SUMMARY. Peach is one of the most important fruit crops, cultivation of which held the third largest areas among all fruit crops, grown in temperate climate zone. Cultivation of this crop under less favourable clime conditions would require the creation of new resistant genotypes via the intra- or interspecific hybridization, including crossing with almond. Efficient breeding of hybrids and their long-term selection will require a rapid and accurate method of genetic barcoding that would be able to distinguish closely-related genotypes or to detect interspecific hybrids. One such approaches is TBP-analysis, which is based on the evaluation of intron length polymorphism of β-tubulin genes. However, the correct interpretation of the results of such an analysis should be based on data on the diversity of β-tubulin genes panel in the genomes of the analyzed species. Thus, here we report on the successful whole-genome identification and on comprehensive analysis of the phylogeny and synteny of the β-tubulin genes of P. persica and P. dulcis, as well as we demonstrate the the possibility to use such data of the genomic search for interpretation of data of TBP genotyping of intra- and interspecific hybrids of peach and almond species. In general, 11 β-tubulin genes were indentified within the P. persica genome, and 10 genes, in the P. dulcis genome, accounting pseudogenes. Additionally, phylogenetic and synteny analyses of the identified genes made it possible to identify the orthologues in the genomes of A. thaliana and A. lyrata, as well as to designate identified β-tubulins to specific isotypes. Genotyping via the TBP-method allowed obtaining distinct molecular profiles for 11 investigated accessions, among which 8 were intra- or interspecific hybrids. Based on obtained results of genotyping, a cluster analysis was carried out, the results of which correlated well with the breeding history of the analysed genotypes, what additionally confirmed the effectiveness and accuracy of the genotyping approach used.
Keywords: peach, almond, interspecific hybrids, ILP, tubulin genes, genotyping, pathogen resistance
Full text and supplemented materials
References
Alioto, T., Alexiou, K.G., Bardil, A., et al., Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence, Plant J., 2020, vol. 101, pp. 455–472. https://doi.org/10.1111/tpj.14538
Altschul, S.F., Basic local alignment search tool, J. Mol. Biol., 1990, vol. 215, no. 3, pp. 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Altschul, S.F., A protein alignment scoring system sensitive at all evolutionary distances, J. Mol. Evol., 1993, vol. 36, no. 3, pp. 290–300. https://doi.org/10.1007/BF00160485
Aranzana, M.J., Garcia-Mas, J., Carbo, J., and Arús, P., Development and variation analysis of microsatellite markers in peach, Plant Breed, 2002, vol. 121, no. 1, pp. 87–92. https://doi.org/10.1046/j.1439-0523.2002.00656.x
Bardini, M., Lee, D., Donini, P., et al., Tubulin based polymorphism (TBP): a new tool, based on functionally relevant sequences, to assess genetic diversity in plant species, Genome, 2004, vol. 47, no. 2, pp. 281–291.https://doi.org/10.1139/g03-132
Benbouza, H., Jean-Marie, J., and Jean-Pierre, B., Otimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels, Biotechnol. Agron. Soc. Environ., 2006, vol. 10, pp. 77–81.
Blume, R.Y., Rabokon, A.N., Postovitova, A.S., et al., Evaluating diversity and breeding perspectives of Ukrainian spring camelina genotypes, Cytol. Genet., 2020, vol. 54, no. 5, pp. 420–436. https://doi.org/10.3103/S0095452720050084
Blume, Ya.B., A journey through plant cytoskeleton: hot spots in signalling and functioning, Cell Biol. Int., 2019, vol. 43, no. 9, pp. 978–982. https://doi.org/10.1002/cbin.11210
Braglia, L., Gavazzi, F., Morello, L., et al., On the applicability of the Tubulin-Based Polymorphism (TBP) genotyping method: a comprehensive guide illustrated through the application on diferent genetic resources in the legume family, Plant Methods, 2020, vol. 16, p. 86. https://doi.org/10.1186/s13007-020-00627-z
Braglia, L., Lauria, M., Appenroth, K.J., et al., Duckweed species genotyping and interspecific hybrid discovery by tubulin-based polymorphism fingerprinting, Front. Plant Sci., 2021, vol. 12, p. 625670.
Breviario, D., Baird, W.V., Sangoi, S., et al., High polymorphism and resolution in targeted fingerprinting with combined β-tubulin introns, Mol. Breed., 2007, vol. 20, no. 3, pp. 249–259. https://doi.org/10.1007/s11032-007-9087-9
Breviario, D., Giani, S., and Morello, L., Multiple tubulins: evolutionary aspects and biological implications, Plant J., 2013, vol. 75, no. 2, pp. 202–218. https://doi.org/10.1111/tpj.12243
Chen, C., Chen, H., Zhang, Y., et al., TBtools: An integrative toolkit developed for interactive analyses of big biological data, Mol. Plant, 2020, vol. 13, no. 8, pp. 1194–1202. https://doi.org/10.1016/j.molp.2020.06.009
Chen, B., Zhao, J., Fu, G., et al., Identification and expression analysis of Tubulin gene family in upland cotton, J. Cotton Res., 2021, vol. 4, p. 20. https://doi.org/10.1186/s42397-021-00097-1
Dar, R.A., Rai, A.N., and Shiekh, I.A., Stigmina carpophyla detected on Prunus americana and Prunus persica in India, Australas. Plant Dis. Notes, 2017, vol. 12, p. 19. https://doi.org/10.1007/s13314-017-0245-6
Didur, O., Kulbachko, Y., Ovchynnykova, Y., et al., Zoogenic mechanisms of ecological rehabilitation of urban soils of the park zone of megapolis: Earthworms and soil buffer capacity, Environ. Res. Eng. Manage., 2019, vol. 75, no. 1, pp. 24–33. https://doi.org/10.5755/j01.erem.75.1.21121
Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acid Res., 2004, vol. 32, no. 5, pp. 1792–1797. https://doi.org/10.1093/nar/gkh340
Findeisen, P., Muhlhausen, S., Dempewolf, S., et al., Six subgroups and extensive recent duplications characterize the evolution of the eukaryotic tubulin protein family, Genome Biol. Evol., 2014, vol. 6, no. 9, pp. 2274–2288. https://doi.org/10.1093/gbe/evu187
Gasanov, E., Jędrychowska, J., Kuźnicki, J., and Korzh, V., Evolutionary context can clarify gene names: Teleosts as a case study, BioEssays, 2021, vol. 43, no. 6, p. e2000258. https://doi.org/10.1002/bies.202000258
Gavazzi, F., Pigna, G., Braglia, L., et al., Evolutionary characterization and transcript profiling of beta-tubulin genes in flax (Linum usitatissimum L.) during plant development, BMC Plant Biol., 2017, vol. 17, p. 237. https://doi.org/10.1186/s12870-017-1186-0
Gertz, E.M., Yu, Y.K., Agarwala, R., et al., Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST, BMC Biol., 2006, vol. 4, p. 41. https://doi.org/10.1186/1741-7007-4-41
Guadalupi, C., Braglia, L., Gavazzi, F., et al., A combinatorial Q-Locus and tubulin-based polymorphism (TBP) approach helps in discriminating Triticum species, Genes, 2022, vol. 13, no. 4, p. 633. https://doi.org/10.3390/genes13040633
Henikoff, S. and Henikoff, J.G., Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci. U. S. A., 1992, vol. 89, no. 22, pp. 10915–10919. https://doi.org/10.1073/pnas.89.22.10915
Hu, B., GSDS 2.0: an upgraded gene feature visualization server, Bioinformatics, 2015, vol. 31, no. 8, pp. 1296–1297. https://doi.org/10.1093/bioinformatics/btu817
Jung, S. and Main, D., Genomics and bioinformatics resources for translational science in Rosaceae, Plant Biotechnol. Rep., 2014, vol. 8, no. 2, pp. 49–64. https://doi.org/10.1007/s11816-013-0282-3
Khokhryakova, A., Classification and characteristic of soils in urban areas (on the example of Odessa city), EUREKA: Life Sci., 2020, vol. 5, pp. 3–15. https://doi.org/10.21303/2504-5695.2020.001404
Khromykh, N.O., Lykholat, Y.V., Kovalenko, I.M., et al., Variability of the antioxidant properties of Berberis fruits depending on the plant species and conditions of habitat, Regul. Mechanisms Biosyst., 2018a, vol. 9, no. 1, pp. 56–61. https://doi.org/10.15421/021807
Khromykh, N., Lykholat, Y., Shupranova, L., et al., Interspecific differences of antioxidant ability of introduced Chaenomeles species with respect to adaptation to the steppe zone conditions, Biosyst. Diversity, 2018b, vol. 26, no. 2, pp. 132–138. https://doi.org/10.15421/011821
Khromykh, N.O., Lykholat, Y.V., Anishchenko, A.A., et al., Cuticular wax composition of mature leaves of species and hybrids of the genus Prunus differing in resistance to clasterosporium disease, Biosyst. Diversity, 2020, vol. 28, no. 4, pp. 370–375. https://doi.org/10.15421/012047
Kumar, S., Stecher, G., Li, M., et al., MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096
Li, S., Cao, P., Wang, C., et al., Genome-wide analysis of tubulin gene family in cassava and expression of family member FtsZ2-1 during various stress, Plants, 2021, vol. 10, no. 4, p. 668. https://doi.org/10.3390/plants10040668
Lykholat, Y.V., Khromykh, N.O., Didur, O.O., et al., Features of the fruit epicuticular waxes of Prunus persica cultivars and hybrids concerning pathogens susceptibility, Ukr. J. Ecol., 2021, vol. 11, no. 1, pp. 261–266. https://doi.org/10.15421/2021_238
Morimoto, T., Inaoka, M., Banno, K., Itai, A., Genetic mapping of a locus controlling the intergeneric hybridization barrier between apple and pear, Tree Genet. Genomes, 2020, vol. 16, p. 5. https://doi.org/10.1007/s11295-019-1397-7
Nei, M., Genetic distance between populations. Am. Nat., 1972, vol. 106, pp. 283–292. https://doi.org/10.1086/282771
Nei, M. and Li, W.H., Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc. Natl. Acad. Sci. U. S. A., 1979, vol. 76, no. 10, pp. 5269–5273. https://doi.org/10.1073/pnas.76.10.5269
Oakley, R.V., Wang, Y.S., Ramakrishna, W., et al., Differential expansion and expression of α- and β- gene families in Populus, Plant Physiol., 2007, vol. 145, no. 3, pp. 961–973. https://doi.org/10.1104/pp.107.107086
Pavlíček, A., Hrdá, Š., and Flegr, J., FreeTree – Freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of the genus Frenkelia, Folia Biol., 1999, vol. 45, pp. 97–99.
Pirko, N.N., Demkovych, A.Y., Kalafat, L.O., et al., Intron length polymorphism of β-tubulin genes in different representatives of Pinaceae Lindl. family, Revista Botanică, 2016, vol. VIII, no. 2/13, pp. 5–9.
Pydiura, N., Pirko, Y., Galinousky, D., et al., Genome-wide identification, phylogenetic classification, and exon-intron structure characterization of the tubulin and actin genes in flax (Linum usitatissimum), Cell Biol. Int., 2019, vol. 43, no. 9, pp. 1010–1019. https://doi.org/10.1002/cbin.11001
Rabokon, A.N., Pirko, Y.V., Demkovych, A.Y., et al., Comparative analysis of the efficiency of intron-length polymorphism of β-tubulin genes and microsatellite loci for flax varieties genotyping, Cytol. Genet., 2018, vol. 52, no. 1, pp. 1–10. https://doi.org/10.3103/S0095452718010115
Radchuk, V.V., The transcriptome of the tubulin gene family in plants, in The Plant Cytoskeleton: a Key Tool for Agro-Biotechnology, Blume, Y.B., Baird, W.V., Yemets, A.I., Breviario, D., Eds., New York: Springer-Verlag, 2008, pp. 219–241. https://doi.org/10.1007/978-1-4020-8843-8_11
Rao, G., Zeng, Y., He, C., and Zhang, J., Characterization and putative post-translational regulation of α- and β-tubulin gene families in Salix arbutifolia, Sci. Rep., 2016, vol. 6, p. 19258. https://doi.org/10.1038/srep19258
Sambrook, J. and Russel, D.W., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Laboratory, 2001, vol. 2.
Spokevicius, A.V., Southerton, S.G., MacMillan, C.P., et al., β-Tubulin affects cellulose microfibril orientation in plant secondary fibre cell walls, Plant J., 2007, vol. 51, no. 4, pp. 717–726. https://doi.org/10.1111/j.1365-313x.2007.03176.x
Stöcker, M., Jordi, G.M., Arús, P., et al., A highly conserved α-tubulin sequence from Prunus amygdalus, Plant Mol. Biol., 1993, vol. 22, pp. 913–916. https://doi.org/10.1007/BF00027377
Swarbreck, D., Wilks, C., Lamesch, P., et al., The Arabidopsis Information Resource (TAIR): gene structure and function annotation), Nucleic Acid Res., 2008, vol. 36, no. 1, pp. 1009–1014. https://doi.org/10.1093/nar/gkm965
Thurow, L.B., Raseira, M.C.B., Bonow, S., et al., Population genetic analysis of brazilian peach breeding germplasm, Rev. Bras. Frutic., 2017, vol. 39, no. 5, p. 166. https://doi.org/10.1590/0100-29452017166
Verde, I., Jenkins, J., Dondini, L., et al., The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity, BMC Genomics, 2017, vol. 18, no. 1, p. 225. https://doi.org/10.1186/s12864-017-3606-9
Wang, Y., Tang, H., Debarry, J.D., et al., MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity, Nucleic Acids Res., 2012, vol. 40, no. 7, p. e49. https://doi.org/10.1093/nar/gkr1293
Yemets, A., Radchuk, V., Bayer, O., et al., Development of transformation vectors based upon a modified plant α-tubulin gene as the selectable marker, Cell Biol. Int., 2008, vol. 32, no. 5, pp. 566–570. https://doi.org/10.1016/j.cellbi.2007.11.012
Zacchino, S.A., Butassi, E., Liberto, M.D., et al., Plant phenolics and terpenoids as adjuvants of antibacterial and antifungal drugs, Phytomedicine, 2017, vol. 37, pp. 27–48. https://doi.org/10.1016/j.phymed.2017.10.018
Zhang, J., Li, Y., Shi, G., et al., Characterization of α-tubulin gene distinctively presented in a cytoplasmic male sterile and its maintainer line of non-heading Chinese cabbage, J. Sci. Food Agric., 2009, vol. 89, no. 2, pp. 274–280. https://doi.org/10.1002/jsfa.3438