1. bookVolume 63 (2014): Issue 1-6 (December 2014)
Journal Details
First Published
22 Feb 2016
Publication timeframe
1 time per year
Open Access

Association mapping for resin yield in Pinus roxburghii Sarg. using microsatellite markers

Published Online: 01 Jun 2017
Volume & Issue: Volume 63 (2014) - Issue 1-6 (December 2014)
Page range: 253 - 266
Received: 27 May 2014
Journal Details
First Published
22 Feb 2016
Publication timeframe
1 time per year

Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding. A total of 240 genotypes of Pinus roxburghii (Himalayan Chir Pine) from a natural population in Chakrata division (Tiunee range), Uttarakhand (India) were evaluated for resin yield. Based on the phenotypic data and stable resin production in consecutive years, 53 genotypes were selected after excluding the individuals with similar resin production. The selected 53 individuals were best representatives of the variation in resin yield in Chakrata population which varied between 0.25 and 8.0 kg/tree/year and were used for genotyping and association analysis using SSR markers. Out of 80 primers initially screened, a total of 19 polymorphic SSRs (11 cpSSR and 8 nSSR) were used in the study. Model based clustering using 19 polymorphic SSR markers identified five subpopulations among these genotypes. LD was evaluated using the entire population. The squared allele frequency correlation, r2 was estimated for each pair of SSR loci. The comparison wise significance (p-values) of SSR marker pairs was determined by performing 100,000 permutations. The genetic divergence ranged from 50 to 100%. The UPGMA based hierarchial clustering grouped the genotypes in accordance with their resin yield. Model based clustering suggested the existence of five subpopulations in the sample. However, the distribution of P. roxburghii genotypes into five subpopulations had no correlation with their resin yield thus ruling out the possibility of any ancestral relationship among the genotypes with similar resin yield. AMOVA suggested that the variation among P. roxburghii genotypes at the molecular level was related with the variation in resin yield and not their site of collection thus highlighting the genetic basis of the trait. LD based association analysis revealed two chloroplast SSRs Pt71936 and Pt87268 and one nuclear SSR pm09a to be in significant association with resin yield. The two associated chloroplast SSRs showed significant LD (p<0.01). One of the chloroplast SSR Pt87268 showing association with resin yield was also found to be in significant LD with the nuclear SSR pm07, further showing the probability of this marker also to be associated with resin yield.


ABDURAKHMONOV, I. Y. and A. ABDUKARIMONOV (2008): Application of association mapping to understanding the genetic diversity of plant germplasm resources. International Journal of Plant Genomics, 2008: 574927.10.1155/2008/574927242341718551188Search in Google Scholar

ASIF, M. J. and C. H. CANNON (2005): DNA Extraction from Processed Wood: A case study for the identification of an endangered timber species (Gonystylus bancanus). Plant Molecular Biology Reporter, 23: 185-192.10.1007/BF02772709Search in Google Scholar

ASMUSSEN, M. A., J. ARNOLD and J. C. AVISE (1987): Definition and properties of disequilibrium statistics for associations between nuclear and cytoplasmic genotypes. Genetics, 115: 755-768.10.1093/genetics/115.4.75512031083582962Search in Google Scholar

BASTEN, C. J. and M. A. ASMUSSEN (1997): The exact test for cytonuclear disequilibria. Genetics, 146: 1165-1171.10.1093/genetics/146.3.116512080449215917Search in Google Scholar

BRADBURY, P. J., Z. ZHANG, D. E. KROON, T. M. CASSTEVENS, Y. RAMDOSS and E. S. BUCKLER (2007): TASSEL: software for association mapping of complex traits in diverse samples. Genetics and Population Analysis, 23(19): 2633-2635.10.1093/bioinformatics/btm30817586829Search in Google Scholar

BROWN, G. R., G. P. GILL, R. J. KUNTZ, J. A. BEAL, D. NELSON, N. C. WHEELER, B. PENTTILA, J. ROERS and D. B. Neale (2004): Associations of candidate gene single nucleotide polymorphisms with wood property phenotypes in loblolly pine. In: Plant and Animal Genomes XII Conference, San Diego, CA, USA. Abstract: W98.Search in Google Scholar

CHAUHAN, P. (2011): Molecular genetic analysis of Chir pine (Pinus roxburghii Sarg.) through microsatellite markers. Ph.D thesis submitted to Forest Research Institute University.Search in Google Scholar

CHURCHILL, G. A. and R. W. DOERGE (1994): Empirical threshold values for quantitative trait mapping. Genetics, 138: 963-971.10.1093/genetics/138.3.96312062417851788Search in Google Scholar

COPPEN, J. J. W. and G. A. HONE (1995): Gum naval stores: turpentine and rosin from pine resin. FAO, Nonwood Forest Products, 2: 62 p.Search in Google Scholar

DOYLE, J. J and J. L. DOYLE (1990): A rapid total DNA preparation procedure for fresh plant tissue. Focus, 12: 13-15.Search in Google Scholar

EBERLE, M. A., K. KUHN, P. C. NG, L. ZHOU, D. A. PEIFFER, L. GALVER, K. A. VIAUD-MARTINEZ, C. T. LAWLEY, K. L. UNDERSON and R. SHEN et al. (2007): Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet, 3(10): 1827-1837.10.1371/journal.pgen.0030170200096917922574Search in Google Scholar

ELSIK, C. G., V. T. MINIHAN, S. E. HALL, A. M. SCARPA andC. G. WILLIAMS (2000): Low-copy microsatellite markers for Pinus taeda L. Genome, 43: 550-555.10.1139/g00-002Search in Google Scholar

EVANNO, G., S. REGNAUT and J. GOUDET (2005): Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14: 2611-2620.10.1111/j.1365-294X.2005.02553.x15969739Search in Google Scholar

EXCOFFIER, L., P. E. SMOUSE and J. M. QUATTRO (1992): Analysis of molecular variance inferred from metric distances among DNA haplotypes; Application to human mitochondrial DNA restriction data. Genetics, 131: 479-491.10.1093/genetics/131.2.47912050201644282Search in Google Scholar

EXCOFFIER, L., G. LAVAL and S. SCHNEIDER (2005): Arlequinver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics online, 1: 47-50.Search in Google Scholar

FARNIR, F., W. COPPIETERS, J. J. ARRANZ, P. BERZI and N. CAMBISANO (2000): Extensive genome wide linkage disequilibrium in cattle. Genome Research, 10: 220-227.10.1101/gr.10.2.22010673279Search in Google Scholar

FELSENSTEIN, J. (1985): Confidence limits in phylogenies: an approach using bootstrap. Evolution, 39: 783-791.10.1111/j.1558-5646.1985.tb00420.x28561359Search in Google Scholar

GEBHARDT, C., A. BALLVORA, B. WALKEMEIER, P. OBERHAGEMANN and K. SCHULER (2004): Assessing genetic potential in germplasm collections of crop plants by markertrait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Molecular Breeding, 13: 93-102.10.1023/B:MOLB.0000012878.89855.dfSearch in Google Scholar

GHILDIYAL, S. K., C. M. SHARMA and S. GAIROLA (2009): Environmental variation in seed and seedling characteristics of Pinus roxburghii Sarg. from Uttarakhand, India. Applied Ecology and Environmental research, 7(2): 121-129.10.15666/aeer/0702_121129Search in Google Scholar

HANSEN, M., T. KRAFT, S. GANESTAM, T. SALL and N. O. NILSSON (2001): Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers, Genetic Research, 77(1): 61-66.10.1017/S001667230000485711279831Search in Google Scholar

HAMRICK, J. L., M. J. W. GODT and S. L. SHERMAN-BROYLES (1992): Factors influencing levels of genetic diversity in woody plant species. New Forests, 6: 95-124.10.1007/BF00120641Search in Google Scholar

HARTL, D. L. and A. G. CLARK (1997): Principles of Population Genetics, 3rd edn. Sinauer Associates, Inc, Sunderland, MA. INGVARSSON, P. K. (2005): Nuceotide polymorphism and linkage disequilibrium within and among natural populations of European Aspen (Populus tremula L. Salicaceae). Genetics, 169: 945-953.Search in Google Scholar

IWATA, H., Y. UGA, Y. YOSHIOKA, K. EBANA and T. HAYASHI (2007): “Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms,” Theoretical and Applied Genetics, 114(8): 1437-1449.10.1007/s00122-007-0529-x17356864Search in Google Scholar

JOYE, N. M. JR. and R. V. LAWRENCE (1967): Resin acidcomposition of pine oleoresins. Journal of Chemical and Engineering Data, 12: 279-282.10.1021/je60033a034Search in Google Scholar

KEDHARNATH, S. (1971): Evolving high oleoresin yielding strains of Chir pine (Pinus roxburghii) through breeding. In: Proceedings of seminar on the role of pine resin in economic and industrial development of India. Sympine. New Delhi, India. 13-14 April, D-1-D-5.Search in Google Scholar

KENNEDY, B. W., M. QUINTON and J. A. M. VANARENDONK (1992): Estimation of effects of single genes on quantitative traits. J. Anim. Sci. 70: 2000-2012.Search in Google Scholar

KIM, Y. B., S. M. KIM, M. K. KANG, T. KUZUYAMA, J. K. LEE, S. C. PARK, S. C. SHIN and S. U. KIM (2009): Regulation of resin acid synthesis in Pinus densiflora by differential transcription of genes encoding multiple 1-deoxy-Dxylulose 5-phosphate synthase and 1-hydroxy-2-methyl- 2(E)-butenyl 4-diphosphate. Tree Physiology, 29: 737-749.10.1093/treephys/tpp00219203978Search in Google Scholar

KRAAKMAN, A. T. W., R. E. NIKS, P. M. M. M. VAN DEN BERG, P. STAM and F. A. VAN EEUWIJK (2004): Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics, 168: 435-446.10.1534/genetics.104.026831144812515454555Search in Google Scholar

KRAAKMAN, A. T. W., F. MARTINEZ, B. MUSSIRALIEV, F. A. VAN EEUWIJK and R. E. NIKS (2006): Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Molecular Breeding, 17: 41-58.10.1007/s11032-005-1119-8Search in Google Scholar

KRUTOVSKY, K. V. and D. B. NEALE (2005): “Nucleotide diversity and linkage disequilibrium in cold-hardinessand wood quality related candidate genes in douglas fir.” Genetics, 171(4): 2029-2041.10.1534/genetics.105.044420Search in Google Scholar

LATTA, R. G., Y. B. LINHART and J. B. MITTON (2001): Cytonuclear disequilibrium and genetic drift in a natural population of Ponderosa pine. Genetics, 158: 843-850.10.1093/genetics/158.2.843Search in Google Scholar

LE MAITRE, D. C. (1998): Pines in cultivation: a global view. In: D. M. RICHARDSON (Eds.), Ecology and biogeography of Pinus, Cambridge University Press, New York, USA. pp. 407-431.Search in Google Scholar

LIU, L., L. WANG, J. YAO, Y. ZHENG and C. ZHAO (2010): Association mapping of six agronomic traits on chromosome 4A of wheat (Triticum aestivum L.) Molecular Plant Breeding, 1(5): 1-10.10.5376/mpb.2010.01.0005Search in Google Scholar

LORENZ, E., S. LEETON and R. J. OWEN (1997): A simple method for sizing large fragments of bacterial DNA separated by PAGE. Cabios, 13: 485-486.Search in Google Scholar

MALOSETTI, M., C. G. VAN DER LINDEN, B. VOSMAN and F. A. VAN EEUWIJK (2007): “A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato,” Genetics, 175(2): 879-889.10.1534/genetics.105.054932Search in Google Scholar

MANOLIO, T. A., L. D. BROOKS and F. S. COLLINS (2008): A HapMap harvest of insights into the genetics of common disease. J. Clin. Invest, 118 (5) (2008), pp. 1590-1605Search in Google Scholar

NAUTIYAL, S., M. TYAGI, S. S. NEGI, R. K. SRIVASTAVA and S. NAUTIYAL (2006): Improvement of Chir pine (Pinus roxburghii Sarg.). In: (Eds.) Studies on Himalayan Pines. Pub. FRI, Dehradun, India. pp. 50-63.Search in Google Scholar

NEGI, S. S. and S. MALIK (2009): Development of prediction models for resin production of Pinus roxburghii. FRI-66(N) funded by ICFRE.Search in Google Scholar

NORDBORG, M. (2000): Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self fertilization. Genetics, 154: 923-29.10.1093/genetics/154.2.923Search in Google Scholar

PERRIER, X. and J. P. JACQUEMOUD-COLLET (2006): DARwin software. Genetic improvement of vegetatively propagated crops. http://darwin.cirad.fr/Home.phpSearch in Google Scholar

POWELL, W., G. MACHRAY and J. PROVAN (1996): Polymorphism revealed by simple sequence repeats. Trends in Plant Sciences, 1: 215-222.10.1016/S1360-1385(96)86898-0Search in Google Scholar

PREVOST, A. and M. WILKINSON (1999): A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics, 98: 107-112.10.1007/s001220051046Search in Google Scholar

PRITCHARD, J. K. and N. A. ROSENBERG (1999): Use of unlinked genetic markers to detect population stratification in association studies. American Journal of Human Genetics, 65: 220-228.10.1086/302449137809310364535Search in Google Scholar

PRITCHARD, J. K., M. STEPHENS and P. DONNELLY (2000a): Inference of population structure using multilocus genotype data. Genetics, 155: 945-959.10.1093/genetics/155.2.945146109610835412Search in Google Scholar

PRITCHARD, J. K., M. STEPHENS, N. A. ROSENBERG andP. DONNELLY (2000b): Association mapping in structured population. American Journal of Human Genetics, 67: 170-181.10.1086/302959128707510827107Search in Google Scholar

RAFALSKI, D. L. and M. MORGANTE (2004): Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends in Genetics, 20: 103-111.10.1016/j.tig.2003.12.00214746992Search in Google Scholar

REN, Y., Z. ZHANG, J. LIU, J. E. STAUB, Y. HAN and Z. CHENG et al. (2009): An Integrated Genetic and Cytogenetic Map of the Cucumber Genome. PLoS ONE 4(6): e5795.10.1371/journal.pone.0005795268598919495411Search in Google Scholar

RISCH, N. J. (2000): Searching for genetic determinants in the new millennium. Nature 405: 847-856.10.1038/3501571810866211Search in Google Scholar

RO, D. K. and J. BOHLMANN (2006): Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol /abietadienal oxidase (PtAO, CYP720B1). Phytochemistry, 67: 1572-1578.10.1016/j.phytochem.2006.01.01116497345Search in Google Scholar

ROLDAN-RUIZ DENDAUW, J., E. VAN BOCKSTAELE, A. DEPICKER and M. DE LOOSE (2000): AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Molecular Breeding, 6: 125-134.10.1023/A:1009680614564Search in Google Scholar

SCHNABEL, A. and M. A. ASMUSSEN (1989): Definition and properties of disequilibria within nuclear-mitochondrial- chloroplast and other nuclear-dicytoplasmic systems. Genetics, 123: 199-215.10.1093/genetics/123.1.19912037842806883Search in Google Scholar

SCRIBNER, K. T., S. DATTA, J. ARNOLD and J. C. AVISE (1999): Empirical evaluation of cytonuclear models incorporating genetic drift, and tests for neutrality of mtDNA variants: data from experimental Gambusia hybrid zones. Genetica, 105: 101-108.10.1023/A:1003656610365Search in Google Scholar

SHARMA, C. M., S. K. GHILDIYAL and D. P. NAUTIYAL (2001): Plus tree selection and their seed germination in Pinus roxburghii from Garhwal Himalaya. Indian Journal of Forestry, 24(1): 48-52.Search in Google Scholar

SHARMA, R., S. KUMAR and K. S. THAKUR (2006): Genetic improvement of Chir pine (Pinus roxburghii Sargent.) in India - A review. The Indian Forester, 132(3): 314-328.Search in Google Scholar

SINGH, V. and S. KUMAR (2004): Seed quality as affected by mid cone diameter in Pinus roxburghii Sarg. Indian Forester, 130(7): 757-761.Search in Google Scholar

STANGE, C., D. PREHN and P. A. JOHNSON (1998): Isolation of Pinus radiata genomic DNA suitable for RAPD analysis. Plant Molecular Biology Reporter, 16: 1-8.10.1023/A:1007540901981Search in Google Scholar

STRANGER, B. E., E. A. STAHL and T. RAJ (2011): Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics. Genetics, 187(2): 367-38310.1534/genetics.110.120907303048321115973Search in Google Scholar

THORNSBERRY, J. M., M. M. GOODMAN, J. DOEBLEY, S. Kresovich, D. NIELSEN and E. S. BUCKLER (2001): Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics, 28: 286-289.10.1038/9013511431702Search in Google Scholar

VENDRAMIN, G. G., P. LELLILR ROSSI and M. MORGANTE (1996): A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecology, 5: 595-598.10.1111/j.1365-294X.1996.tb00353.x8794566Search in Google Scholar

VENDRAMIN, G. G., B. DEGEN, R. J. PETIT, M. ANZIDIE, A. MADAGHIELE and B. ZIEGENHAGEN (1999): High level of variation at Abies alba chloroplast microsatellite loci in Europe. Molecular Ecology, 8: 1117-1126.10.1046/j.1365-294x.1999.00666.x10447853Search in Google Scholar

WEIR, B. S. (1996): Genetic data analysis II. Methods for discrete population genetic data. Sinauer Associates, Sunderland. University of Washington, 376 p.Search in Google Scholar

WRIGHT, S. (1978): Evolution and the Genetics of Populaton, Variability Within and Among Natural Populations. The University of Chicago Press, Chicago.Search in Google Scholar

XUELIAN, S., Y. TAO, H. JUNJIE, Z. XIAOYAN, F. REBECCA, J. JUNYE, A. FANG, G. JIANPING and Z. XUXIAO (2014): SSR genetic linkage map construction of pea (Pisum sativum L.) based on Chinese native varieties, The Crop Journal 2, 170-174.Search in Google Scholar

YANG, H., Y. TAO, Z. ZHENG, Q. ZHANG, G. ZHOU, M. W.SWEETINGHAM, J. G. HOWIESON and C. LI (2013): Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L. PLoS One. 8(5): e64799.10.1371/journal.pone.0064799366717423734219Search in Google Scholar

YIN, T. M., S. P. DIFAZIO, L. E. GUNTER, S. S. JAWDY, W. BOERJAN and G. A. TUSKAN (2004): “Genetic andphysical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence,” New Phytologist, 164(1): 95-105.10.1111/j.1469-8137.2004.01161.x33873470Search in Google Scholar

ZHAO, Y., H. WANG, W. CHEN and Y. LI (2014): Genetic Structure, Linkage Disequilibrium and Association Mapping of Verticillium Wilt Resistance in Elite Cotton (Gossypium hirsutum L.) Germplasm Population. PLoS ONE 9(1): e86308. doi:10.1371/journal.pone.0086308Search in Google Scholar

ZONDERVAN, K. T. and L. R. CARDON (2004): The complex interplay among factors that influence allelic association. Nat. Rev. Genet. 5: 89-100.Search in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo