Open Access

Development and validation of Acacia koa and A. koaia nuclear SSRs using Illumina sequencing


Cite

Adamski DJ, NS Dudley, CW Morden and D Borthakur (2012) Genetic differentia­tion and diversity of Acacia koa populations in the Hawaiian Islands. Plant Species Biol. 27(3): 181-190. https://doi.org/10.1111/j.1442-1984.2011.00359.x 10.1111/j.1442-1984.2011.00359.xOpen DOISearch in Google Scholar

Adamski DJ, NS Dudley, CW Morden and D Borthakur (2013) Cross-amplification of nonnative Acacia species in the Hawaiian Islands using microsatellite markers from Acacia koa. Plant Biosyst. 147(4): 1088-1091. https://doi.org/10.1080/11263504.2012.749958 10.1080/11263504.2012.749958Open DOISearch in Google Scholar

Butcher PA and GF Moran (2000) Genetic linkage mapping in Acacia mangium. 2. Development of an integrated map from two outbred pedigrees using RFLP and microsatellite loci. Theor Appl Genet. 101(4): 594-605. https://doi.org/10.1007/s001220051521 10.1007/s001220051521Open DOISearch in Google Scholar

Cappa EP, J Klapste, MN Garcia, PV Villalba and SN Marcucci Poltri (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(7): 96-114. https://doi.org/10.1007/s11032-016-0522-7 10.1007/s11032-016-0522-7Open DOISearch in Google Scholar

Cheng J, Z Zhao, B Li, C Qin, Z Wu, DL Trejo-Saavedra, X Luo, J Cui, RF Rive­ra-Bustamante, S Li and K Hu (2016) A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Scientific Reports. 6(1): 1-12. https://doi.org/10.1038/srep18919 10.1038/srep18919470397126739748Open DOISearch in Google Scholar

Fredua-Agyeman R, D Adamski, RJ Liao, C Morden and D Borthakur (2008) Development and characterization of microsatellite markers for analysis of population differentiation in the tree legume Acacia koa (Fabaceae: Mimo­soideae) in the Hawaiian Islands. Genome. 51(12): 1001-1015. https://doi.org/10.1139/g08-087 10.1139/g08-08719088813Open DOISearch in Google Scholar

Guillemaud T, L Broadhurst, I Legoff, M Henery, A Blin, C Ducatillion, N Ferrando and T Malausa (2015) Development of 23 Polymorphic Microsatellite Loci in Invasive Silver Wattle, Acacia dealbata (Fabaceae). Applications in Plant Sciences. 3(5): A1500018. https://doi.org/10.3732/apps.1500018 10.3732/apps.1500018443546925995979Search in Google Scholar

Gugger PF, CT Liang, VL Sork, P Hodgskiss, and JW Wright (2017) Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment. Evolutionary Applications. 0(0): 1-12. https://doi.org/10.1111/eva.12534 10.1111/eva.12534577549029387158Search in Google Scholar

Hopley T, LM Broadhurst and MG Gardner (2015) Isolation via 454 sequencing and characterisation of microsatellites for Acacia montana (Fabaceae), Mallee wattle: an endemic shrub from southeastern Australia. Conserv Genet Resour. 7(1): 171-172. https://doi.org/10.1007/s12686-014-0321-6 10.1007/s12686-014-0321-6Open DOISearch in Google Scholar

Le S, R Wickneswari, CE Harwood, MJ Larcombe, RA Griffin, A Koutoulis, JL Har­bard, KS Cyer, LW Yee, TH Ha and RE Vaillancourt (2016) A multiplexed set of microsatellite markers for discriminating Acacia mangium, A. auriculiformis, and their hybrid. Tree Genet Genomes. 12(2): A31. https://doi.org/10.1007/s11295-016-0990-2 10.1007/s11295-016-0990-2Open DOISearch in Google Scholar

Lepais O and CFE Bacles (2011) Comparison of random and SSR-enriched shot­gun pyrosequencing for microsatellite discovery and single multiplex PCR optimization in Acacia harpophylla F. Muell. Ex Benth. Mol Ecol Resour. 11(4): 711-724. https://doi.org/10.1111/j.1755-0998.2011.03002.x 10.1111/j.1755-0998.2011.03002.x21466660Open DOISearch in Google Scholar

Levy E, M Byrne, DJ Coates, SJ van Leeuwen, S McArthur, B Macdonald and MG Gardiner (2014) Isolation via 454 sequencing, and characterisation of micro­satellite markers for the Pilbara endemic Acacia atkinsiana (Fabaceae). Con­serv Genet Resour. 6(3): 585-587. https://doi.org/10.1007/s12686-014-0146-3 10.1007/s12686-014-0146-3Open DOISearch in Google Scholar

Magoč T and SL Salzberg (2011) FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 27(21): 2957-2963. https://doi.org/10.1093/bioinformatics/btr507 10.1093/bioinformatics/btr507319857321903629Open DOISearch in Google Scholar

Millar MA and M Byrne (2007) Characterization of polymorphic microsatellite DNA markers for Acacia saligna (Labill.) H.L.Wendl. (Mimosaceae). Mol Ecol Notes. 7(6): 1372-1374. https://doi.org/10.1111/j.1471-8286.2007.01890.x 10.1111/j.1471-8286.2007.01890.xOpen DOISearch in Google Scholar

Millar MA, M Byrne, I Nuberg and M Sedgley (2008) High outcrossing and random pollen dispersal in a planted stand of Acacia saligna subsp. saligna re­ vealed by paternity analysis using microsatellites. Tree Genet Genomes. 4(3): 367-377. https://doi.org/10.1007/s11295-007-0115-z. 10.1007/s11295-007-0115-zOpen DOISearch in Google Scholar

Morgante M and AM Olivieri (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J. 3(1):175-182. https://doi.org/10.1111/j.1365-313x.1993.tb00020.x. 10.1111/j.1365-313x.1993.tb00020.xOpen DOISearch in Google Scholar

Nevill PG, JM Anthony and SL Krauss (2010) Isolation and characterization of microsatellite markers for the banded ironstone endemic Acacia karina (Legu­minosae: Mimosaceae) and cross-species amplification with A. stanleyi and A. jibberdingensis. Conserv Genet Resour. 2(1): 321-323. https://doi.org/10.1007/s12686-010-9219-0. 10.1007/s12686-010-9219-0Open DOISearch in Google Scholar

Ng CH, SC Koh, SL Lee, KKS Ng, A Mark, M Norwati and R Wickneswari (2005) Isolation of 15 polymorphic microsatellite loci in Acacia hybrid (Acacia mangi­um x Acacia auriculiformis). Mol Ecol Notes. 5(3): 572-575. https://doi.org/10.1111/j.1471-8286.2005.00994.x 10.1111/j.1471-8286.2005.00994.xOpen DOISearch in Google Scholar

Otero-Arnaiz A, A Schnabel, TC Glenn, NA Schable, C Hagen and L Ndong (2005) Isolation and characterization of microsatellite markers in the East African tree, Acacia brevispica (Fabaceae: Mimosoideae). Mol Ecol Notes. 5(2): 366- 368. https://doi.org/10.1111/j.1471-8286.2005.00929.x. 10.1111/j.1471-8286.2005.00929.xOpen DOISearch in Google Scholar

Ozyigit II, I Dogan and E Filiz (2015) In silico analysis of simple sequence repeats (SSRs) in chloroplast genomes of Glycine species. POJ. 8(1): 24-29. doi: http://www.pomics.com/FILITZ_8_1_2015_24_29.pdf. Search in Google Scholar

Rohlf FJ. (2000) NTSYSpc Numerical Taxonomy and Multivariate Analysis System version 2.2. User Guide. Exeter Software. https://www.researchgate.net/publication/246982444_NTSYS-pc_-_Numerical_Taxonomy_and_Multivariate_Analysis_System. Accessed 26 August 2017 Search in Google Scholar

Ruiz-Guajardo JC, A Otero-Arnaiz, T Taylor, G Stone, TC Glenn, NA Schable, JT Miller, S Preuss, and A Schnabel (2007) Isolation of polymorphic microsatellite markers in the sub-Saharan tree, Acacia (Senegalia) mellifera (Fabaceae: Mimosoideae). Mol Ecol Notes. 7(6): 1138-1140. https://doi.org/10.1111/j.1471-8286.2007.01809.x 10.1111/j.1471-8286.2007.01809.xOpen DOISearch in Google Scholar

Rushanaedy I, TC Jones, NS Dudley, RJF Liao, R Agbayani, and D Borthakur (2012) Chitinase is a Potential Molecular Biomarker for Detecting Resistance to Fusarium oxysporum in Acacia koa. Trop Plant Biol. 5(3):244-252. https://doi.org/10.1007/s12042-012-9108-7. 10.1007/s12042-012-9108-7Open DOISearch in Google Scholar

Shiraishi A, JF Leslie, S Zhong, and JY Uchida (2012) AFLP, pathogenicity, and VCG analyses of Fusarium oxysporum and Fusarium pseudocircinatum from Acacia koa. Plant Dis. 96(8): 1111-1117. https://doi.org/10.1094/pdis-06-11-0491 10.1094/PDIS-06-11-049130727049Search in Google Scholar

Shyu C, JA Foster and LJ Forney (2002) Electronic polymerase chain reaction (ePCR) search algorithm. Proceedings of the IEEE Computer Society Bioin­formatics Conference (CSB’02). https://doi.org/10.1109/csb.2002.1039361 10.1109/CSB.2002.1039361Search in Google Scholar

Smulders MJM, G Bredemeijer, W Rus-Kortekaas, P Arens and B Vosman (1997) Use of short microsatellites from database sequences to generate polymor­phisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet. 94(2): 264-272. https://doi.org/10.1007/s001220050409 10.1007/s001220050409Open DOISearch in Google Scholar

Sonah H, RK Deshmukh, A Sharma, VP Singh, DK Gupta, RN Gacche, JC Rana, NK Singh and TR Sharma (2011) Genome-wide distribution and organization of microsatellites in plants: An insight into marker development in Brachypo­dium. PLoS One. 6(6): e21298. https://doi.org/10.1371/journal.pone.0021298 10.1371/journal.pone.0021298311969221713003Open DOISearch in Google Scholar

Staton M, T Best, S Khodwekar, S Owusu, T Xu, Y Xu, R Jennings, R Cronn, A Kathiravetpilla, M Coggeshall, O Gailing, H Liang, J Romero-Severson, S Schlarbaum and JE Carlson (2015) Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome se­quencing. PLoS One. 10(12): e0145031. https://doi.org/10.1371/journal.pone.0145031 10.1371/journal.pone.0145031468944426698853Search in Google Scholar

Tamura K, G Stecher, D Peterson, A Filipski and S Kumar (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30(12): 2725- 2729. https://doi.org/10.1093/molbev/mst197. 10.1093/molbev/mst197384031224132122Search in Google Scholar

Young ND. (1996) QTL mapping and quantitative disease resistance in plants. Annu Rev Phytopathol. 34(1): 479-501. https://doi.org/10.1146/annurev.phyto.34.1.479 10.1146/annurev.phyto.34.1.47915012553Open DOISearch in Google Scholar

Zhang Q, B Ma, H Li, Y Chang, Y Han, J Li, G Wei, S Zhao, A Awas Khan, Y Zhou, C Gu, X Zhang, Z Han, S Korban, S Li and Y Han (2012) Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple. BMC Genom. 13(1): a537. https://doi.org/10.1186/1471-2164-13-537.10.1186/1471-2164-13-537370494023039990Open DOISearch in Google Scholar

eISSN:
2509-8934
Language:
English
Publication timeframe:
Volume Open
Journal Subjects:
Life Sciences, Molecular Biology, Genetics, Biotechnology, Plant Science