Morphological and genetic variation of Amaranthus spinosus L.: an adaptation evidence of climate differences and gene interaction

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Research Paper 01/11/2013
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Morphological and genetic variation of Amaranthus spinosus L.: an adaptation evidence of climate differences and gene interaction

Arik Arubil Fatinah, Estri Laras Arumingtyas, Retno Mastuti
Int. J. Biosci.3( 11), 205-212, November 2013.
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Abstract

Amaranthus spinosus (spiny amaranth) natively live in America, Africa, Australia, Europe and Asia. This plant can be used as medicinal plant and also as food or feed. A. spinosus has phenotypic variation, especially in leave and stem type. It is because of plant adaptation. Plant adaptations impact to variation on morphological and genetic. Chloroplast DNA (cpDNA) is a common molecular marker that used in the genetic variability analyses. Phenotypic variation was analyzed using morphological and molecular data. The trnL intron, matK and rbcL genes were amplified and sequenced. The sequence data analyses using MEGA5, Bioedit and DNAsp software’s. The molecular data shown that A. spinosus from tropical zone was higher genetic variability then temperate zone. Plant in the tropical zone easy to be colonized and there isn’t gene flow barrier. So that, A. spinosus that adapt to different habitat have different morphological character and have higher genetic variability.

VIEWS 7

Backer A. 1968. Flora of Java Volume I. Walters Noordhoff. Netherland.

Bakker FT, Culham A, Gomez-Martinez R, Carvalho J,Compton J, Dawtrey R, Gibby M. 2000. Pattern of nucleotide substitution in angiosperm cpDNA trnL(UAA)-trnF(GAA) regions. Molecular Biology and Evolution 17(8), 1146-1155.

Bares JC, Rodriguez AG, Pahlich A, Koehler K, Deacon N. 2011. Phylogeography and climatic niche evolution in live oaks (Quercus series Virentes) from the tropics to the temperata zone. Journal of Biogeography 38, 962-981.

Baumgarthner BJ, Rapp JC, Mullet JE. 1993. Plastid genes encoding the transcription/translation apparatus are differentially transcribes early in barley (Hordeum vulgare) chloroplast development. Plant Physiology 101, 781-791.

Boza, G, Scheuring. 2004. Envitonmental heterogeineity  and  the  evolution  of  mutualism.  J. Ecocomp 1,239-339. http://dx.doi.org/10.1016/j.ecocom.2004.07.002

Brown WM, Prager EM, Wang A, Wilson AC. 1982. Mitochondrial DNA sequences of primates: the tempo and mode of evolution. Journal of Molecular Evolution 18, 225–239.

CBOL. 2009. CBOL approves matK and rbcL as the DNA barcode regions for land plants. Statemen oleh Executive Committee, CBOL (Proceedings) of the National Academy of Science 2009.

Clegg MT, Zurawski G. 1991. Chloroplast DNA and study of plant phylogeny. Dalam P.S. Soltis, D.E. Soltis & J.J. Doyle (Eds). Molecular Systematics of Plants. Champman & Hall. New York.

Coleman, JS, McConnaughay KDM, Ackerley DD. 1994. Interpreting phenotypic variation in plants: Perspective. TREE, 9(5), 187-191.

Costea M, Weaver ES, Tardif JF. 2004. The biology of Canadian weed: 130. Amaranthus retroflexus L., A. poewllii S. Waston and A. hibridus L. Can. Journal of Plant Science 84, 631-668.

De Las Rivas J, Lozano JJ, Ortiz AR. 2002. Comparative analysis of chloroplast genomes: functional annotation, genome based phylogeny, and deduced evolutionary patterns. Genome Research. 2(30), 567-583.

Echols H, Goodman MF. 1991. Fidelity mechanisms in DNA replication. Annual Review of Biochemistry 60, 477–511.

Ellis RJ. 1979. The most abundant protein in the world. Trends in Biochemistry 4, 241-244.

Farlow A, Medurian E, Schloterer C. 2010. DNA double-stand break repair and the evolution of intron density. Trends in Genetics: 1-6. http://dx.doi.org/10.1016/j.tig.2010.10.004

Fatinah AA, Arumingtyas EL, Mastuti R. 2012. Genetic diversity study among six genera of Amaranth Family found in Malang based on RAPD marker. Jornal of Tropical Life Science 2(3), 81-86.

Fatinah AA, Arumingtyas EL, Mastuti R. 2013. Infraspecific classification in Amaranthus spinosus based on morphological and molecular data. Proceeding. BASIC seminar 2013 in Malang.

Fisher RA. 1930. The Genetical Theory of Natural Selection. Clarendon Press. Inggris.

Galmez J, Flexas J, Keys AJ, Cifre J, Mitchell RAC, Madgwick PJ, Haslam RP, Medrano H, Parry MAH. 2005. Rubisco specificity factors tends to be larger in plant species from drier habitats and in species with persistent leaves. Plant, Cell and Environment 28, 517-579.

Gonza`lez-Rodriguez A, Baffin JF, Golden JL, Oyama K. 2004. Chloroplast DNA variation in the Quercus affinis- Q. laurina complex in Mexico: geographical structure and associations with nuclear and morphological variation. Molecular Ecology 13, 3467-3476.

Gojobori T, Li WL, Graur D. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. Journal of Molecular Evolution 18, 360–369.

Haldane JBS, Jayakar SD. 1963. Polymorphism due to selection of varying direction. Journal of Genetic 58, 237-242.

Hao DC, Mu J, Chen SL, Xiao PG. 2010. Physicochemical evolution and positive selection of the gymnosperm matK protein. Journal of Genetic. 89, 1-9.

Hilu KW, Liang H. 1997. The matK gene: sequence variation and application in plant systematics. American Journal of Botany 84, 830-839.

Holmquist R. 1983. Transitions and transversion in evolutionary descent: an approach to understanding. Journal of Molecular Evolution 19, 134-144.

INA, Y. 1998. Estimation of the transition/transversion ratio. Journal of Molecular Evolution 46, 521–533.

Jaramillo-Correa JP, Beaulieu J, Khasa DP, Bousquet J. 2009. Inferring the past from the present phylogeographic structure of North American forest trees: seeing the forest for the genes. Canadian Journal of Forest Research 39, 286-307.

Kusumaningtyas R., Kobayashi, Takeda S. 2006. Mixed species gardens in Java and the transmigration areas of Sumatra, Indonesia: a comparison. Journal of Tropical Agriculture 44 (1-2), 15-22.

Kumar A, Lakshman BS, Jayaveera K, Nandeesh KN, Manoj N, Ranganayakulu. 2010. Comparative in vitro atihelminthic activity of three plants from Amaranthaceae family. Biological science 62(1), 185-189. http://dx.doi.org/102298/ABS1001185K

Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceeding of National Academic Science of USA, 102, 8369-8374. http://dx.doi.org/10.1073/pnas.0503123102

Leimu R, Fischer M. 2008. A meta analysis of local adaptation in plants. Plos One 3(12), 1-8.

Levene H. 1953. Genetic equilibrium when more than one ecological niche is available. The American Naturalist 87, 331-333.

Levins R. 1968. Evolution in Changing Environments. Princeton University Press. New Jersey.

Li WH, Graur D. 1991. Fundamentals of molecular evolution. Sinauer, Sunderland, MA.

Murray MJ. 1940. The genetics of sex determination in the family Amaranthaceae. Genetics 25, 409-431.

Newmaster   SG,   Fazekas  AJ,    Ragupathy   S. 2006. DNA barcoding in land plants: evaluation of rbcL in multigene tiered approach. Canadian Journal of Botany 84, 335-341.

Popa G, Cornea CP, Ciuca M, Babeanu N, Popa O, Marin D. 2010. Studies among genetic diversity in Amaranthus species using the RAPD markers. TOM, XVII(2), 280-285.

Purvis A, Bromham L. 1997. Estimating the transition/transversion ratio from independent pairwise comparisons with an assumed phylogeny. Journal of Molecular Evolution. 44, 112–119.

Radford AE. 1986. Fundamentals of Plant Systematics. Harper & Row, publisher, Inc. New York.

Roy SW, Penny D. 2007. Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of  O. sativa and A. thaliana.  Molecular  Biology  and  Evolution  24(1), 171-181. http://dx.doi.org/10.1093/molbev/msl159

Schlichting CD, Pigliucci M. 1998. Phenotypic Evolution: A Reaction Norm Perspective. Sinauer Associates, Inc. Massachusetts.

Sem L, Fares MA, Liang B, Gao L, Wang B, Wang T, Su YJ. 2011. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns. Biology Direct 2(29), 1-19. http://dx.doi.org/10.1186/1745-6150-6-29

Soltis D, Morris JP, McLachlan S, Soltis PS. 2006. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology 15, 4261-4293.

Sugiura M. 1995. The chloroplast genome assays. Biochemistry 30, 49-57.

Taberlet P, Gielly L, Poutou G, Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17(5), 1105-1109.

Vardhana H. 2011. In vitro antibacterial activity of Amaranthus spinosus root extracts. Pharmacophore 2(5), 266-270.

Vogel J, Börner T, Hess WR. 1999. Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants. Nucleic Acids Research : 3866-3874.

Wright S. 1931. Evolution in Mendelian populations. Genetics 16, 97-159.