and the numbers of methylated and nonmethylated DNA loci for yield traits. Our results indicate that cross-hybridization may favor epiallelic modifications in F₁ hybrids, presumably responsible for heterosis. Thus, epigenetic DNA variation may explain the absence of a linear relationship between the level of structural DNA divergence and F₁ heterosis, as well as the manifestation of heterosis in crosses of related (genetically similar) accessions.

1. Ashikawa I. Surveying CpG methylation at 5'-CCGG in the genomes of rice cultivars. Plant Mol. Biol. 2001;45:31-39. DOI 10.1023/A:1006457321781.

2. Becker C., Hagmann J., Muller J., Koenig D., Stegle O., Borgwardt K., Weigel D. Spontaneous epigenetic variation in the Arabidopsis thali-ana methylome. Nature. 2011;480(7376):245-249. DOI 10.1038/nature10555.

3. Becker C., Weigel D. Epigenetic variation: origin and transgenerational inheritance. Curr. Opin. Plant Biol. 2012;15(5):562-567. DOI 10.1016/j.pbi.2012.08.004.

4. Bruce A.B. The Mendelian theory of heredity and the augmentation of vigor. Science. 1910;32:627-628. DOI 10.1126/science.32.827.627-a.

5. Charlesworth D., Willis J. The genetics of inbreeding depression. Nat. Rev. Genet. 2009;10:783-796. DOI 10.1038/nrg2664.

6. Chodavarapu R.K., Feng S., Ding B., Simon S.A., Lopez D., Jia Y., Wang G.L., Meyers B.C., Jacobsen S.E., Pellegrini M. Transcriptome and methylome interactions in rice hybrids. Proc. Natl. Acad. Sci. USA. 2012;109(30):12040-12045. DOI 10.1073/pnas.1209297109.

7. Crabb A.R. The Hybrid-Corn Makers: Prophets of Plenty. New Brunswick, NJ: Rutgers Univ. Press, 1947.

8. East E.M., Hayes H.K. Heterozygosis in evolution and in plant breeding. U.S. Dept. Agric. Plant Industr. Bull. 1912;243:1879-1938. DOI 10.5962/bhl.title.119161.

9. Greaves I.K., Gonzalez-Bayon R., Wang L., Zhu A., Liu P.-Ch., Grosz -mann M., Peacock W.J., Dennis E.S. Epigenetic changes in hybrids. Plant Physiol. 2015;168(4):1197-1205. DOI 10.1104/pp.15.00231.

10. Groszmann M., Greaves I., Albertyn Z., Scofield G., Peacock W., Dennis E. Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc. Natl. Acad. Sci. USA. 2011;108:2617-2622. DOI 10.1073/pnas.1019217108.

11. Gutierrez O.A., Basu S., Saha S., Jenkins J.N., Shoemaker D.B., Cheathman C.L., McCarty J.C. Genetic distance among selected cotton genotypes and its relationship with F2 performance. Crop Sci. 2002;42:1841-1847. DOI 10.2135/cropsci2002.1841.

12. He G., He H., Deng X.W. Epigenetic variations in plant hybrids and their potential roles in heterosis. J. Genet. Genomics. 2013;40:205-210. DOI 10.1016/j.jgg.2013.03.011.

13. Jones D. Dominance of linked factors as a means of accounting for heterosis. Proc. Natl. Acad. Sci. USA. 1917;3(4):310-312. DOI 10.1073/pnas.3.4.310.

14. Kaeppler Sh. Heterosis: Many genes, many mechanisms - end the search for an undiscovered unifying theory. ISRN Botany. 2012;Ar-ticle ID:682824. DOI 10.5402/2012/682824.

15. Kawamura K., Kawanabe T., Shimizua M., Naganoc A.J., Saeki N., Okazaki K., Kaji M., Dennis E.S., Osabe K., Fujimoto R. Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis. Plant Gene. 2016;5:1-7. DOI 10.1016/j.plgene.2015.10.003.

16. Kawanabe T., Ishikura S., Miyaji N., Sasaki T., Wu L.M., Itabashi E., Takada S., Shimizu M., Takasaki-Yasuda T., Osabe K., Peacock W.J., Dennis E.S., Fujimoto R. Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA. 2016:E6704-E6711. DOI 10.1073/pnas.1613372113.

17. Krieger U., Lippman Z.B., Zamir D. The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat. Genet. 2010;42:459-463. DOI 10.1038/ng.550.

18. Lauria M., Piccinini S., Pirona R., Lund G., Viotti A., Motto M. Epigenetic variation, inheritance, and parent-of-origin effects of cytosine methylation in maize (Zea mays). Genetics. 2014;96(3):653-666. DOI 10.1534/genetics.113.160515.

19. Lee S., Nahm H., Kim Y.M., Kim D.D. Characterisation and molecular genetic mapping of microsatellite loci in pepper. Theor. Appl. Genet. 2004;108:619-627. DOI 10.1007/s00122-003-1467-x.

20. Li Q., Li Y., Moose S.P., Hudson M.E. Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants. BMC Plant Biol. 2015;15:168. DOI 10.1186/s12870-015-0549-7.

21. Melchinger A.E. Genetic diversity and heterosis. In: Coors J.G., Stuab J.E. (Eds.). The Genetics and Exploitation of Heterosis and Crop Plants. Crop Sci. Soc. of America, Madison, 1999:99-118.

22. Mimura Y., Inoue T., Minamiyama Y., Kubo N. An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps. Breed. Sci. 2012;62(1):93-98. DOI 10.1270/jsbbs.62.93.

23. Minamiyama Y., Tsuro M., Hirai M. An SSR-based linkage map of Capsicum annuum. Mol. Breed. 2006;18(2):157. DOI 10.1007/s11032-006-9024-3.

24. Nei M., Li M.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA. 1979;76(10):5269-5273. DOI 10.1073/pnas.76.10.5269.

25. Nei M., Tajima F., Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J. Mol. Evol. 1983; 19:153-170. DOI 10.1007/BF01840887.

26. Ong-Abdullah M., Ordway J.M., Jiang N., ... Alwee S.S., Sambant-hamurthi R., Martienssen R.A. Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature. 2015;525(7570):533-537. DOI 10.1038/nature15365.

27. Perenzin M., Corbellini M., Accerbi M., Vaccino P., Borghi B. Bread wheat: Fj hybrid performance and parental diversity estimates using molecular markers. Euphytica. 1998;100:273-279. DOI 10.1023/A:1018324811038.

28. Reif J.C., Hahn V., Melchinger A.E. Genetic bases of heterosis and prediction of hybrid performance. Helia. 2012;35(57):1-8. DOI 10.2298/hel1257001r.

29. Reyna-Lopez G.E., Simpson J., Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol. Gen. Genet. 1997;253(6):703-710. DOI 10.1007/s004380050374.

30. Ryder P., McKewon C., Fort A., Spillane Ch. Epigenetics and heterosis in crop plants. In: Epigenetics in Plants of Agronomic Importance: Fundamental and Applications. Springer, Cham, 2014;13-31. DOI 10.1007/978-3-319-07971-4_2.

31. Sanghera G.S., Wani S.H., Hussain W., Shafi W., Haribhushan A., Singh N.B. The magic of heterosis: New tools and complexities. Nat. Sci. 2011;9(11):42-53.

32. Schrag T.A., Mohring J.M., Maurer H.P., Dhillon B.S., Melchinger A.E., Piepho H.-P., S0rensen A.P., Frisch M. Molecular marker-based prediction of hybrid performance in maize using unbalanced data from multiple experiments with factorial crosses. Theor. Appl. Genet. 2009;118:741-751. DOI 10.1007/s00122-008-0934-9.

33. Shen H., He H., Li J., Chen W., Wang X., Guo L., Peng Z., He G., Zhong S., Qi Y., Terzaghi W., Deng X.W. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell. 2012;24(3):875-892. DOI 10.1105/tpc.111.094870.

34. Shpak E.D., Berthiaume C.T., Hill E.J., Torii K.U. Synergistic interaction of three ERECTA-family receptor-like kinases controls Ara-bidopsis organ growth and flower development by promoting cell proliferation. Development. 2004;131(7):1491-1501. DOI 10.1242/dev.01028.

35. Shull G.H. The composition of a field of maize. J. Hered. 1908;4:296-301. DOI 10.1093/jhered/os-4.1.296.

36. Shull G.H. Beginnings of the heterosis concept. In: Gowen J.W. (Ed.). Heterosis. Ames, IA, Iowa State College Press, 1952;14-48.

37. Singh R., Low E.-T., Ooi L., ... Ordway J.M., Sambanthamurthi R., Martienssen R.A. The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature. 2013;500:340-344. DOI 10.1038/nature12356.

38. Springer N., Stupar R. Allelic variation and heterosis in maize: How do two halves make more than whole? Genome Res. 2007;17:264-275. DOI 10.1101/gr.5347007.

39. Swanson-Wagner R.A., Jia Y., DeCook R., Borsuk L.A., Nettleton D., Schnable P.S. All possible modes of gene action are observed in a global comparison of gene expression in a maize Fj hybrid and its inbred parents. Proc. Natl. Acad. Sci. USA. 2006;103(18):6805-6810. DOI 10.1073/pnas.0510430103.

40. Tsaftaris A.S., Kafka M., Polidoros A., Tani E. Epigenetic changes in maize DNA and heterosis. In: Abstracts of the Int. Symp. on “The Genetics and Exploitation of Heterosis in Crops”. Mexico City, 1997;112-113.

41. Usatov A.V., Klimenko A.I., Azarin K.V., Gorbachenko O.F., Markin N.V., Tikhobaeva V.E., Kolosov Yu.A., Usatova O.A., Ba-koev S., Makarenko M., Getmantseva L. The relationships between heterosis and genetic distances based on SSR markers in Heliantus annuus. Am. J. Agric. Biol. Sci. 2014;9(3):270-276. DOI 10.3844/ajabssp.2014.270.276.

42. Vergeer P., Wagemaker N., Ouborg N.J. Evidence for an epigenetic role in inbreeding depression. Biol. Lett. 2012;8(5):798-801. DOI 10.1098/rsbl.2012.0494.

43. Xu W., Virmani S.S., Hernandez J.E., Sebastian L.S., Redona E.D., Li Zh. Genetic diversity in the parental lines and heterosis of the tropical rice hybrids. Euphytica. 2002;127:139-148. DOI 10.1023/A:1019960625003.

44. Zhang M., Kimatu J.N., Xu K., Liu B. DNA cytosine methylation in plant development. J. Genet. Genomics. 2010;37:1-12. DOI 10.1016/S1673-8527(09)60020-5.