Have a personal or library account? Click to login
Association mapping for resin yield in Pinus roxburghii Sarg. using microsatellite markers Cover

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

Open Access
|Jun 2017

References

  1. 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: 574927.10.1155/2008/574927242341718551188
  2. 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/BF02772709
  3. 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/115.4.75512031083582962
  4. BASTEN, C. J. and M. A. ASMUSSEN (1997): The exact test for cytonuclear disequilibria. Genetics, 146: 1165-1171.10.1093/genetics/146.3.116512080449215917
  5. 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/btm30817586829
  6. 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.
  7. CHAUHAN, P. (2011): Molecular genetic analysis of Chir pine (Pinus roxburghii Sarg.) through microsatellite markers. Ph.D thesis submitted to Forest Research Institute University.
  8. CHURCHILL, G. A. and R. W. DOERGE (1994): Empirical threshold values for quantitative trait mapping. Genetics, 138: 963-971.10.1093/genetics/138.3.96312062417851788
  9. 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.
  10. DOYLE, J. J and J. L. DOYLE (1990): A rapid total DNA preparation procedure for fresh plant tissue. Focus, 12: 13-15.
  11. 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.0030170200096917922574
  12. 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/g00-002
  13. 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.x15969739
  14. 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/131.2.47912050201644282
  15. 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.
  16. 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.10.2.22010673279
  17. FELSENSTEIN, J. (1985): Confidence limits in phylogenies: an approach using bootstrap. Evolution, 39: 783-791.10.1111/j.1558-5646.1985.tb00420.x28561359
  18. 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.df
  19. 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_121129
  20. 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/S001667230000485711279831
  21. 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/BF00120641
  22. 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.
  23. 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-x17356864
  24. 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/je60033a034
  25. 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.
  26. 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.
  27. 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/tpp00219203978
  28. 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.104.026831144812515454555
  29. 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/s11032-005-1119-8
  30. 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.105.044420
  31. 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/158.2.843
  32. 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.
  33. 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.2010.01.0005
  34. 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.
  35. 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.105.054932
  36. 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. 1590-1605
  37. 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.
  38. NEGI, S. S. and S. MALIK (2009): Development of prediction models for resin production of Pinus roxburghii. FRI-66(N) funded by ICFRE.
  39. NORDBORG, M. (2000): Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self fertilization. Genetics, 154: 923-29.10.1093/genetics/154.2.923
  40. PERRIER, X. and J. P. JACQUEMOUD-COLLET (2006): DARwin software. Genetic improvement of vegetatively propagated crops. http://darwin.cirad.fr/Home.php
  41. 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)86898-0
  42. 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/s001220051046
  43. 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: 220-228.10.1086/302449137809310364535
  44. PRITCHARD, J. K., M. STEPHENS and P. DONNELLY (2000a): Inference of population structure using multilocus genotype data. Genetics, 155: 945-959.10.1093/genetics/155.2.945146109610835412
  45. PRITCHARD, J. K., M. STEPHENS, N. A. ROSENBERG andP. DONNELLY (2000b): Association mapping in structured population. American Journal of Human Genetics, 67: 170-181.10.1086/302959128707510827107
  46. 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.2003.12.00214746992
  47. 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.0005795268598919495411
  48. RISCH, N. J. (2000): Searching for genetic determinants in the new millennium. Nature 405: 847-856.10.1038/3501571810866211
  49. 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.2006.01.01116497345
  50. 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:1009680614564
  51. 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/123.1.19912037842806883
  52. 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:1003656610365
  53. 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.
  54. 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.
  55. SINGH, V. and S. KUMAR (2004): Seed quality as affected by mid cone diameter in Pinus roxburghii Sarg. Indian Forester, 130(7): 757-761.
  56. 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:1007540901981
  57. 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.110.120907303048321115973
  58. 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: 286-289.10.1038/9013511431702
  59. 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.x8794566
  60. 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.x10447853
  61. WEIR, B. S. (1996): Genetic data analysis II. Methods for discrete population genetic data. Sinauer Associates, Sunderland. University of Washington, 376 p.
  62. WRIGHT, S. (1978): Evolution and the Genetics of Populaton, Variability Within and Among Natural Populations. The University of Chicago Press, Chicago.
  63. 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.
  64. 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.0064799366717423734219
  65. 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.x33873470
  66. 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.0086308
  67. ZONDERVAN, K. T. and L. R. CARDON (2004): The complex interplay among factors that influence allelic association. Nat. Rev. Genet. 5: 89-100.
DOI: https://doi.org/10.1515/sg-2014-0033 | Journal eISSN: 2509-8934 | Journal ISSN: 0037-5349
Language: English
Page range: 253 - 266
Submitted on: May 27, 2014
Published on: Jun 1, 2017
Published by: Johann Heinrich von Thünen Institute
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2017 Anita Rawat, S. Barthwal, H. S. Ginwal, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.