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Single Nucleotide Polymorphism (SNP) Markers Discovery within Musa spp (Plantain Landraces, AAB Genome) for Use in Beta Carotene (Provitamin A) Trait Mapping
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Volume 1, 2013
Issue 1 (December)
Pages: 11-19   |   Vol. 1, No. 1, December 2013   |   Follow on         
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MMEKA, Ebelechukwu C, Department of Botany, university of Ibadan, Ibadan, Nigeria; Bioscience Centre, International Institute of Tropical Agriculture, IITA, Ibadan, Nigeria; Department of Botany, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria.
ADESOYE, Adenubi I, Department of Botany, university of Ibadan, Ibadan, Nigeria.
VROH, Bi I, Bioscience Centre, International Institute of Tropical Agriculture, IITA, Ibadan, Nigeria.
UBAOJI, Kingsley I, Department of Biochemistry, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria.
The need for biofortification of staple crops has become the concern of Modern Nutritional Genomics in producing staple crops with the ability of accumulating high micronutrients. Beta-carotene (Provitamin A) biosynthesis pathway is a stepwise process which is coded by two main genes; phytoene synthase (PSY) and lycopene beta-cyclase (LYB). These two important genes LYB 7 and PSY 1 1 were amplified, sequenced and analyzed within various diploid and triploid plantain landraces to identify SNPs present and to study their potentials for mapping the quantitative trait loci in those genes brought about by climatic variation within plantain landraces over time and also reveal their phylogenetic relationship. A total of 7 SNPs were found in the two genes from 68 genotypes used for PSY 11 and 35 plantain genotypes for LYB 7 gene. A frequency of 1 SNP per 80bp was detected in LYB 7 and I SNP per 32bp in PSY 11 gene of 160 bp sequences each. The allelic diversity was 0.0286 in LYB 7 and 0.0147 to 0.0294 in PSY 11. The phylogenetic relationship revealed that the genotypes for LYB 7 gene follow two distinct lines of evolution whereas in PSY 11 gene, the genotypes are similar with Zue and Sel advancing a bit. From the research, the high frequency of SNPs detected showed that it is sufficient in mapping the quantitative trait loci associated with high beta-carotene synthesis and could be incorporated in plantain breeding program.
LYB 7, PSY 11, Indels, Musa Species, ORF, Quantitative Trait, SNPs, Transition, Transversion
Adesoye, A., Mmeka, E. and Vroh, B. (2012). Single Nucleotide Polymorphism Markers Discovery in Musa Spp (Plantain Landraces, AAB Genome) and its Potentials for Use in Gibberellic Acid and Parthenocarpy Trait Mapping. J Plant Mol Biol Biotechnol 3(1): 9-21
Bhat, K.V. (2005). DNA fingerprinting and cultivar identification. National Research Center on DNA fingerprinting, N.B.P.G.R, New Delhi -011 012
Carreel, F., Fauré, S., Gonzalez De Leon, D., Lagoda, P., Perrier, X., Bakry, F., Tézenas du Montcel, H., Lanaud, C. and Horry, J.P. (1994). Evaluation de la diversité génétique chez les bananiers diploïdes (Musa sp.). Genetics Selection Evolution 26:125-136.
Creste, S., A. Tulmann , N., Vencovsky, S.O. Silva and Figueira, A. (2004). Genetic diversity of Musa diploid and triploid accessions from the Brazilian banana breeding program estimated by microsatellite markers. Genetic Resources and Crop Evolution 51:723-733.
De Langhe, E., Hribova, E., Carpentier, S., Dolezel, J., and Swennen, R. (2010). Did backcrossing contribute to the origin of hybrid edible bananas? Annals of Botany Page 1 of 9 doi:10.1093/aob/mcq187, available online at www.aob.oxfordjournals.org
Dereeper, A., Guignon, V, Blanc, G., Audic S, Buffet S, Chevenet F, Dufayard, J.F, Guindon, S, Lefort V, Lescot M, Claverie J.M, Gascuel, O. (2008). Phylogeny.fr: robust phyogenetic analysis for the non-specialist. Nucleic Acids Res, 1; 36 (Web server issue) W 465-9 (http://www.phylogeny.fr/version 2_cgi.index.cgi)
Doyle J J, Doyle J L, 1990. Isolation of plant DNA from fresh tissue. Focus 12:13-15
EBI (2011). European Bioinformatics Institution (http://www.ebi.ac.uk/Tools/Services/ web_Clustal2).
FAOSTAT (2009). Acting together against banana diseases. Food and Agricultural Organization Statistics. Available online at http://www.fao.org
Gawel, N.J., Jarret, R and Wittemore, A.P. (1992). Restriction fragment length polymorphism (RFLP)-based phylogenetic analysis of Musa. Theoretical and Applied Genetics 84:286-290.
GeneDoc (2011). www.psc.edu/biomed/genedoc
Grapin, A., Noyer,J.J., Carreel, F., Dambier, D., Baurens, F.C., Lanaud, C and Lagoda, P.J.L. (1998). Diploid Musa acuminata genetic diversity assayed with sequence tagged microsatellite sites. Electrophoresis 19:1374- 1380.
Handelman, G.J. (2001). The evolving role of carotenoids in human biochemistry. Nutrition 17:818-822.
Hearne, S. J., Lorenzen , J., Town, C., and Zhuang, E. (2009). EST derived genomic resources for Musa. IITA Report .2008. www.IITA.org.
Henry R, Edwards K. 2009. New tools for single nucleotide polymorphism (SNP) discovery and analysis accelerating plant biotechnology. Plant Biotechnology Journal 7(4): 311
Hippolyte, I. and Roux,N. (2005). Molecular Markers for Allele Mining Proceedings of a workshop, 22–26 August 2005, MS Swaminathan Research Foundation, Chennai, India M. Carmen de Vicente, M and Glaszmann, J editors International Plant Genetic Resources Institute, Generation Challenge Programme. P26.
Jarret, R., Gawel, N., Wittemore, A.P., and Sharrock, S. (1994). RFLP-based phylogeny of Musa species in Papua New Guinea. Theoretical and Applied Genetics 84:579-584
Kloosteman , A. D., Budowle, B. and Daselaar, P.(1993). PCR-amplification and detection of the human DIS80 VNTR locus. Amplification conditions, population genetics and amplification in forensic analysis. International Journal for Legal Medicine, 7: 257-264.
Kumar, P. (2010). Biotech Bananas. Biotech Protecting the Banana Plant from Diseases. Available online at http://www.biotecharticles.com/
Lagoda, P.J.L., Noyer, J.L., Dambier, D., Baurens, F.C., Grapin, A. and Lanaud, C. (1998). Primer note – Sequence tagged microsatellite site (STMS) markers in the Musaceae. Molecular Ecology 7:659-663
Magnid, C. R. (2006). Comparing techniques Review: AFLP Data Interpretation and Analysis. Sequence-tagged site markers, RFLPs, RAPDs/Arbitrary techniques, SNPs, Diversity Arrays, Microsatellite. Dr. Cs. Forestales Depto. de Silvicultura Facultad de Cs. Forestales Universidad de Chile Santiago de Chile
Mayer, J. E., Pfeiffer, W.H. and Beyer, P. (2008). Biofortified Crops to Alleviate Micronutrient Malnutrition. Journal of Current Opinion in Plant Biology 11:166-170.
Mayer, J.E. (2007). Golden Rice, Golden Crops, Golden Prospects. Rev. Colomb. Biotecnol. 9 (1): 22-34.
Nageswara-Rao, M. and Soneji, J. R. (2008). Molecular Genetic Markers: What? Why? Which one for Exploring Genetic Diversity? Retrieved online from www.scienceboard.net/community/perspectives.210.html
National Center for Biotechnology Information, NCBI. (2011). http://www.ncbi.nlm.nih.gov
Noyer, J.L., Causse, S., Tomekpe, K., Bouet, A. and Baurens, F.C. (2005). A new image of plantain diversity assessed by SSR, AFLP and MSAP markers. Genetica 124: 61–69.
Perrier, X., Bakry, F., Carreel, F., Jenny, C., Horry, J., Lebot, V. and Hippolyte, I (2009). Combining Biological Approaches to Shed Light on the Evolution of Edible Bananas Ethnobotany Research & Applications 7:199-216. Available online at www.ethnobotanyjournal.org/vol7/i1547-3465-07-199.pdf
Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo MC, Peng J. (2013). Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci. 14(4):7061-88.
Shaheen, T., Zafar, Y. and Mehboob-ur, R. (2010). Detection of Single Nucleotide Polymorphisms in the conserved ESTs regions of Gossypium arboretum. Electronic Journal of Biotechnology, 13: 1-10. Available online at http://www.ejbiotechnology.info.
Ude, G., Pillay, M., Nwakanma D. and Tenkouano, A. (2002b). Genetic diversity in Musa acuminata Colla and Musa balbisiana Colla and some of their natural hybrids using AFLP markers. Theoretical and Applied Genetics 104:1246-1252.
Ude, G., Pillay, M., Nwakanma D. and Tenkouano, A. (2002a). Analysis of genetic diversity and sectional relationships in Musa using AFLP markers. Theoretical and Applied Genetics 104:1239-1245.
Utomo, H. S. and Linscombe, S. D. (2009). Current Patents and Future Development Underlying Marker –Assisted Breeding in Major Grain Crops. Recent Patents on DNA & Gene Sequences 3: 53-62.
Wang, D. G., Fan J. B., Siao, C. J, Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Wincheter, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson ,E., Mittmann, M., Morris M.S., Shen, N. P., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T. J, Lipshutz, R., Chee, M., Lander E. S. (1998). Large-scale identification, mapping and genotyping of SNP in the human genome. Science, 280:1077-1082.
Warburton, M. L. (2010). Identification and Use of Rare Natural Genetic Sequence Variation to Improve Levels of β-Carotene in Maize. ISB News Reports June 2010.
Welsch, R., Arango, J., Bar. C., Salazar. B., Al-Babili. S., Beltra. J., Ba. R., Salazar. B., Chavanrriaga. P., Ceballos. H., Tohme. J., and Beyer. P. (2010). Provitamin A Accumulation in cassava (Manihot esculenta) Roots Driven by a Single Nucleotide Polymorphism in a Phytoene Synthase Gene. Plant Cell. 22(10) 3348-3356.
Welsch. R. (2011). A Single Nucleotide Polymorphism in a Phytoene Synthase Gene can Simplify Provitamin A Biofortification of Cassava. ISB News Reports March 2011. 1-3
WHO database of vitamin A deficiency; http://www.who.int/vmnis/vitamina/data/en/index.html).
Wikipedia encyclopedia (2011). Banana. Retrieved online on 18th May, 2011 from http://en.wikipedia.org/wiki/Banana
Wong. C., Kiew, R., Argent, G., Set, O. Lee , S.K and Gan, Y.Y. (2002). Assessment of the validity of the sections in Musa (Musaceae) using AFLP. Annals of Botany 90:231-238.
Wong. J. (2011)."The Pursuit of Happiness (A.K.A. It Appears That The Writer Wrote About Bananas After Eating A Few Too Many)". The Science Creative Quarterly, University of British Columbia. Available online at http://www.scq.ubc.ca/the-pursuit-of-happiness-aka-it-appears-that-the-writer-wrote-about-bananas-after-eating-a-few-too-many/.
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