Marker-assisted selection and protein identification in Eucalyptus

Authors

DOI:

https://doi.org/10.33448/rsd-v11i6.29227

Keywords:

Bibliometrics; Forest improvement; MAS; Teaching.

Abstract

Marker-assisted selection aims to improve quantitative traits in Eucalyptus, and molecular markers allow the identification of (the expression) of challenging alleles. Aiming to overcome this challenge our work presents a systematic review of the use of marker-assisted selection and candidate proteins to identify markers associated with traits of Eucalyptus. The research carried out a prospection of content obtained by keywords in the scientific databases Scopus and Web of Science. The bibliographic data generated was imported using the Bibliometrix package in R software. The nucleic acid sequences were prospected in the Genetic Sequence Database – GenBank. The proteins were prospected in UNIPROT and the 3D structures were obtained at the Swiss Bioinformatics Institute - SIB. The prospection resulted in 63 scientific articles after duplicates were removed, from 41 journals, with an average publication of 12.4 articles per year and an average of 25.2 citations per document. China and Brazil stand out in the number of publications. RAPD technique was the most used in studies to obtain alleles with traits of interest in Eucalyptus. The ISSR and SSR markers were highlighted for studies on genotype resistance. The sequences associated with resistance to galling organisms in Eucalyptus are related to TAC1 transcription regulatory proteins, mediator 2; zinc finger protein 11, associated with the expressed genes TAC1, At5g64680, and ZFP11.

References

Agarwal, M., Shrivastava, N., & Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27(4), 617-631. https://doi.org/10.1007/s00299-008-0507-z

Arcade, A., Faivre-Rampant, P., Pâques, L. E., & Prat, D. (2002). Localisation of genomic regions controlling microdensitometric parameters of wood characteristics in hybrid larches. Annals of Forest Science, 59(5-6), 607-615. https://doi.org/10.1051/forest:2002046

Ballesta, P., Mora, F., Ruiz, E., & Contreras-Soto, R. (2015). Marker-trait associations for survival, growth, and flowering components in Eucalyptus cladocalyx under arid conditions. Biologia plantarum, 59(2), 389-393.

Bandaranayake, C. K., & Kearsey, M. J. (2005). Genome mapping, QTL analysis and MAS: Importance, principle, constraints and application in coconut. Plant Genetic Resources Newsletter, (142), 47.

Chagné, D., Batley, J., Edwards, D., & Forster, J. W. (2007). Single Nucleotide Polymorphism Genotyping in Plants. In: Oraguzie, N. C., Rikkerink, E. H. A., Gardiner, S. E., Silva, H. N. (eds) Association Mapping in Plants. Springer, New York, NY. https://doi.org/10.1007/978-0-387-36011-9_5

Contreras-Soto, R., Ballesta, P., Ruiz, E., & Mora, F. (2016). Identification of ISSR markers linked to flowering traits in a representative sample of Eucalyptus cladocalyx. Journal of forestry research, 27(2), 239-245.

Domingues, S. D., Neves, A. F., Mangolin, C. A., & Machado, M. F. P. S. (2017). Seleção de primers para análise de Inter Simple Sequence Repeats (ISSR) em Cereus sp. (Cactaceae) Selection of primers for Inter Simple Sequence Repeats (ISSR) in Cereus sp.(Cactaceae). Revista Biotecnologia & Ciência v, 6(2), 46-54.

e-Plant. (2022). The bio-analytic resource for plant biology. Recovered in jan, 22, 2022 of http://bar.utoronto.ca/

Farro, A. P., Bortoloto, T. M., Oda, S., Mello, E., & Marino, C. L. (2013). Identification of molecular marker linked to early flowering in Eucalyptus grandis. Rev Ins Fla, (24), 149-157.

Food and Agriculture Organization of the United Nations. (2021). Eucalyptus Species. Recovered in jan, 22, 2022 of http://www.fao.org/3/AC121E/ac121e04.htm

Freeman, J. S., Potts, B. M., Downes, G. M., Pilbeam, D., Thavamanikumar, S., & Vaillancourt, R. E. (2013). Stability of quantitative trait loci for growth and wood properties across multiple pedigrees and environments in Eucalyptus globulus. New Phytologist, 198(4), 1121-1134.

Freeman, J. S., Whittock, S. P., Potts, B. M., & Vaillancourt, R. E. (2009). QTL influencing growth and wood properties in Eucalyptus globulus. Tree Genetics & Genomes, 5(4), 713-722.

Fuchs, M. C. P., Tambarussi, E. V., Lourenção, J. C., Nogueira, L. M., Bortoloto, T. M., González, E. R., Oda, S., & Marino, C. L. (2015). Molecular marker associated with a deleterious recessive anomaly in Eucalyptus grandis seedlings. Annals of Forest Science, 72(8), 1043–1052. https://doi.org/10.1007/s13595-015-0502-9

Gan, S., Shi, J., Li, M., Wu, K., Wu, J., & Bai, J. (2003). Moderate-density molecular maps of Eucalyptus urophylla S. T. Blake and E. tereticornis Smith genomes based on RAPD markers. Genetica, 118(1), 59-67. https://doi.org/10.1023/A:1022966018079

Goetze, M., Passaia, G., & Sperb-Ludwig, F. (2017). Marcadores moleculares baseados em restrição: AFLP e suas variações. In Marcadores Moleculares na Era genômica: Metodologias e Aplicações (p.181). Recovered in jan, 22, 2022 of https://www.lume.ufrgs.br/bitstream/handle/10183/206114/001056131.pdf?sequence=1%0Ahttps://www.sbg.org.br/sites/default/files/e_book_marcadores_moleculares_sbg_2017_final.pdf

Gomes, C. A. F. C., Pereira, F. B., De Oliveira Garcia, F. A., Garret, A. T. D. A., De Siqueira, L., & Tambarussi, E. V. (2019). Inoculation of Ceratocystis fimbriata ellis & halsted in Eucalyptus spp. And evaluation pf genetic diversity by ISSR markers. Scientia Forestalis/Forest Sciences, 47(123), 579-587. https://doi.org/10.18671/scifor.v47n123.19

Grattapaglia, D., Bertolucci, F. L. G., Penchel, R., & Sederoff, R. R. (1996). Genetic mapping of quantitative trait loci controlling growth and wood quality traits in Eucalyptus grandis using a maternal half-sib family and RAPD markers. Genetics, 144(3), 1205-1214.

Grattapaglia, D., Ribeiro, V. J., & Rezende, G. D. S. P. (2004). Retrospective selection of elite parent trees using paternity testing with microsatellite markers: An alternative short term breeding tactic for Eucalyptus. Theoretical and Applied Genetics, 109(1), 192-199. https://doi.org/10.1007/s00122-004-1617-9

Hall, T. M. Multiple modes of RNA recognition by zinc finger proteins. Curr Opin Struct Biol. 15(3):367-373. 2005.

Jaccoud, D., Peng, K., Feinstein, D., & Kilian, A. (2001). Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Research, 29(4), 25. https://doi.org/10.1093/nar/29.4.e25

Jaleta, D., Mbilinyi, B., Mahoo, H., & Lemenih, M. (2016). Eucalyptus Expansion as Relieving and Provocative Tree in Ethiopia. Journal of Agriculture and Ecology Research International, 6(3), 1-12.

Kumar, P., Gupta, V., Misra, A., Modi, D., & Pandey, B. (2009). Potential of Molecular Markers in Plant Biotechnology. Plant Omics, 2(4), 141–162.

Laity, J. H., Lee, B. M., & Wright, P. E. (2001). Zinc finger proteins: new insights into structural and functional diversity. Current opinion in structural biology, 11(1), 39-46.

Lee, S. H., Clark, S., & Werf, J. H. J. V. D. (2017). Estimation of genomic prediction accuracy from reference populations with varying degrees of relationship. PLoS ONE, 12(12), 1-22. https://doi.org/10.1371/journal.pone.0189775

Li, F., Zhou, C., Weng, Q., Li, M., Yu, X., Guo, Y., Wang, Y., Zhang, X., & Gan, S. (2015). Comparative genomics analyses reveal extensive chromosome colinearity and novel quantitative trait loci in eucalyptus. PLoS ONE, 10(12). https://doi.org/10.1371/journal.pone.0145144

Maldonado, C., Contreras-Soto, R. I., Gerhardt, I. F. S., Amaral, A. T. Jr., & Mora, F. (2018). Stable marker-trait associations for growth across different ages in Eucalyptus cladocalyx through the use of microsatellites. Scientia Forestalis, 46(119). https://doi.org/10.18671/scifor.v46n119.04

Marques, C. M., Vasquez-Kool, J., Carocha, V. J., Ferreira, J. G., O’Malley, D. M., Liu, B. H., & Sederoff, R. (1999). Genetic dissection of vegetative propagation traits in Eucalyptus tereticornis and E. globulus. Theoretical and Applied Genetics, 99(6), 936-946. https://doi.org/10.1007/s001220051400

Matthews, J. M., & Sunde, M. (2002). Zinc fingers‐‐folds for many occasions. IUBMB life, 54(6), 351-355.

Moher, D., Shamseer, L., Clarke, M., Ghersi, D., Liberati, A., Petticrew, M., & Stewart, L. A. (2015). Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Systematic reviews, 4(1), 1-9. https://doi.org/10.1186/2046-4053-4-1

Mora, F., Arriagada, O., Ballesta, P., & Ruiz, E. (2017). Genetic diversity and population structure of a drought-tolerant species of Eucalyptus, using microsatellite markers. Journal of Plant Biochemistry and Biotechnology, 26(3), 274-281.

Naidoo, S., Külheim, C., Zwart, L., Mangwanda, R., Oates, C. N., Visser, E. A., Wilken, F. E., Mamni, T. B., & Myburg, A. A. (2014). Uncovering the defence responses of eucalyptus to pests and pathogens in the genomics age. Tree Physiology, 34(9), 931-943. https://doi.org/10.1093/treephys/tpu075

Nicolle, D. (2019). Classification of the Eucalypts (Angophora, Corymbia and Eucalyptus). Version 4.

R Core Team. (2020). R: A Language and environment for statistical computing. [Software]. Vienna: R Foundation on Statistical Computing (1.3.1073).

Savelkoul, P. H. M., Aarts, H. J. M., Haas, J., Dijkshoorn, L., Duim, B., Otsen, M., & Lenstra, J. A. (1999). Amplified-fragment length polymorphism analysis: the state of an art. Journal of clinical microbiology, 37(10), 3083-3091.

Shanmugapriya, A., Bachpai, V. K. W., Ganesan, M., & Yasodha, R. (2015). Association analysis for vegetative propagation traits in Eucalyptus tereticornis and Eucalyptus camaldulensis using simple sequence repeat markers. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 85(2), 653-658.

Swiss Institute of Bioinformatics. (2022). The 3D structures of the proteins. Recovered in jan, 22, 2022 of https://www.sib.swiss/

Ribeiro, D. O., Silva-Mann, R., Carvalho, S. V. Á., Souza, E. M. S. D., Vasconcelos, M. C., & Blank, A. F. (2017). Genetic variability in Jatropha curcas L. from diallel crossing. Genetics and Molecular Research, 16(2): gmr16029651.

Rocha, R. B., Barros, E. G., Cruz, C. D., Rosado, A. M., & Araújo, E. F. (2007). Mapping of QTLs related with wood quality and developmental characteristics in hybrids (Eucalyptus grandis x Eucalyptus urophylla). Revista Árvore, 31(1), 13-24. https://doi.org/10.1590/S0100-67622007000100003

Rosado, T. B., Tomaz, R. S., Ribeiro Junior, M. F., Rosado, A. M., Guimarães, L. M. D. S., Araújo, E. F. D., & Cruz, C. D. (2010). Detection of QTL associated with rust resistance using IBD-based methodologies in exogamic Eucalyptus spp. populations. Crop Breeding and Applied Biotechnology, 10, 321-328.

Sansaloni, C., Petroli, C., Jaccoud, D., Carling, J., Detering, F., Grattapaglia, D., & Kilian, A. (2011). Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proceedings, 5(7), 1-2. https://doi.org/10.1186/1753-6561-5-s7-p54

Samal, B., Vanapalli, K. R., Dubey, B. K., Bhattacharya, J., Chandra, S., & Medha, I. (2021). Influence of process parameters on thermal characteristics of char from co-pyrolysis of eucalyptus biomass and polystyrene: Its prospects as a solid fuel. Energy, 232, 121050.

Sarkis-Onofre, R., Catalá-López, F., Aromataris, E., & Lockwood, C. (2021). How to properly use the PRISMA Statement. Systematic Reviews, 10(1), 1-3. https://doi.org/10.1186/s13643-021-01671-z

Silva-Mann, R., Vieira, M. G., Machado, J. C., Bernardino Filho, J. R., Salgado, K. C., & Stevens, M. R. (2005). AFLP markers differentiate isolates of Colletotrichum gossypii from C. gossypii var. cephalosporioides. Fitopatologia Brasileira, 30, 169-172.

Souza, D. C. L. (2015). Técnicas moleculares para caracterização e conservação de plantas medicinais e aromáticas: uma revisão. Revista Brasileira de Plantas Medicinais, 17(3), 495-503. https://doi.org/10.1590/1983-084X/13_071

Souza, G. A., Carvalho, M. R.O., Martins, E. R., Guedes, R. N. C., & Oliveira, L. O. (2008). Diversidade genética estimada com marcadores ISSR em populações brasileiras de Zabrotes subfasciatus. Pesquisa Agropecuária Brasileira, 43(7), 843-849. https://doi.org/10.1590/S0100-204X2008000700008

Thamarus, K., Groom, K., Bradley, A., Raymond, C. A., Schimleck, L. R., Williams, E. R., & Moran, G. F. (2004). Identification of quantitative trait loci for wood and fibre properties in two full-sib pedigrees of Eucalyptus globulus. Theoretical and Applied Genetics, 109(4), 856-864.

Thamarus, K., Groom, K., Murrell, J., Byrne, M., & Moran, G. (2002). A genetic linkage map for Eucalyptus globulus with candidate loci for wood, fiber, and floral traits. Theoretical and Applied Genetics, 104, 379-387.

Theoretical and Applied Genetics. International Journal of Plant Breeding Research. Recovered in jan, 22, 2022 of https://www.springer.com/journal/122/aims-and-scope

Thumma, B.R., Nolan, M.F., Evans, R., & Moran, G. (2005). Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics, 171, 1257-1265.

Trevorah, R. M., Huynh, T., Vancov, T., & Othman, M. Z. (2018). Bioethanol potential of Eucalyptus obliqua sawdust using gamma-valerolactone fractionation. Bioresource Technology, 250, 673-682. https://doi.org/10.1016/j.biortech.2017.11.084

Verhaegen, D., Plomion, C., Gion, J. M., Poitel, M., Costa, P., & Kremer, A. (1997). Quantitative trait dissection analysis in Eucalyptus using RAPD markers: Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages. Theoretical and Applied Genetics, 95(4), 597-608.

Viana, J. M. S., Cruz, C. D., & Barros, E. G. (2012). Genética - Fundamentos. Universidade Federal de Viçosa (2a). Editora UFV.

Waese, J., & Provart, N. J. (2017). “The bio-analytic resource for plant biology,” in Plant Genomics Databases. Humana Press, New York, 119–148.

Williams, J. G., Hanafey, M. K., Rafalski, J. A., & Tingey, S. V. (1993). Genetic analysis using random amplified polymorphic DNA markers. In Methods in enzymology. Academic Press, 218, 704-740.

Young, N. D., Tanksley, S. D. (1989). Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theoret. Appl. Gene Theoretical and Applied Genetics, 77, 95-101. https://doi.org/10.1007/BF00292322

Zhang, M., Zhou, C., Song, Z., Weng, Q., Li, M., Ji, H., Mo, X., Huang, H., Lu, W., Luo, J., Li, F., & Gan, S. (2018). The first identification of genomic loci in plants associated with resistance to galling insects: A case study in Eucalyptus L’Hér. (Myrtaceae). Scientific Reports, 8(1), 1-10. https://doi.org/10.1038/s41598-018-20780-9

Zhang, M., Zhou, C., Song, Z., Weng, Q., Li, M., Ji, H., & Gan, S. (2018). The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér (Myrtaceae). Scientific reports, 8(1), 1-10.

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03/05/2022

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CALAZANS, C. C.; NUNES, V. V. .; SOUZA, J. L.; SANTANA, N. A.; ALMEIDA, F. E. de .; SILVA-MANN, R. Marker-assisted selection and protein identification in Eucalyptus. Research, Society and Development, [S. l.], v. 11, n. 6, p. e45311629227, 2022. DOI: 10.33448/rsd-v11i6.29227. Disponível em: https://rsdjournal.org/index.php/rsd/article/view/29227. Acesso em: 22 nov. 2024.

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Vol. 11 No. 6

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Agrarian and Biological Sciences

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Copyright (c) 2022 Crislaine Costa Calazans; Valdinete Vieira Nunes; Juliana Lopes Souza; Natali Aparecida Santana; Fernanda Evangelista de Almeida; Renata Silva-Mann

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