Genomics studies for trait improvement in four important tree species: Current status and future prospects

Almeida P, Proux-Wera E, Churcher A, Soler L et al. (2019) Single-molecule genome assembly of the Basket Willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biology, 18(1), 1-18. https://doi.org/10.1101/589804.10.1101/589804 Search in Google Scholar

Alves FC, Balmant KM, Resende MFR et al. (2020) Accelerating forest tree breeding by integrating genomic selection and greenhouse phenotyping. The Plant Genome,13(3). https://doi.org/10.1002/tpg2.20048.10.1002/tpg2.2004833217213 Search in Google Scholar

Andersson-Gunnerås S, Mellerowicz E et al. (2006) Biosynthesis of cellulose-enriched tension wood in Populus global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. The Plant Journal, 45(2), 144-65. https://doi.org/10.1111/j.1365-313x.2005.02584.x10.1111/j.1365-313X.2005.02584.x16367961 Search in Google Scholar

Badenes ML, Martí AF, Ríos G, Rubio-Cabetas MJ et al. (2016) Application of genomic technologies to the breeding of trees. Frontiers in Genetics, 7(198), 1–13. https://doi.org/10.3389/fgene.2016.00198.10.3389/fgene.2016.00198510902627895664 Search in Google Scholar

da-Silva B, Adriano, Wanderley-Nogueira AC, Silva RRM et al. (2005) In silico survey of resistance (R) genes in Eucalyptus transcriptome. Genetics and Molecular Biology, 28(3), 562–574. https://doi.org/10.1590/S1415-47572005000400011.10.1590/S1415-47572005000400011 Search in Google Scholar

Eugenia B, Carol-Ann VS, Lezar S (2009) A microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis. BMC Biotechnology, 9(1), 51. https://doi.org/10.1186/1472-6750-9-51.10.1186/1472-6750-9-51269888219473481 Search in Google Scholar

Bhambhani S, Lakhwani D, Gupta P et al. (2017) Transcriptome and metabolite analyses in Azadirachta indica Identification of genes involved in biosynthesis of bioactive triterpenoids. Scientific Reports, 7(1), 1–12. https://doi.org/10.1038/s41598-017-05291-3.10.1038/s41598-017-05291-3550599128698613 Search in Google Scholar

Triboulot B, Béatrice M, Brosché M, Renaut J et al. (2007) Gradual Soil Water Depletion Results in Reversible Changes of Gene Expression, Protein Profiles, Ecophysiology, and Growth Performance in Populus euphratica, a Poplar Growing in Arid Regions. Plant Physiology,143(2), 876–892. https://doi.org/10.1104/pp.106.088708.10.1104/pp.106.088708180372817158588 Search in Google Scholar

Boyle B, Levée V, Hamel LP, Nicole MC et al. (2010) Molecular and histochemical characterisation of two distinct poplar Melampsora leaf rust pathosystems. Plant Biology, 12(2), 364–376. https://doi.org/10.1111/j.1438-8677.2009.00310.x.10.1111/j.1438-8677.2009.00310.x20398242 Search in Google Scholar

Brosché M, Vinocur B, Alatalo ER, et al. (2005) Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biology, 6(12), 1-17. https://doi.org/10.1186/gb-2005-6-12-r101.10.1186/gb-2005-6-12-r101141407216356264 Search in Google Scholar

Cappa EP, El-Kassaby YA, Garcia MN et al. (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). https://doi.org/10.1371/journal.pone.0081267.10.1371/journal.pone.0081267383993524282578 Search in Google Scholar

Chen, Zhi-Qiang, Zan Y, Milesi P et al. (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/s13059-021-02421-z10.1186/s13059-021-02421-z828166534266449 Search in Google Scholar

Chhetri HB, Furches A, Macaya-Sanz D, et al. (2020) 1Frontiers in Plant Science, 11, 1–20. https://doi.org/10.3389/fpls.2020.545748.10.3389/fpls.2020.545748750916833013968 Search in Google Scholar

Chhetri, Hari B, Macaya-Sanz D, Kainer D et al. (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.org10.1111/NPH.1577710.1111/nph.1577730843213 Search in Google Scholar

Constabel CP, Lindroth RL (2010) The Impact of Genomics on Advances in Herbivore Defense and Secondary Metabolism in Populus. Genetics and Genomics of Populus, 279–305. Springer. New York. https://doi.org/10.1007/978-1-4419-1541-2_13.10.1007/978-1-4419-1541-2_13 Search in Google Scholar

Dai X, Hu Q, Cai Q et al. (2014) The willow genome and divergent evolution from poplar after the common genome duplication. Cell Research, 24(10), 1274–1277. https://doi.org/10.1038/cr.2014.83.10.1038/cr.2014.83418535224980958 Search in Google Scholar

Dasgupta GM, Bari MPA, Shanmugavel S et al. (2021) Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis× E. grandis. Genomics. Elsevier, 113(6), 4276–4292. https://doi.org/10.1016/j.ygeno.2021.11.01310.1016/j.ygeno.2021.11.01334785351 Search in Google Scholar

Dillon SK, Brawner JT, Meder R et al. (2012) Association genetics in Corymbia citriodora subsp. variegata identifies single nucleotide polymorphisms affecting wood growth and cellulosic pulp yield. New Phytologist, 195(3), 596–608. https://doi.org/10.1111/j.1469-8137.2012.04200.x.10.1111/j.1469-8137.2012.04200.x22680066 Search in Google Scholar

Diningrat DS, Widiyanto SM, Pancoro A, Iriawati et al. (2015) Transcriptome of Teak (Tectona grandis, L.f) in Vegetative to Generative Stages Development. Journal of Plant Sciences, 10(1), 1–14. https://doi.org/10.3923/jps.2015.1.14.10.3923/jps.2015.1.14 Search in Google Scholar

Du Y, Song W, Yin Z et al. (2021) Genomic analysis based on chromosome-level genome assembly reveals an expansion of terpene biosynthesis of Azadirachta indica. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.11.11.46820710.1101/2021.11.11.468207 Search in Google Scholar

Duplessis S, Pierre-Emmanuel C (2005) Transcript patterns associated with ectomycorrhiza development in Eucalyptus globulus and Pisolithus microcarpus. New Phytologist, 165(2), 599–611. https://doi.org/10.1111/j.1469-8137.2004.01248.x10.1111/j.1469-8137.2004.01248.x15720670 Search in Google Scholar

El-Fattah AD, Sikora RA (2007) Induced resistance by the mutualistic endophyte, Fusarium oxysporum strain 162, toward Meloidogyne incognita on tomato. Biocontrol Science and Technology, 17(9), 969–975. https://doi.org/10.1080/09583150701582057.10.1080/09583150701582057 Search in Google Scholar

Elshire RJ, Glaubitz JC, Qi Sun et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS One 6(5). https://doi.org/10.1371/journal.pone.001937910.1371/journal.pone.0019379308780121573248 Search in Google Scholar

Fan C, Qiu Z, Zeng B, Liu Y et al. (2017) Selection of reference genes for quantitative real-time PCR in Casuarina equisetifolia under salt stress. Biologia plan-tarum, 61(3), 463–472. https://doi.org/10.1007/s10535-016-0670-y10.1007/s10535-016-0670-y Search in Google Scholar

FAO Global Forest Resources Assessment (2020), Rome FAO. https://doi.org/10.4060/ca9825en.10.4060/ca9825en Search in Google Scholar

Foresta, de H, Somarriba E, Temu A (2013) Towards the Assessment of Trees Outside Forests. Resources Assessment. Rome. Search in Google Scholar

Frost CJ, Mescher MC, Dervinis C et al. (2008) Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis -3-hexenyl acetate. New Phytologist, 180(3), 722–734. https://doi.org/10.1111/j.1469-8137.2008.02599.x.10.1111/j.1469-8137.2008.02599.x18721163 Search in Google Scholar

Galeano E, Vasconcelos TS, Oliveira PND et al. (2019) Physiological and molecular responses to drought stress in teak (Tectona grandis L.f.). PLoS ONE, 14(9), 1–26. https://doi.org10.1371/journal.pone.0221571.10.1371/journal.pone.0221571673347131498810 Search in Google Scholar

Galeano E, Vasconcelos TS, Vidal M et al. (2015) Large-scale transcriptional profiling of lignified tissues in Tectona grandis. BMC Plant Biology, 15(1), 1–21. https://doi.org/10.1186/s12870-015-0599 Search in Google Scholar

El-Dien OG, Ratcliffe B, Klápště J et al. (2015) Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing. BMC Genomics, 16(1), 370. https://doi.org/10.1186/s12864-015-1597-y.10.1186/s12864-015-1597-y442489625956247 Search in Google Scholar

Goué N, Lesage-Descauses MC, Mellerowicz EJ et al. (2008) Microgenomic analysis reveals cell type-specific gene expression patterns between ray and fusi-form initials within the cambial meristem of Populus. New Phytologist, 180(1), 45–56. https://doi.org/10.1111/j.1469-8137.2008.02556.x.10.1111/j.1469-8137.2008.02556.x18631289 Search in Google Scholar

Graça I, Mendes VM, Marques I et al. (2019) Comparative proteomic analysis of nodulated and non-nodulated Casuarina glauca Sieb. ex Spreng. grown under salinity conditions using sequential window acquisition of all theoretical mass spectra (SWATH-MS). International journal of molecular sciences, 21(1), 78. https://doi.org/10.3390/ijms2101007810.3390/ijms21010078698204931861944 Search in Google Scholar

Grattapaglia and Dario (2014) Breeding forest trees by genomic selection: current progress and the way forward. Genomics of plant genetic resources. Springer, 651–682. https://doi.org/10.1007/978-94-007-7572-5_2610.1007/978-94-007-7572-5_26 Search in Google Scholar

Grattapaglia, Dario (2017) Status and perspectives of genomic selection in forest tree breeding. Genomic selection for crop improvement Springer, 199–249. Springer. https://doi.org/10.1007/978-3-319-63170-7_910.1007/978-3-319-63170-7_9 Search in Google Scholar

Grattapaglia, Dario, Silva-Junior OB, Resende RT et al. (2018) Quantitative genetics and genomics converge to accelerate forest tree breeding. Frontiers in Plant Science, 9, 1693. https://doi.org/10.3389/fpls.2018.0169310.3389/fpls.2018.01693626202830524463 Search in Google Scholar

Grönlund A, Bhalerao RP, Karlsson J (2009) Modular gene expression in Poplar a multilayer network approach. New Phytologist, 181(2), 315–322. https://doi.org/10.1111/j.1469-8137.2008.02668.x.10.1111/j.1469-8137.2008.02668.x19121030 Search in Google Scholar

Groover A, Quentin Cronk (2017) Comparative and evolutionary genomics of angiosperm trees. (Ed.) Andrew Groover & Quentin Cronk Springer, 21, https://doi.org/10.1007/978-3-319-49329-910.1007/978-3-319-49329-9 Search in Google Scholar

Jungmin H, Shim S, Lee T, Kang YJ et al. (2019) Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. Plant Biotechnology Journal, 17(2), 517–530. https://doi.org/10.1111/pbi.12995.10.1111/pbi.12995633507230059608 Search in Google Scholar

Hallingbäck HR, Berlin S, Nordh NE et al. (2019) Genome wide associations of growth, phenology, and plasticity traits in willow [Salix viminalis (L.)]. Frontiers in Plant Science, 10, P.753. https://doi.org/10.3389/fpls.2019.00753.10.3389/fpls.2019.00753658275431249579 Search in Google Scholar

Hanley SJ, Karp A (2014) Genetic strategies for dissecting complex traits in bio-mass willows (Salix spp.). Tree Physiology, 34(11), 1167–1180. https://doi.org/10.1093/treephys/tpt089.10.1093/treephys/tpt08924218244 Search in Google Scholar

Pan H, Zhong C, Zhang Y, Jiang Q (2016) Geographic variation in seedling morphology of Casuarina equisetifolia subsp. equisetifolia (Casuarinaceae). Australian Journal of Botany, 64(2), 160–170. https://doi.org/10.1071/BT1504910.1071/BT15049 Search in Google Scholar

Correa J, Juan P, Prunier J, Vázquez-Lobo A et al. (2015) Molecular Signatures of Adaptation and Selection in Forest Trees. Advances in Botanical Research, 74, 265–306. https://doi.org/10.1016/bs.abr.2015.04.003.10.1016/bs.abr.2015.04.003 Search in Google Scholar

Kainer, David, Padovan A, Degenhardt J et al. (2019) High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus. New Phytologist, 223(3), 1489–1504. https://doi.org/10.1111/nph.15887.10.1111/nph.1588731066055 Search in Google Scholar

Keller, Guylaine, Marchal T, SanClemente H (2009) Development and functional annotation of an 11,303-EST collection from Eucalyptus for studies of cold tolerance. Tree Genetics & Genomes, 5(2), 317–327. https://doi.org/10.1007/s11295-008-0184-7.10.1007/s11295-008-0184-7 Search in Google Scholar

Khan, M Awais, Korban SS (2012) Association mapping in forest trees and fruit crops. Journal of Experimental Botany, 63(11), 4045–4060. https://doi.org/10.1093/jxb/ers10510.1093/jxb/ers10522511806 Search in Google Scholar

King, James D, Roslyn M. Gleadow et al. (2006) Regulation of oil accumulation in single glands of Eucalyptus polybractea. New Phytologist, 172(3) 440–451. https://doi.org/10.1111/j.1469-8137.2006.01842.x.10.1111/j.1469-8137.2006.01842.x17083675 Search in Google Scholar

Kress, WJ, Douglas ES, Paul JK, Jill LW, James HLM, Morgan RG, Xin L, Pamela SS (2022) “Green plant genomes: What we know in an era of rapidly expanding opportunities.” Proceedings of the National Academy of Sciences 119 (4).10.1073/pnas.2115640118879553535042803 Search in Google Scholar

Kreuzwieser J, Hauberg J, Howell KA et al. (2009) Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant physiology, 149(1), 461–473. https://doi.org/10.1104/pp.108.12598910.1104/pp.108.125989261373219005089 Search in Google Scholar

Neeraja KM, Jain P, Gupta S et al. (2016) An Improved Genome Assembly of Azadirachta indica A. Juss. G3: Genes, Genomes, Genetics, 6(7), 1835–1840. https://doi.org/10.1534/g3.116.03005610.1534/g3.116.030056493863827172223 Search in Google Scholar

Neeraja KM, Pattnaik S, Jain P, Gaur P et al. (2012) A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. BMC genomics, 13(1), 1–13. https://doi.org/10.1186/1471-2164-13-46410.1186/1471-2164-13-464350778722958331 Search in Google Scholar

Kumar R, Mehta S, Pathak SR (2018) Bioactive constituents of neem. Synthesis of medicinal agents from plants. Elsevier, 75–103. https://doi.org/10.1016/B978-0-08-102071-5.00004-010.1016/B978-0-08-102071-5.00004-0 Search in Google Scholar

Kuravadi NA, Gowda M (2019), 53–57. Springer. https://doi.org/10.1007/978-3-030-16122-4_610.1007/978-3-030-16122-4_6 Search in Google Scholar

Kuravadi NA, Yenagi V, Rangiah K, Mahesh HB et al. (2015) Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree. PeerJ, 3. https://doi.org/10.7717/peerj.106610.7717/peerj.1066454002826290780 Search in Google Scholar

Lafarguette F, Lepl JC, Dejardin A, Laurans F et al. (2004) Poplar Genes Encoding Fasciclin-Like Arabinogalactan Proteins Are Highly Expressed in Tension Wood. The New Phytologist, 164(1), 107–121. https://doi.org/10.1111/j.1469-8137.2004.01175.x10.1111/j.1469-8137.2004.01175.x33873473 Search in Google Scholar

Lebedev VG, Lebedeva TN, Chernodubov AI, Shestibratov KA (2020) Genomic selection for forest tree improvement: Methods, achievements and perspectives. Forests, 11(11), 1–36. https://doi.org/10.3390/f11111190.10.3390/f11111190 Search in Google Scholar

Li HB, Li N, Yang SZ, Peng HZ et al. (2017) Transcriptomic analysis of Casuarina equisetifolia L. in responses to cold stress. Tree Genetics & Genomes, 13(1), 1–15. https://doi.org/10.1007/s11295-016-1090-z.10.1007/s11295-016-1090-z Search in Google Scholar

Metzker ML (2010) Sequencing technologies—the next generation. Nature reviews genetics, 11(1), 31–46.10.1038/nrg262619997069 Search in Google Scholar

Michael T P, Jackson S (2013) The First 50 Plant Genomes. The Plant Genome, Crop Science Society of America, 6(2), 1–7. https://doi.org/10.3835/plantgenome2013.03.0001in.10.3835/plantgenome2013.03.0001in Search in Google Scholar

Miranda M, Ralph SG, Mellway R, White R et al. (2007) The Transcriptional Response of Hybrid Poplar ( Populus trichocarpa x P. deltoids ) to Infection by Melampsora medusae Leaf Rust Involves Induction of Flavonoid Pathway Genes Leading to the Accumulation of Proanthocyanidins. Molecular Plant-Microbe Interactions, 20(7), 816–831. https://doi.org/10.1094/MPMI-20-7-0816.10.1094/MPMI-20-7-081617601169 Search in Google Scholar

Modhumita GD, Radha V, Karpaga RSB (2017) Characterization of genes expressed in Casuarina equisetifolia in response to elicitation by cell wall components of Trichosporium vesiculosum. Silvae Genetica, 62(1–6), 161–172. https://doi.org/10.1515/sg-2013-0021.10.1515/sg-2013-0021 Search in Google Scholar

Mphahlele MM, Isik F, Mostert-O’Neill MM, Reynolds SM et al. (2020) Expected benefits of genomic selection for growth and wood quality traits in Eucalyptus grandis. Tree Genetics & Genomes, 16(4), 49. https://doi.org/10.1007/s11295-020-01443-1.10.1007/s11295-020-01443-1 Search in Google Scholar

Muchero W, Sondreli KL, Chen JG, Urbanowicz BR et al. (2018) Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree. Proceedings of the National Academy of Sciences, 115(45), 11573–11578.10.1073/pnas.1804428115623311330337484 Search in Google Scholar

Myburg AA, Grattapaglia D, Tuskan GA et al. (2014) The genome of Eucalyptus grandis, Nature. 510(7505), 356–362.10.1038/nature1330824919147 Search in Google Scholar

Naidoo S, Külheim C, Zwart L, Mangwanda R et al. (2014) Uncovering the de-fence responses of Eucalyptus to pests and pathogens in the genomics age. Tree physiology, 34(9), 931–943.10.1093/treephys/tpu07525261123 Search in Google Scholar

Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nature Reviews Genetics, 12(2), 111–122. Search in Google Scholar

Norwati A, Norlia B, Rosli HM, Norwati M et al. (2011) Development of transgenic teak (Tectona grandis) expressing a cry1AB genefor control of the skeletoniser. Asia-Pacific Journal of Molecular Biology and Biotechnology, 19(4), 149–156. Search in Google Scholar

O’Connor K, Hayes B, Topp B (2018) Prospects for increasing yield in macadamia using component traits and genomics. Tree Genetics and Genomes, 14(1), 7. https://doi.org/10.1007/s11295-017-1221-1.10.1007/s11295-017-1221-1 Search in Google Scholar

Ogunwande IA, Flamini G, Adefuye AE et al. (2011) Chemical compositions of Casuarina equisetifolia L., Eucalyptus toreliana L. and Ficus elastica Roxb. ex Hornem cultivated in Nigeria. South African Journal of Botany, 77(3), 645–649. Search in Google Scholar

Park S, Keathley DE, Han KH (2008) Transcriptional profiles of the annual growth cycle in Populus deltoides. Tree Physiology, 28(3), 321–329. https://doi.org/10.1093/treephys/28.3.321.10.1093/treephys/28.3.32118171656 Search in Google Scholar

Pégard M, Segura V, Muñoz F, Bastien C et al. (2020) Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar. Frontiers in Plant Science, 11, 1–23. https://doi.org/10.3389/fpls.2020.581954.10.3389/fpls.2020.581954765590333193528 Search in Google Scholar

Poland JA and Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. The Plant Genome, 5(3), 92–102.10.3835/plantgenome2012.05.0005 Search in Google Scholar

Qiu D, Wilson IW, Gan S, Washusen R et al. (2008) Gene expression in Eucalyptus branch wood with marked variation in cellulose microfibril orientation and lacking G-layers. New Phytologist, 179(1), 94–103. https://doi.org/10.1111/j.1469-8137.2008.02439.x.10.1111/j.1469-8137.2008.02439.x18422902 Search in Google Scholar

Quesada T, Li Z, Dervinis C, Li Y et al. (2008) Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytologist, 180(2), 408–420. https://doi.org/10.1111/j.1469-8137.2008.02586.x.10.1111/j.1469-8137.2008.02586.x18694447 Search in Google Scholar

Rae AM, Pinel MPC, Bastien C, Sabatti M et al. (2008) QTL for yield in bioenergy Populus: identifying G× E interactions from growth at three contrasting sites. Tree Genetics and Genomes. Springer, 4(1), 97–112. Search in Google Scholar

Rae AM, Tricker PJ, Bunn SM, Taylor G (2007) Adaptation of tree growth to elevated CO2: quantitative trait loci for biomass in Populus. New Phytologist, 175(1), 59–69.10.1111/j.1469-8137.2007.02091.x17547667 Search in Google Scholar

Ralph S, Oddy C, Cooper D, Yueh H et al. (2006) Genomics of hybrid poplar (Populus trichocarpa× deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences. Molecular Ecology, 15(5), 1275–1297. https://doi.org/10.1111/j.1365-294X.2006.02824.x.10.1111/j.1365-294X.2006.02824.x16626454 Search in Google Scholar

Ranik M, Creux NM, Myburg AA (2006) Within-tree transcriptome profiling in wood-forming tissues of a fast-growing Eucalyptus tree. Tree Physiology, 26(3), 365–375. https://doi.org/10.1093/treephys/26.3.365.10.1093/treephys/26.3.36516356907 Search in Google Scholar

Resende MDV, Resende MFR, Sansaloni CP, Petroli CD et al. (2012) Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytologist, 194(1), 116–128. https://doi.org/10.1111/j.1469-8137.2011.04038.x.10.1111/j.1469-8137.2011.04038.x22309312 Search in Google Scholar

Roy J, Mooney HA, Saugier B (2001) Terrestrial global productivity. Elsevier. Sarah R, Tabassum B, Idrees N, Hussain MK (2019) Bio-active Compounds isolated from Neem tree and their applications. Natural bio-active compounds, 509–528. Springer.10.1007/978-981-13-7154-7_17 Search in Google Scholar

Savolainen O, Pyhäjärvi T, Knürr T (2007) Gene flow and local adaptation in trees. Annual Reviews of Ecology Evolution and Systemetics, 38. 595–619.10.1146/annurev.ecolsys.38.091206.095646 Search in Google Scholar

Sjödin A, Street NR, Sandberg G, Gustafsson Pet al. (2009) The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome. New Phytologist, 182(4), 1013–1025. https://doi.org/10.1111/j.1469-8137.2009.02807.x.10.1111/j.1469-8137.2009.02807.x19383103 Search in Google Scholar

Solomon OL, Berger DK, Myburg AA (2010) Diurnal and circadian patterns of gene expression in the developing xylem of Eucalyptus trees. South African Journal of Botany, 76(3), 425–439. https://doi.org/10.1016/j.sajb.2010.02.087.10.1016/j.sajb.2010.02.087 Search in Google Scholar

Sousa TV, Caixeta ET, Alkimim ER, Oliveira ACB et al. (2017) Population structure and genetic diversity of coffee progenies derived from Catuaí and Híbrido de Timor revealed by genome-wide SNP marker. Tree Genetics & Genomes, 13(6), 124. https://doi.org/10.1007/s11295-017-1208-y.10.1007/s11295-017-1208-y Search in Google Scholar

Souza LM, Francisco FR, Gonçalves PS, Junior EJS et al. (2019) Genomic selection in rubber tree breeding: a comparison of models and methods for managing G× E interactions. Frontiers in plant science, 1353. https://doi.org/10.3389/fpls.2019.0135310.3389/fpls.2019.01353682423431708955 Search in Google Scholar

Stanton BJ, Neale DB, Li S, Stanton BJ et al. (2010) Genetics and Genomics of Populus. Springer, 8. https://doi.org/10.1007/978-1-4419-1541-2.10.1007/978-1-4419-1541-2 Search in Google Scholar

Tagu D, Bastien C, Faivre-Rampant P, Garbaye J et al. (2005) Genetic analysis of phenotypic variation for ectomycorrhiza formation in an interspecific F1 poplar full-sib family. Mycorrhiza. Springer, 15(2), 87–91. https://doi.org/10.1007/s00572-004-0302-910.1007/s00572-004-0302-915015061 Search in Google Scholar

Tan QG and Luo XD (2011) Meliaceous limonoids: chemistry and biological activities. Chemical reviews, 111(11), 7437–7522.10.1021/cr900402321894902 Search in Google Scholar

Thumma BR, Baltunis BS, Bell JC, Emebiri LC et al. (2010) Quantitative trait locus (QTL) analysis of growth and vegetative propagation traits in Eucalyptus ni-tens full-sib families. Tree Genetics & Genomes, 6(6), 877–889. https://doi.org/10.1007/s11295-010-0298-6.10.1007/s11295-010-0298-6 Search in Google Scholar

Tripathi AM, Yadav A, Saikia SP Roy S (2017) Global gene expression pattern in a forest tree species, Tectona grandis (Linn. F.), under limited water supply. Tree Genetics & Genomes, 13(3), 66. https://doi.org/10.1007/s11295-017-1151-y.10.1007/s11295-017-1151-y Search in Google Scholar

Tschaplinski TJ, Tuskan GA, Sewell MM, Gebre GM et al. (2006) Phenotypic variation and quantitative trait locus identification for osmotic potential in an interspecific hybrid inbred F2 poplar pedigree grown in contrasting environments. Tree Physiology, 26(5), 595–604. https://doi.org/10.1093/treephys/26.5.59510.1093/treephys/26.5.59516452073 Search in Google Scholar

Tuskan GA, DiFazio S, Jansson S, Bohlmann J et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). American Association for the Advancement of Science, 313(5793), 1596–1604. https://doi.org/10.1126/science.1128691.10.1126/science.112869116973872 Search in Google Scholar

Tuskan GA., Andrew TG, Jeremy S, Stephen PD, Alexander M, Grattapaglia D, Lawrence B. Smart et al. (2018) “Hardwood tree genomics: unlocking woody plant biology.” Frontiers in plant science 9, p1799.10.3389/fpls.2018.01799630436330619389 Search in Google Scholar

Varshney RK, Sinha P, Singh VK, Kumar A, Zhang Q, Bennetzen JL (2020) “5Gs for crop genetic improvement.” Current Opinion in Plant Biology 56, 190-196.10.1016/j.pbi.2019.12.004745026932005553 Search in Google Scholar

Waheed S, Zeng L (2020) The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development. Genes (Basel),11(3), 319. doi: 10.3390/genes11030319. PMID: 32192095; PMCID: PMC7140873.10.3390/genes11030319714087332192095 Search in Google Scholar

Varshney RK, Sinha P, Singh VK, Kumar A, Zhang Q, Bennetzen JL (2020) “5Gs for crop genetic improvement.” Current Opinion in Plant Biology 56, 190-196.10.1016/j.pbi.2019.12.004 Search in Google Scholar

Wang H, Wang N, Huo Y (2020) Multi-tissue transcriptome analysis using hybrid-sequencing reveals potential genes and biological pathways associated with azadirachtin A biosynthesis in neem (azadirachta indica). BMC genomics, 21(1), 1–17. https://doi.org/10.1186/s12864-020-07124-610.1186/s12864-020-07124-6759252333115410 Search in Google Scholar

Wang J, Ding J, Tan B, Robinson KM et al. (2018) A major locus controls local adaptation and adaptive life history variation in a perennial plant. Genome biology, 19(1), 1–17. https://doi.org/10.1186/s13059-018-1444-y10.1186/s13059-018-1444-y598559029866176 Search in Google Scholar

Wang M, Qi X, Zhao S, Zhang S et al. (2009) Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays. BMC genomics. Springer, 10(1), 215. https://doi.org/10.1186/1471-2164-10-21510.1186/1471-2164-10-215268540919426563 Search in Google Scholar

Wang S, Zhang H, Li X, Zhang J (2016) Gene expression profiling analysis reveals a crucial gene regulating metabolism in adventitious roots of neem (Azadirachta indica). RSC Advances, 6(115), 114889–114898. https://doi.org/10.1039/C6RA20494E.10.1039/C6RA20494E Search in Google Scholar

Wegrzyn JL, Falk T, Grau E, Buehler S et al. (2020) Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evolutionary Applications, 13(1), 228–241. https://doi.org/10.1111/eva.12860.10.1111/eva.12860693559331892954 Search in Google Scholar

Westbrook JW, Zhang Q, Mandal MK, Jenkins EV et al. (2020) Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade-off with American chestnut ancestry implies resistance is polygenic. Evolutionary applications, 13(1), 31–47. https://doi.org/10.1111/eva.1288610.1111/eva.12886693559431892942 Search in Google Scholar

Wheeler GS, Taylor GS, Gaskin JF, Purcell MF (2011) Ecology and management of Sheoak (Casuarina spp.), an invader of coastal Florida, USA. Journal of Coastal Research, 27(3), 485–492. https://doi.org/10.2112/JCOASTRES-D-09-00110.110.2112/JCOASTRES-D-09-00110.1 Search in Google Scholar

Yang X, Qian X, Wang Z (2019) The complete chloroplast genome of Casuarina glauca. Mitochondrial DNA Part B: Resources. Taylor & Francis, 4(1), 357–358. https://doi.org/10.1080/23802359.2018.1536476.10.1080/23802359.2018.1536476 Search in Google Scholar

Yasodha R, Vasudeva R, Balakrishnan S, Sakthi AR et al. (2018) Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation. DNA Research, 25(4), 409–419. Search in Google Scholar

Ye G, Zhang H, Chen B, Nie S (2019) De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth. Plant Journal, 97(4), 779–794. https://doi.org/10.1111/tpj.14159.10.1111/tpj.1415930427081 Search in Google Scholar

Zhang H, Yin W, Xia X (2008) Calcineurin B-Like family in Populus: comparative genome analysis and expression pattern under cold, drought and salt stress treatment. Plant Growth Regulation. Springer, 56(2), 129–140. https://doi.org/10.1007/s10725-008-9293-410.1007/s10725-008-9293-4 Search in Google Scholar

Zhang H, Yin T (2016) Identifying candidate genes for wood formation in poplar based on microarray network analysis and graph theory. Tree Genetics and Genomes, 12(3), 61. https://doi.org/10.1007/s11295-016-1016-9.10.1007/s11295-016-1016-9 Search in Google Scholar

Zhang J, Yuan H, Yang Q, Li M et al. (2017) The genetic architecture of growth traits in Salix matsudana under salt stress. Horticulture Research, 4. https://doi.org/10.1038/hortres.2017.2410.1038/hortres.2017.24546994228638623 Search in Google Scholar

Zhao D, Hamilton JP, Bhat WW, Johnson SR et al. (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), 1–10. https://doi.org/10.1093/gigascience/giz005.10.1093/gigascience/giz005639420630698701 Search in Google Scholar

Zhao Y, Sun J, Xu P, Zhang R et al. (2014) Intron-mediated alternative splicing of WOOD-ASSOCIATED NAC TRANSCRIPTION FACTOR1B regulates cell wall thickening during fiber development in Populus species. Plant physiology. American Society of Plant Biologists, 164(2), 765–776.10.1104/pp.113.231134391210424394777 Search in Google Scholar