References
- Allwright MR, Payne A, Emiliani G, Milner S, Viger M, Rouse F, Keurentjes JJ, Bérard A, Wildhagen H, Faivre-Rampant P (2016) Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.). Biotechnology for biofuels 9(1): 1-22. https://doi.org/10.1186/s13068-016-0603-1
- Ansari SA, Narayanan C, Wali SA, Kumar R, Shukla N, Rahangdale SK (2012) ISSR markers for analysis of molecular diversity and genetic structure of Indian teak (Tectona grandis Lf) populations. Annals of forest research: 11-23. https://doi.org/10.15287/afr.2012.71
- Badilla Y, Xavier A, Murillo O, Paiva HN (2016) IBA efficiency on mini-cutting rooting from Teak (Tectona grandis Linn F.) clones. Revista Árvore 40: 477-485. https://doi.org/10.1590/0100-67622016000300011
- Badilla-Valverde Y, Murillo-Gambo O, Espinoza-Pizarro M (2023) Optimization of controlled pollination techniques in Tectona grandis, Linn isf. Revista Forestal Mesoamericana Kurú 20(46): 1-9. https://doi.org/10.18845/rfmk.v20i46.6597
- Balakrishnan S, Ramasamy Y, Dev SA (2023) An overview of teak genetic improvement towards conservation of genetic resources in a changing climate with special emphasis on India. Tree Genetics & Genomes 19(3): 1-17. https://doi.org/10.1007/s11295-023-01604-y
- Ballesta P, Bush D, Silva FF, Mora F (2020) Genomic predictions using low-density SNP markers, pedigree and GWAS information: a case study with the non-model species Eucalyptus cladocalyx. Plants 9(1): 99.
- Bian Y, Holland JB (2017) Enhancing genomic prediction with genome-wide association studies in multiparental maize populations. Heredity 118(6): 585-593. https://doi.org/10.1038/hdy.2017.4
- Burdon RD, Klápště J (2019) Alternative selection methods and explicit or implied economic-worth functions for different traits in tree breeding. Tree Genetics & Genomes 15(6): 79. https://doi.org/10.1007/s11295-019-1384-z
- Callister AN (2013) Genetic parameters and correlations between stem size, forking, and flowering in teak (Tectona grandis). Canadian Journal of Forest Research 43: 1145-1150. https://doi.org/10.1139/cjfr-2013-0226
- Callister AN (2021) Genetic Improvement of Teak. The Teak Genome. Ramasamy Y, Galeano E, Win TT, Springer International Publishing: 191-218.
- Callister AN, Bradshaw BP, Elms S, Gillies RW, Sasse JM, Brawner JT (2021) Single-step genomic BLUP enables joint analysis of disconnected breeding programs: an example with Eucalyptus globulus Labill. G3 Genes|Genomes|Genetics 11(10). https://doi.org/10.1093/g3journal/jkab253
- Callister AN, Collins SL (2008) Genetic parameter estimates in a clonally replicated progeny test of teak (Tectona grandis Linn. f.). Tree Genetics & Genomes 4(2): 237-245. https://doi.org/10.1007/s11295-007-0104-2
- Cappa EP, El-Kassaby YA, Garcia MN, Acuña C, Borralho NM, Grattapaglia D, Marcucci Poltri SN (2013) Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus. PloS one 8(11): e81267. https://doi.org/10.1371/journal.pone.0081267
- Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular ecology 22(11): 3124-3140. https://doi.org/10.1111/mec.12354
- Chamberland V, Robichaud F, Perron M, Gélinas N, Bousquet J, Beaulieu J (2020) Conventional versus genomic selection for white spruce improvement: a comparison of costs and benefits of plantations on Quebec public lands. Tree Genetics & Genomes 16(1): 17. https://doi.org/10.1007/s11295-019-1409-7
- Chen Z-Q, Zan Y, Milesi P, Zhou L, Chen J, Li L, Cui B, Niu S, Westin J, Karlsson B (2021) Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis. Genome biology 22(1): 1-30. https://doi.org/10.1186/s13059-021-02392-1
- Chen Z-Q, Zan Y, Zhou L, Karlsson B, Tuominen H, García-Gil MR, Wu HX (2022) Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce. Frontiers in Plant Science 13: 927673. https://doi.org/10.3389/fpls.2022.927673
- Chhetri HB, Macaya-Sanz D, Kainer D, Biswal AK, Evans LM, Chen JG, Collins C, Hunt K, Mohanty SS, Rosenstiel T (2019) Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytologist 223(1): 293-309. https://doi.org/10.1111/nph.15777
- Danarto S, Hardiyanto EB (2001) Results of the progeny test of teak at 12 years of age at Jember, East Java. Potentials and Opportunities in Marketing and Trade of Plantation Teak: Challenge for the New Millennium. Proceedings of the Third Regional Seminar on Teak July 31 - August 4, 2000, Yogyakarta, Indonesia, Faculty of Forestry Gadjah Mada University.
- Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST (2011) The variant call format and VCFtools. Bioinformatics 27(15): 2156-2158. https://doi.org/10.1093/bioinformatics/btr330
- Darmawan W, Nandika D, Sari RK, Sitompul A, Rahayu I, Gardner D (2015) Juvenile and mature wood characteristics of short and long rotation teak in Java. IAWA journal 36(4): 428-442. https://doi.org/10.1163/22941932-20150112
- Desta ZA, Ortiz R (2014) Genomic selection: genome-wide prediction in plant improvement. Trends in plant science 19(9): 592-601. https://doi.org/10.1016/j.tplants.2014.05.006
- Dev SA, Ramasamy Y (2021) Genome of Teak: Structure and Features. The Teak Genome, Springer: 237-251.
- Fahrenkrog AM, Neves LG, Resende Jr MF, Vazquez AI, de Los Campos G, Dervinis C, Sykes R, Davis M, Davenport R, Barbazuk WB (2017) Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides. New Phytologist 213(2): 799-811. https://doi.org/10.1111/nph.14154
- Fallas JL (2017) Funciones alométricas, de volumen y de crecimiento para clones de teca (Tectona grandis L.f) en Costa Rica. M. Sc., Escuela de Ingeniería Forestal. Cartago, Costa Rica.
- Fofana IJ, Ofori D, Poitel M, Verhaegen D (2009) Diversity and genetic structure of teak (Tectona grandis L.f) in its natural range using DNA microsatellite markers. New Forests 37: 175-195. https://doi.org/10.1007/s11056-008-9116-5
- Galli G, Gezan SA, Murillo DA, Murray D (2022) ASRgwas: An R package to perform complex Genome-Wide Association Studies (GWAS). Version 1.0.0. . VSN International, Hemel Hempstead, United Kingdom. VSN International, Hemel Hempstead, United Kingdom.
- Gezan SA, de Oliveira AA, Murray D (2021) ASRgenomics: An R package with Complementary Genomic Functions. Version 1.0.0 VSN International, Hemel Hempstead, United Kingdom.
- Gianola D (2013) Priors in whole-genome regression: the Bayesian alphabet returns. Genetics 194(3): 573-596. https://doi.org/10.1534/genetics.113.151753
- Goddard M (2009) Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136(2): 245-257. https://doi.org/10.1007/s10709-008-9308-0
- Goh DKS, Chaix G, Baillères H, Monteuuis O (2007) Mass production and quality control of teak clones for tropical plantations: The Yayasan Sabah Group and Forestry Department of Cirad Joint Project as a case study. Bois et Forêts des Tropiques 293: 65-77. https://doi.org/10.19182/bft2007.293.a20343
- Grattapaglia D (2022) Twelve years into genomic selection in forest trees: climbing the slope of enlightenment of marker assisted tree breeding. Forests 13(10): 1554. https://doi.org/10.3390/f13101554
- Grattapaglia D, Resende MD (2011) Genomic selection in forest tree breeding. Tree Genetics & Genomes 7: 241-255. https://doi.org/10.1007/s11295-010-0328-4
- Habier D, Fernando RL, Kizilkaya K, Garrick DJ (2011) Extension of the Bayesian alphabet for genomic selection. BMC bioinformatics 12(1): 1-12. https://doi.org/10.1186/1471-2105-12-186
- Hansen O, Changtragoon S, Ponoy B, Kjaer E, Minn Y, Finkeldey R, Nielsen K, Graudal L (2015) Genetic resources of teak (Tectona grandis Linn. f.)— strong genetic structure among natural populations. Tree Genetics and Genomes. 11: 802.
- Hansen OK, Changtragoon S, Ponoy B, Lopez J, Richard J, Kjaer ED (2017) Worldwide translocation of teak - origin of landraces and present genetic base. Tree Genetics & Genomes 13(87). https://doi.org/10.1007/s11295-017-1170-8
- Huang G, Liang K, Zhou Z, Ma H (2016) SSR genotyping—genetic diversity and fingerprinting of teak (Tectona grandis) clones. Journal of Tropical Forest Science 28(1): 48-58. https://doi.org/http://www.jstor.org/stable/43748078
- Husen A, Pal M (2003) Effect of serial bud grafting and etiolation on rejuvenation and rooting cutttings of mature trees of Tectona grandis Linn. f. Silvae Genetica 52(2): 84-88.
- Isik F (2022). Genomic Prediction of Complex Traits Complex traits in Perennial Plants: A Case for Forest Trees Forest trees. Genomic prediction of complex traits: Methods and Protocols, Springer: 493-520.
- Izekor D, Fuwape J, Oluyege A (2010) Effects of density on variations in the mechanical properties of plantation grown Tectona grandis wood. Archives of Applied Science Research 2(6): 113-120.
- Kokutse AD, Stokes A, Baillères H, Kokou K, Baudasse C (2006) Decay resistance of Togolese teak (Tectona grandis L.f) heartwood and relationship with colour. Trees 20: 219-223. https://doi.org/10.1007/s00468-005-0028-0
- Korte A, Farlow A (2013) The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9(1): 29. https://doi.org/10.1186/1746-4811-9-29
- Lebedev VG, Lebedeva TN, Chernodubov AI, Shestibratov KA (2020) Genomic selection for forest tree improvement: Methods, achievements and perspectives. Forests 11(11): 1190. https://doi.org/10.3390/f11111190
- Lefouili M, Nam K (2022) The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species. Scientific Reports 12(1): 11331. https://doi.org/10.1038/s41598-022-15563-2
- Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27(21): 2987-2993. https://doi.org/10.1093/bioinformatics/btr509
- Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows– Wheeler transform. bioinformatics 25(14): 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP (2009) The sequence alignment/map format and SAMtools. bioinformatics 25(16): 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
- Mandal AK, Chawhan PH (2005) Investigations on inheritance of growth and wood properties and their interrelationships in teak. International Conference on Quality Timber products of Teak from Sustainable Forest management. Peechi, Thrissur, Kerala, India, Kerala Forest Research Institute, India and International Tropical Timber Organisation, Japan 506-510.
- Mandal AK, Rambabu N (2001) Quantitative Genetic Aspects of Teak Improvement. Genetics and Silviculture of Teak. Mandal AK, Ansari SA. Dehra Dun, International Book Distributors: 134-145.
- McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J (2014) Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. New Phytologist 203(2): 535-553. https://doi.org/10.1111/nph.12815
- Metzker ML (2010) Sequencing technologies—the next generation. Nature reviews genetics 11(1): 31-46. https://doi.org/10.1038/nrg2626
- Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819–1829. https://doi.org/10.1093/genetics/157.4.1819
- Money D, Gardner K, Migicovsky Z, Schwaninger H, Zhong G-Y, Myles S (2015) LinkImpute: Fast and Accurate Genotype Imputation for Non-Model Organisms. G3: Genes, Genomes, Genetics g3.115.021667. https://doi.org/10.1534/g3.115.021667
- Monteuuis O, Goh DKS, Garcia C, Alloysius D, Gidiman J, Bacilieri R, Chaix G (2011) Genetic variation of growth and tree quality traits among 42 diverse genetic origins of Tectona grandis planted under humid tropical conditions in Sabah, East Malaysia. Tree Genetics & Genomes 7(6): 1263-1275. https://doi.org/10.1007/s11295-011-0411-5
- Monteuuis O, Vallauri D, Poupard C, Hazard L, Yusof Y, Wahap Latip A, Garcia C, Chauviere M (1995). Propagation clonale de tecks matures par bouturage horticole. Bois et Forêts des Tropiques 243: 25-39.
- Moya R, Marin JD, Murillo O, Leandro L (2013) Wood physical properties, color, decay resistance and stiffness in Tectona grandis clones with evidence of genetic control. Silvae Genetica 62(3): 142-152. https://doi.org/10.1515/sg-2013-0019
- Moya R, Tenorio C (2021) Wood properties and their variations in teak. The Teak Genome, Springer: 103-137.
- Mphahlele MM, Isik F, Mostert-O’Neill MM, Reynolds SM, Hodge GR, Myburg AA (2020) Expected benefits of genomic selection for growth and wood quality traits in Eucalyptus grandis. Tree Genetics and Genomes 16(4): 49. https://doi.org/10.1007/s11295-020-01443-1
- Müller BS, de Almeida Filho JE, Lima BM, Garcia CC, Missiaggia A, Aguiar AM, Takahashi E, Kirst M, Gezan SA, Silva-Junior OB (2019) Independent and Joint-GWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations. New Phytolo-gist 221(2): 818-833. https://doi.org/10.1111/nph.15449
- Murillo O (2011) Forest Evaluation and Appraisal. Software Version 2023
- Murillo O, Resende MDV, Badilla Y, Gamboa JP (2019) Genotype by environment interaction and teak (Tectona grandis L.) selection in Costa Rica. Silvae Genetica 68: 116-121. https://doi.org/10.2478/sg-2019-0020
- Murillo O, Wright J, Monteuuis O, Montenegro F (2013) Mejoramiento genético de la teca en América Latina. Las plantaciones de teca en América Latina: Mitos y realidades. Camino R, Aymerich JM. Costa Rica, CATIE: 86-111.
- Naranjo SS, Moya R, Chauhan S (2012) Early selection of morphology and some wood properties of Tectona grandis L. clones. Silvae Genetica 61(1/2): 58-65. https://doi.org/10.1515/sg-2012-0008
- Narayanan C, Wali S, Shukla N, Kumar R, Mandal A, Ansari S (2007) RAPD and ISSR markers for molecular characterization of teak (Tectona grandis) plus trees. Journal of Tropical Forest Science: 218-225. https://doi.org/https://www.jstor.org/stable/43595390
- Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nature Reviews Genetics 12(2): 111-122. https://doi.org/10.1038/nrg2931
- Pandey D, Brown C (2000) Teak: a global overview. Unasylva 201 51: 3-13.
- Park T, Casella G (2008) The bayesian lasso. Journal of the American Statistical Association 103(482): 681-686. https://doi.org/10.1198/016214508000000337
- Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS genetics 2(12): e190. https://doi.org/10.1371/journal.pgen.0020190
- Pérez P, de Los Campos G (2014) Genome-wide regression and prediction with the BGLR statistical package. Genetics 198(2): 483-495. https://doi.org/10.1534/genetics.114.164442
- Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS one 7(5): e37135. https://doi.org/10.1371/journal.pone.0037135
- Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, DiFazio SP, Muchero W, Ranjan P, Tuskan GA (2013) Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. New Phytologist 200(3): 710-726. https://doi.org/10.1111/nph.12422
- Resende MDV (2016) Software Selegen-REML/BLUP: a useful tool for plant breeding. Crop Breeding and Applied Biotechnology 16: 330-339. https://doi.org/10.1590/1984-70332016v16n4a49
- Rizanti DE, Darmawan W, George B, Merlin A, Dumarcay S, Chapuis H, Gérardin C, Gelhaye E, Raharivelomanana P, Kartika Sari R (2018) Comparison of teak wood properties according to forest management: short versus long rotation. Annals of Forest Science 75(2): 1-12. https://doi.org/10.1007/s13595-018-0716-8
- Sasidharan S (2021) Teak plantations and wood production. The Teak Genome, Springer: 13-25.
- Shukla S, Viswanath S (2023) Comparison of growth and few wood quality parameters of 24–25-year-old Tectona grandis (teak) trees raised under three agroforestry practices. Agroforestry Systems 97(4): 631-645. https://doi.org/10.1007/s10457-023-00815-5
- VanRaden PM (2008) Efficient methods to compute genomic predictions. Journal of Dairy Science 91(11): 4414-4423. https://doi.org/10.3168/jds.2007-0980
- Verhaegen D, Fofana IJ, Logossa ZA, Ofori D (2010) What is the genetic origin of teak (Tectona grandis L.) introduced in Africa and Indonesia? Tree Genetics and Genomes 6(5): 717-733. https://doi.org/10.1007/s11295-010-0286-x
- Win TT (2021) Genetic Diversity and Population Genetic Structure of Teak. The Teak Genome, Springer: 181-190.
- Wu HX (2019) Benefits and risks of using clones in forestry – a review. Scandinavian Journal of Forest Research 34(5): 352-359. https://doi.org/10.1080/02827581.2018.1487579
- Younessi-Hamzekhanlu M, Gailing O (2022) Genome-wide SNP markers accelerate perennial forest tree breeding rate for disease resistance through marker-assisted and genome-wide selection. International Journal of Molecular Sciences 23(20): 12315. https://doi.org/10.3390/ijms232012315
- Zhao D, Hamilton JP, Bhat WW, Johnson SR, Godden GT, Kinser TJ, Boachon B, Dudareva N, Soltis DE, Soltis PS (2019) A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. Gigascience 8(3): giz005. https://doi.org/10.1093/gigascience/giz005