New validated Eucalyptus SSR markers located in candidate genes involved in growth and plant development
Abstract
Aim of study: To validate and characterize new microsatellites or Simple Sequence Repeats (SSR) markers, located within genomic transcribed sequences related to growth and plant developmental traits, in Eucalyptus species.
Area of study: Eucalyptus species from different Australian origins planted in Argentina.
Materials and methods: In total, 134 SSR in 129 candidate genes (CG-SSR) involved in plant development were selected and physically mapped to the E. grandis reference genome by bioinformatic tools. Experimental validation and polymorphism analysis were performed on 48 individuals from E. grandis and interspecific hybrids (E. grandis x E. camaldulensis; E. grandis x E. tereticornis), E. globulus, E. maidenii, E. dunnii and E. benthamii.
Main results: 131 out of 134 CG-SSR were mapped on the 11 chromosomes of E. grandis reference genome. Most of the 134 analyzed SSR (> 75%) were positively amplified and 39 were polymorphic in at least one species. A search of annotated genes within a 25 kbp up and downstream region of each SSR location retrieved 773 genes of interest.
Research highlights: The new validated and characterized CG-SSR are potentially suitable for comparative QTL mapping, molecular marker-assisted breeding (MAB) and population genetic studies across different species within Symphyomyrtus subgenus.
Keywords: CG-SSR; cross-transferability; EST; eucalypts; microsatellite.
Downloads
References
Acuña C, Fernandez P, Villalba P, García M, Hopp E, Marcucci Poltri S, 2012a. Discovery, validation and in silico functional characterization of EST-SSR markers in Eucalyptus globulus. Tree Genet Genomes 8:289-301. https://doi.org/10.1007/s11295-011-0440-0
Acuña C, Villalba P, Pathauer P, Hopp E, Marcucci Poltri S, 2012b. Characterization of novel microsatellite markers in candidate genes for wood properties for application in functional diversity assessment in Eucalyptus globulus. Electron J Biotechnol 15 (2): 12-28. https://doi.org/10.2225/vol15-issue2-fulltext-3
Acuña C, Villalba P, Hopp E, Marcucci Poltri S, 2014. Transferability of microsatellite markers located in candidate genes for wood properties between Eucalyptus species. Forest Systems 2014 23(3): 506-512. https://doi.org/10.5424/fs/2014233-05279
Aguirre N, Filippi C, Zaina G, Rivas J, Acuña C, Villalba P, García M, González S, Rivarola M, Martínez M, et al., 2019. Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden. Agronomy 2019, 9, 484. https://doi.org/10.3390/agronomy9090484
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al., 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29. https://doi.org/10.1038/75556
Azpilicueta MM, El Mujtar VA, Gallo L, 2016. A Searching for molecular insight on hybridization in Nothofagus spp. forests at Lagunas de Epulauquen, Argentina. Bosque 2016, 37(3), 591-601. https://doi.org/10.4067/S0717-92002016000300016
Bauhus J, van der Meer P and Kanninen M, 2010. Ecosystem goods and services from plantation forests. London, Great Brittain: Earthscan. 254 pp. (Earthscan forest library). https://doi.org/10.4324/9781849776417
Bechtold U, Feld B, 2018. Molecular mechanisms controlling plant growth during abiotic stress. J Exp Bot 69 (11): 2753-2758. https://doi.org/10.1093/jxb/ery157
Boerjan W, Ralph J, Baucher M, 2003. Lignin Biosynthesis. Annu Rev Plant Biol 54 (1):519-546. https://doi.org/10.1146/annurev.arplant.54.031902.134938
Cappa EP, Klápště J, Garcia, MN, Villalba PV, Marcucci Poltri, SN, 2016. SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters: precision from a small half-sib sample population of Eucalyptus grandis. Mol Breeding 36:97. https://doi.org/10.1007/s11032-016-0522-7
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M, 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676. https://doi.org/10.1093/bioinformatics/bti610
Du Q, Lu W, Quan M, Xiao L, Song F, Li P, Zhou D, Xie J, Wang L, Zhang D, 2018. Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects. Front Plant Sci 29: 1912. https://doi.org/10.3389/fpls.2018.01912
Faria DA, Mamani EMC, Pappas MR, Pappas jr GJ, Grattapaglia D, 2010. A selected set of EST-derived microsatellites, polymorphic and transferable across 6 species of Eucalyptus. J Hered 101: 512-520. https://doi.org/10.1093/jhered/esq024
Faria DA, Mamani EMC, Pappas GJ, Grattapaglia D, 2011. Genotyping systems for Eucalyptus based on tetra-, penta-, and hexanucleotide repeat EST microsatellites and their use for individual fingerprinting and assignment tests. Tree Genet Genomes 7, 63-77. https://doi.org/10.1007/s11295-010-0315-9
Foucart C, Paux E, Ladouce N, San-Clemente H, Grima-Pettenati J, Sivadon P, 2006. Transcript profiling of a xylem vs phloem cDNA subtractive library identifies new genes expressed during xylogenesis in Eucalyptus. New Phytol 170: 739-752. https://doi.org/10.1111/j.1469-8137.2006.01705.x
Gion J, Chaumeil P, Plomion C, 2015. EucaMaps: linking genetic maps and associated QTLs to the Eucalyptus grandis genome. Tree Genet Genomes 11, 795. https://doi.org/10.1007/s11295-014-0795-0
Govindan M, 2005. Eucalyptus: the Genus Eucalyptus. Edited by John J. W. Coppen (Natural Resources Institute, University of Greenwich, UK). Taylor and Francis, London. 2002. ISBN 0-415-27879-1. J. Nat. Prod. 68: 151-152. https://doi.org/10.1021/np0307789
Grattapaglia D, Mamani E, Silva-Junior O, Faria D, 2015. A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence. Mol Ecol Resour 15 (2): 437-448. https://doi.org/10.1111/1755-0998.12317
Gudeta TB, 2018. Molecular marker based genetic diversity in forest tree populations. Forest Res Eng Int J. 18;2(4):176-182. https://doi.org/10.15406/freij.2018.02.00044
He X, Wang Y, Li F, Weng Q, Li M, Xu L A, Gan S, 2012. Development of 198 novel EST-derived microsatellites in Eucalyptus (Myrtaceae). Am J Bot 99(4), e134-e148. https://doi.org/10.3732/ajb.1100442
Hodel RGJ, Segovia-Salcedo MC, Landis JB, Crowl AA, Sun M, Liu X, Gitzendanner MA, Douglas NA, Germain-Aubrey CC, Chen S, Soltis, D E, Soltis PS, 2016. The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century. Appl Plant Sci 4(6): 1600025. https://doi.org/10.3732/apps.1600025
Jia Z, Zhao B, Liu S, Lu Z, Chang B, Jiang H, Cui H, He Q, Li W, Jin B, Wang L, 2020. Embryo transcriptome and miRNA analyses reveal the regulatory network of seed dormancy in Ginkgo biloba. Tree Physiol. tpaa023. https://doi.org/10.1093/treephys/tpaa023
Kainer D, Padovan A, Degenhardt J, Krause S, Mondal P, Foley WJ, Külheim C, 2019. High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus. New Phytol, 223: 1489-1504. https://doi.org/10.1111/nph.15887
Kirst M, Cordeiro CM, Rezende G, Grattapaglia D, 2005. Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. J Hered 96(2):161-166. https://doi.org/10.1093/jhered/esi023
Langmead B, Salzberg SL, 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 94: 9, 357. https://doi.org/10.1038/nmeth.1923
Lehouque G, Sanhueza R, Melo F, 2008. Development of MultiTAAG: an Automated Genotyping System for Eucalyptus Species Using Multiplex Amplification of Microsatellite Markers. Boletín del CIDEU 6-7: 25-34.
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), e0145144. https://doi.org/10.1371/journal.pone.0145144
Marcucci Poltri SN, Zelener N, Rodriguez Traverso J, Gelid P, Hopp HE, 2003. Selection of a seed orchard of Eucalyptus dunnii based on genetic diversity criteria calculated using molecular markers. Tree Physiol 23(9): 625-632. https://doi.org/10.1093/treephys/23.9.625
Müller BSF, de Almeida Filho JE, Lima BM, García CC, Missiaggia A, Aguiar AM, Takahashi E, Kirst M, Gezan SA, Silva-Junior OB, et al., 2019. Independent and Joint GWAS for growth traits in Eucalyptus by assembling genome: wide data for 3373 individuals across four breeding populations. New Phytol, 221: 818-833. https://doi.org/10.1111/nph.15449
Myburg A, Grattapaglia D, Tuskan G, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, et al., 2014. The genome of Eucalyptus grandis. Nat 510: 356-362.
Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J, 2004. Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol Biol 55: 263-80. https://doi.org/10.1007/s11103-004-0621-4
Pomponio M, Acuña C, Petreath VL, Lauenstein D, Marcucci Poltri S, Torales S, 2015. Characterization of functional SSR markers in Prosopis alba and their transferability across Prosopis species. Forest Systems, 24(2), eRC04. https://doi.org/10.5424/fs/2015242-07188
Powell W, Machray GC, Provan J, 1996. Polymorphisms revealed by simple sequence repeats. Trends Plant Sci 1 (7): 215-222. https://doi.org/10.1016/S1360-1385(96)86898-0
Rengel D, Clemente HS, Servant F, Ladouce N, Paux E, Wincker P, Couloux A, Sivadon P, Grima-Pettenati J, 2009. A new genomic resource dedicated to wood formation in Eucalyptus. BMC Plant Biol 9: 36. https://doi.org/10.1186/1471-2229-9-36
Silva-Junior OB, Grattapaglia D, 2015. Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis. New Phytol 208: 830-845. https://doi.org/10.1111/nph.13505
Silva-Junior OB, Faria DA, Grattapaglia D, 2015. A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species. New Phytol. 2015, 206, 1527-1540. https://doi.org/10.1111/nph.13322
Varshney RK, Graner A, Sorrells ME, 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23: 48-55. https://doi.org/10.1016/j.tibtech.2004.11.005
Wingfield MJ, Brockerhoff EG, Wingfield BD, Slippers B, 2015. Planted forest health: The need for a global strategy. Sci 349: 832-836. https://doi.org/10.1126/science.aac6674
Yasodha R, Sumathi R, Chezhian P, Kavitha S, Ghosh M, 2008. Eucalyptus microsatellites mined in silico: survey and evaluation. J Genet 87:21-25. https://doi.org/10.1007/s12041-008-0003-9
Zhou C, He X, Li F, Weng Q, Yu X, Wang Y, Li M, Shi J, Gan S, 2014. Development of 240 novel EST-SSRs in Eucalyptus L'Hérit. Mol Breeding 33: 221-225. https://doi.org/10.1007/s11032-013-9923-z
© CSIC. Manuscripts published in both the printed and online versions of this Journal are the property of Consejo Superior de Investigaciones Científicas, and quoting this source is a requirement for any partial or full reproduction.
All contents of this electronic edition, except where otherwise noted, are distributed under a “Creative Commons Attribution 4.0 International” (CC BY 4.0) License. You may read here the basic information and the legal text of the license. The indication of the CC BY 4.0 License must be expressly stated in this way when necessary.
Self-archiving in repositories, personal webpages or similar, of any version other than the published by the Editor, is not allowed.
