Research article

A preliminary investigation on AFLP marker-wood density trait association in teak (Tectona grandis L. f.)

Vivek Vaishnav, Syed Arif Wali, Shashi Bhushan Tripathi, Mahender Singh Negi, Shamim Akhtar Ansari

Vivek Vaishnav
Institute of Forest Productivity, Lalgutwa, NH-23, Ranchi 835303, India
Syed Arif Wali
The Energy Resource Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110 003, India
Shashi Bhushan Tripathi
The Energy Resource Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110 003, India
Mahender Singh Negi
The Energy Resource Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110 003, India
Shamim Akhtar Ansari
Flat #206, Gemini Apartment, Khurram Nagar, Lucknow 226022, India. Email:

Online First: July 03, 2018
Vaishnav, V., Wali, S., Tripathi, S., Negi, M., Ansari, S. 2018. A preliminary investigation on AFLP marker-wood density trait association in teak (Tectona grandis L. f.). Annals of Forest Research DOI:10.15287/afr.2018.1018

Association between 276 AFLP loci and wood density of 46 teak (Tectona grandis L. f.) genotypes was evaluated, confirming the genetic structure among the genotypes and significant (p < 0.01) linkage disequilibrium between 9.4% loci-pair. AFLP markers with Bayesian correction for inbreeding coefficient detected a low genetic structure vis-à-vis high genetic diversity (0.23) and high polymorphism (57.41 ± 9.62%). AMOVA allocated 26.34% variation among the populations and 73.65% variation among the genotypes with FST = 0.16. The wood density with 8.71% variation displayed significant normal distribution. The careful control of statistical estimates incorporating Q and K to avoid the false discovery resulted in four AFLP loci significantly associated with the wood density trait. This is the first report dealing with marker-trait association in teak against the scarcity of background genomic information in this species. The AFLP markers associated with the wood density trait may be developed into STS
markers for marker-assisted selection and breeding for genetic improvement of the species.

Alemdag, I. S. 1984. Wood density variation of 28 tree species from ontario. Canada: Petawawa National Forestry Institute, Canadian Forest Service.

Amos, W., Driscoll, E., Hoffman, J. I., 2011. Candidate genes versus genome-wide associations: which are better for detecting genetic susceptibility to infectious disease? Proceedings of the Royal Society of London Series B 278: 1183-1188. DOI: 10.1098/rspb.2010.1920

Ansari, S. A., Narayanan, C., Wali, S. A., Kumar, R., Shukla, N., Kumar, S. R. 2012. ISSR markers for analysis of molecular diversity and genetic structure of Indian teak (Tectona grandis L f) locations. Annals of Forest Research 55 (1): 1-13.

Araya, E., Murillo, O., Agullar, G., Rocha, O., Woolbright, S., Kelm, P. 2005. Possibilities of breeding teak (Tectona grandis L.f.) in Costa Rica assisted by AFLP markers. Kurú: Revista Forest (Costa Rica) 2(5): 1-8.

Beaulieu, J., Doerksen, T., Boyle, B., Clément, S., Deslauriers, M., Beauseigle, S., Poulin, P., Lenz, P., Caron, S., Rigault, P., Bicho, P., Bousquet, J., Mackay, J. 2011. Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression. Genetetics 110: 197-214. DOI: 10.1534/genetics.110.125781

Bonin, A., Ehrich, D., Manel, S. 2007. Statistical analysis of amplified fragment length polymorphisms data: a tool box for molecular ecologists and evolutionists. Molecular Ecology 16: 3737 – 3758. DOI: 10.1111/j.1365-294X.2007.03435.x

Botstein, D., White, R. L., Skolnick, M., Davis, R. W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphism. American Journal of Human Genetics 32: 314 - 331.

Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., Buckler, E. S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23 (19): 2633-2635. DOI: 10.1093/bioinformatics/btm308

Breseghello, F., Sorrells, M. S. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177. DOI: 10.1534/genetics.105.044586

Chave, J. 2005. Measuring wood density for tropical forest trees: A field manual for the CTFS sites.[1].pdf

Dillon, S.K., Nolan, M., Li, W., Bell, C., Wu, H. X., Southerton, S. G. 2010. Allelic variation in cell wall candidate genes affecting solid wood properties in natural populations and land races of Pinus radiata. Genetics 185 (4): 1477-1487. DOI: 10.1534/genetics.110.116582

Eckert, A. J., Pande, B., Ersoz, E. S., Wright, M. H., Rashbrook, V. K., Neale, D. B. 2009. High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genetics & Genomes 5: 225-234. DOI: 10.1007/s11295-008-0183-8

Evanno, G., Regnaut, S., Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620. DOI: 10.1111/j.1365-294X.2005.02553.x

Excoffier, L., Lischer, H. E. L. 2010. ARLEQUIN suite ver 3.5: A new series of programs to perform population genetics analyses under LINUX and WINDOWS. Molecular Ecology Notes 10: 564–567. DOI: 10.1111/j.1755-0998.2010.02847.x

Falush, D., Stephens, M., Pritchard, J. K. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.

Falush, D., Stephens, M., Pritchard, J. K. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7: 574–578. DOI: 10.1111/j.1471-8286.2007.01758.x

Fofana, I., Ofori, D., Poitel, M., Verhaegen, D. 2009: Diversity and genetic structure of teak (Tectona grandis Linn f) in its natural range using DNA microsatellite markers. New Forest 37: 175-195. DOI: 10.1007/s11056-008-9116-5

Fofana, I. J., Lidah, Y. J., Diarrassouba, N., N'guetta, S. P. A. 2008. Genetic structure and conservation of teak (Tectona grandis ) plantations in Cote d'Ivoire, revealed by site specific recombinase (SSR). Tropical Conservation Science 1(3): 279-292. DOI: 10.1177/194008290800100308

Furlotte, N. A., Kang, E. Y., Van Nas, A., Farber, C. R., Lusis, A. J., Eskin, E. 2012. Increasing association mapping power and resolution in mouse genetic studies through the use of meta-analysis for structured populations. Genetics 191: 959-967. DOI: 10.1534/genetics.112.140277

Gonza’lez-Martı’nez, S.C., Huber, D., Ersoz, E., Davis, J. M., Neale, D. B. 2008. Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101: 19-28. DOI: 10.1038/hdy.2008.21

Gonza’lez-Martı’nez, S.C., Wheeler, N. C., Ersoz, E., Nelson, C. D., Neale, D. B. 2007. Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175: 399–409. DOI: 10.1534/genetics.106.061127

Griffiths, R., Orr, K. 1999. The use of amplified fragment length polymorphism (AFLP) in the isolation of sex-specific markers. Molecular Ecology 8: 671–674. DOI: 10.1046/j.1365-294x.1999.00578.x

Hammer, Ø., Harper, D.A.T., Ryan, P.D. 2001. Past: paleontological statistics software package for education and data analysis. Palaeontology Electronica 4: 9.

Hansen, O. K., Changtragoon, S., Ponoy, B., Kjær, E. D., Minn, Y., Finkeldey, R., Nielsen, K. B., Graudal, L. 2015. Genetic resources of teak (Tectona grandis Linn f ) strong genetic structure among natural populations. Tree Genetics & Genomes 11 DOI:10 1007/s11295-014-0802-5

Holliday, J.A., Ritland, K., Aitken, S. N. 2010. Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis). New Phytolology 188: 501- 514. DOI: 10.1111/j.1469-8137.2010.03380.x

Holsinger, K. E, Lewis, P. O. 2007. Hickory, software for analysis of geographic structure in genetic data. http://darwin.eeb.uconn. edu/hickory/hickory.html

Hubisz, M. J., Falush, D., Stephens, M., Pritchard, J. K. 2009. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Research 9: 1322- 1333. DOI: 10.1111/j.1755-0998.2009.02591.x

Indira, E. P., Bhat, K. M. 1998. Effects of site and place of origin on wood density of teak. Journal of Tropical Forest Science 10 (4): 537-541.

Ingvarsson, P. K., Garcia, M. V., Luquez, V. Hall, D., Jansson, S. 2008. Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European Aspen (Populus tremula, Salicaceae). Genetics 178: 2217–2226. DOI: 10.1534/genetics.107.082354

Jansen, R. C. 1994. Controlling the type I and type II errors in mapping quantitative trait loci. Genetics 138: 871-881.

Kaosa-ard, A. 1981. Teak (Tectona grandis L.f.) - its natural distribution and related factors. Natural History Bulletin of Siam Society 29: 55–74.

Khan, M.A., Korban, S. S. 2012. Association mapping in forest trees and fruit crops. Journal of Experimental Botany 63: 4045–4060. DOI: 10.1093/jxb/ers105

Kokutse, A. D., Bailleres, H., Stokes, A., Kokou, K. 2004. Proportion and quality of heartwood in Togolese teak (Tectona grandis L. f.). Forest Ecology Management 189: 37–48.

DOI: 10.1016/j.foreco.2003.07.041

Kumar, V., Kotrange, H. R., Dhotekar, U. P. 1998. Genetic improvement of teak. Indian Forester 124 (9): 687 – 695.

Lepoittevin, C., Harvengt, L., Plomion, C., Garnier-Gere, P. 2012. Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population. Tree Genetics & Genomes 8: 113-126. DOI: 10.1007/s11295-011-0426-y

Li, Z., Mottonen, J., Sillanpaa, M. J. 2015. A robust multiple locus method for quantitative trait locus analysis of non-normally distributed multiple traits. Heredity 115: 556-564. DOI: 10.1038/hdy.2015.61

Liu, K., Muse, S. V. 2005. Integrated analysis environment for genetic marker data. Bioinformatics 21(9): 2128-2129. DOI: 10.1093/bioinformatics/bti282

Ma, X., Hall, D., St.Onge, K. R., Jansson, S., Ingvarsson, P. K. 2010. Genetic differentiation, clinal variation and phenotypic associations with growth cessation across the Populus tremula photoperiodic pathway. Genetics 186: 1033-1044. DOI: 10.1534/genetics.110.120873

Mackay, T. F. C. 2001. Quantitative trait loci in Drosophila. Nature Review of Genetics 2: 11-20. DOI: 10.1038/35047544

McCarthy, M.I., Abecasis, G. R., Cardon, L. R. et al. 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature Review 9: 356–369. DOI: 10.1038/nrg2344

Moya, R., Marin, J. D., 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. DOI: 10.1515/sg-2013-0019

Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z., Costich, D. E., Buckler, E. S. 2009. Association maping: critical considerations shift from genotyping experimental design. Plant Cell 21: 2194 – 2202. DOI: 10.1105/tpc.109.068437

Narayanan, C., Wali, S. A., Shukla, N., Kumar, R., Mandal, A. K., Ansari, S. A. 2007. RAPD and ISSR markers for molecular characterization of teak (Tectona grandis) plus trees. Journal of Tropical Forest Science 19 (4): 218 -225.

Nazareno, A. G., Bemmels, J. B., Dick, C. W., Lohmann, L. G. 2017. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Molecular Ecology Resources 17(6): 1136 – 1147. DOI: 10.1111/1755-0998.12654

Neale, D. B., Savolainen, O. 2004. Association genetics of complex traits in conifers. Trends in Plant Science 9: 325–330. DOI: 10.1016/j.tplants.2004.05.006

Oraguzie, N.C., Rikkerink, E.H.A., Gardiner, S.E. 2007. Association mapping in plants. Springer Science +Business Media, LLC, New York. DOI: 10.1007/978-0-387-36011-9

Peakall, R., Smouse, P. E. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28: 2537-2539. DOI: 10.1093/bioinformatics/bts460

Perrier, X., Jacquemond-Collet, J. P. 2006. DARwin software.

Prevost, A., Wilkinson, M.J. 1999: A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical & Applied Genetics 98: 107–112. DOI: 10.1007/s001220051046

Pritchard, J. K., Stephens, J. K., Rosenberg, N. A., Donnelly, P. 2000. Association mapping in structured populations. American Journal of Humen Genetics 67: 170–181. DOI: 10.1086/302959

Quesada, T., Gopal, V., Cumbie, W. P., Echert, J A. J., Wegrzyn, L., Neale, D. B. 2010. Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L) .Genetics 186: 677–686. DOI: 10.1534/genetics.110.117549

Rao, N. K. 2004: Plant genetic resources: Advancing conservation and use through biotechnology. African Journal of Biotechnology 3(2): 136- 145.

Rydholm, C., Szakacs, G., Lutzoni, F. 2006. Low genetic variation and no detectable population structure in Aspergillus fumigatus compared to closely related Neosartorya species. Eukaryotic Cell 5: 650–657. DOI: 10.1128/EC.5.4.650-657.2006

Slatkin, M. 2008. Linkage disequilibrium–understanding the evolutionary past and mapping the medical future. Nature Reviews of Genetics 9: 477–485. DOI: 10.1038/nrg2361

Spiegelhalter, D. J., Best, N. G., Carlin, B. P., van der Linde, A. 2002. Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society Series B Statistical Methodology 64: 583– 689. DOI: 10.1111/1467-9868.00353

Sreekanth, P. M., Balasundaran, M., Nazeem, P. A., Suma, T. B. 2012. Genetic diversity of nine natural Tectona grandis L. f. populations of the Western Ghats in Southern India. Conservation Genetics 13: 1409-1419. DOI: 10.1007/s10592-012-0383-5

Thumma, B. R., Nolan, M. F., Evans, R., Moran, G. F. 2005. Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171: 1257–1265. DOI: 10.1534/genetics.105.042028

Thumma, B. R., Matheson, B. A., Zhang, D., Meeske, C., Meder, R., Downes, G. M., Southerton, S. G. 2009. Identification of a Cis-acting regulatory polymorphism in a Eucalypt COBRA-Like gene affecting cellulose content. Genetics 183 (3): 1155-1164. DOI: 10.1534/genetics.109.106591

Vaishnaw, V., Mohammad, N., Wali, S. A., Kumar, R., Tripathi, S. B., Negi, M. S., Ansari, S. A. 2015. AFLP markers for analysis of genetic diversity and structure of teak (Tectona grandis L f) in India. Canadian Journal of Forest Research 44: 297- 306. DOI: 10.1139/cjfr-2014-0279

Vekemans, X. 2002. AFLP-SURV version 1.0. Laboratoire de Génétique et Ecologie Végétale. In. Université Libre de Bruxelles, Belgium

Verhaegan, D., Ofori, D., Fofana, I. J., Poitel, M., Vaillant, A. 2005. Development and characterization of microsatellite markers in Tectona grandis (Linn. f). Molecular Ecology Note. 5: 945– 947. DOI: 10.1111/j.1471-8286.2005.01124.x

Verhaegen, D., Fofana, I. J., Logossa, Z. A., Ofori, D. 2010. What is the genetic origin of teak (Tectona grandis L) introduced in Africa and Indonesia? Tree Genetics & Genomes 6: 717-733. DOI: 10.1007/s11295-010-0286-x

Vos, P., Hogers, R., Bleeker, M., Reijans, M., Vandelee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., Zabeau, M. 1995. AFLP — a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407– 4414. DOI: 10.1093/nar/23.21.4407

Vos, P. G., Paulo, M. J., Voorrips, R. E., Visser, R. G., van Eck, H. J., van Eeuwijk, F. A. 2017. Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato. Theoretical & Applied Genetics 130(1): 123–135. DOI: 10.1007/s00122-016-2798-8

Wilcox, P. L., Echt, C. E., Burdon, R. D. 2007. Application of association genetics for forest tree breeding, in Oraguzie NC, EHA Rikkerink, DE Gardiner, and HN De Silva (eds). Association mapping in plants. Springer. New York, USA, 213–249. DOI: 10.1007/978-0-387-36011-9_10

Yu, J., Pressoir, G., Briggs, W. H., Bi, I. V., Yamasaki, M., Doebley, J. F., McMullen, M. D., Gaut, B. S., Nielsen, D. M., Holland, J. B. 2006. A unified mixed –model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38: 203-208. DOI: 10.1038/ng1702

Zhivotovsky, L.A. 1999. Estimating population structure in diploids with multilocus dominant DNA markers. Molecular Ecology 8: 907–913. DOI: 10.1046/j.1365-294x.1999.00620.x

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