Functional significance of genetic polymorphisms

Abstract

Natural genetic polymorphisms are gifts from nature and sources of variations at all levels. The post-genomic era permits new perspectives on interpreting genetic polymorphisms and also poses challenges for scientists to answer system questions. Rather than a comprehensive coverage of genetic polymorphisms up-to-date, this review attempts to present some of the results in a somewhat coherent manner to highlight the needs and potentials of pertinent studies.

Keywords

omics / genetic polymorphism / metabolic pathway / functional significance / neutral status

References

[1] Aguade M (2001). Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes, in Arabidopsis thaliana. Mol Biol Evol, 18: 1-9

[2] Akyildiz M, Gowik U, Engelmann S, Koczor M, Streubel M, Westhoff P (2007). Evolution and function of a cis-regulatory module for mesophyll-specific gene expression in the C-4 dicot Flaveria trinervia. Plant Cell, 19: 3391-3402

[3] Bernatchez L, Landry C (2003). MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?J Evol Biol, 16: 363-377

[4] Bonafè M, Barbieri M, Marchegiani F, Olivieri F, Ragno E, Giampieri C, Mugianesi E, Centurelli M, Franceschi C, Paolisso G (2003). Polymorphic variants of insulin-like growth factor I (IGF-I) receptor and phosphoinositide 3-kinase genes affect IGF-I plasma levels and human longevity: cues for an evolutionarily conserved mechanism of life span control. J Clin Endocrinol Metab, 88: 3299-3304

[5] Borevitz J O, Hazen S P, Michael T P, Morris G P, Baxter I R, Hu T T, Chen H, Werner J D, Nordborg M, Salt D E, Kay S A, Chory J, Weigel D, Jones J D G, Ecker J R (2007). Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci USA, 104: 12057-12062

[6] Bugni J M, Han J, Tsai M, Hunter D J, Samson L D (2007). Genetic association and functional studies of major polymorphic variants of MGMT. DNA Repair, 6: 1116-1126

[7] Clark R M, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu T T, Fu G, Hinds D A, Chen H, Frazer K A, Huson D H, Schölkopf B, Nordborg M, Rätsch G, Ecker J R, Weigel D (2007). Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science, 317: 338-342

[8] Corona G, Toffoli G (2004). High throughput screening of genetic polymorphisms by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Comb Chem High Throughput Screen, 7: 707-725

[9] Crosbie P A, McGown G, Thorncroft M R, O'Donnell P N, Barber P V, Lewis S J, Harrison K L, Agius R M, Santibáñez-Koref M F, Margison G P, Povey A C (2008). Association between lung cancer risk and single nucleotide polymorphisms in the first intron and codon 178 of the DNA repair gene, O-6-alkylguanine-DNA alkyltransferase. Int J Cancer, 122: 791-795

[10] Dauwe R, Morreel K, Goeminne G, Gielen B, Rohde A, Van Beeumen J, Ralph J, Boudet A M, Kopka J, Rochange S F, Halpin C, Messens E, Boerjan W (2007). Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration. Plant J, 52: 263-285

[11] Eanes W F (1999). Analysis of selection on enzyme polymorphisms. Annu Rev Ecol Syst, 30: 301-326

[12] Emerson J J, Cardoso-Moreira M, Borevitz J O, Long M (2008). Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science, 320: 1629-1631

[13] Fiehn O (2002). Metabolomics-the link between genotypes and phenotypes. Plant Mol Biol, 48: 155-171

[14] Flowers J M, Sezgin E, Kumagai S, Duvernell D D, Matzkin L M, Schmidt P S, Eanes W F (2007). Adaptive evolution of metabolic pathways in Drosophila. Mol Biol Evol, 24: 1347-1354

[15] Franceschi C, Olivieri F, Marchegiani F, Cardelli M, Cavallone L, Capri M, Salvioli S, Valensin S, Benedictis G D, Iorio A D, Caruso C, Paolisso G, Monti D (2005). Genes involved in immune response/inflammation, IGF1/insulin pathway and response to oxidative stress play a major role in the genetics of human longevity: the lesson of centenarians. Mech Ageing Dev, 126: 351-361

[16] Gregory B D, Yazaki J, Ecker J R (2008). Utilizing tiling microarrays for whole-genome analysis in plants. Plant J, 53: 636-644

[17] Hanson M A, Gaut B S, Stec A O, Fuerstenberg S I, Goodman M M, Coe E H, Doebley J F (1996). Evolution of anthocyanin biosynthesis in maize kernels: The role of regulatory and enzymatic loci. Genetics, 143: 1395-1407

[18] Hedrick P W (2006). Genetic polymorphism in heterogeneous environments: the age of genomics. Annu Rev Ecol Evol Syst, 37: 69-93

[19] Hennig L (2007). Patterns of beauty-omics meets plant development. Trends Plant Sci, 12: 287-293

[20] Hudson M E (2008). Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Res, 8: 3-17

[21] Ibeagha-Awemu E M, Kgwatalala P, Ibeagha A E, Zhao X (2008). A critical analysis of disease-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig. Mamm Genome, 19: 226-245

[22] Keurentjes J J, Koornneef M, Vreugdenhil D (2008). Quantitative genetics in the age of omics. Curr Opin Plant Biol, 11: 123-128

[23] Keurentjes J J B, Fu J, de Vos C H R, Lommen A, Hall R D, Bino R J, Plas L H W, Jansen R C, Vreugdenhil D, Koornneef M (2006). The genetics of plant metabolism. Nature Genet, 38: 842-849

[24] Klein J, Sato A, Nikolaidis N (2007). MHC, TSP, and the origin of species:from immunogenetics to evolutionary genetics. Annu Rev Genet, 41: 281-304

[25] Lay J O, Borgmann S, Liyanage R, Wilkins C L (2006). Problems with the “omics”. Trends Anal Chem, 25: 1046-1056

[26] Lee D O, Jee B C, Ku S-Y, Suh C S, Kim S H, Choi Y M, Moon S Y, Kim J G (2008). Relationships between the insulin-like growth factor I (IGF-I) receptor gene G3174A polymorphism, serum IGF-I levels, and bone mineral density in postmenopausal Korean women. J Bone Miner Metab, 26: 42-46

[27] Lu Y (2002). Molecular Evolution at the Self-Incompatibility Locus of Physalis longifolia (Solanaceae). J Mol Evol, 54: 784-793

[28] Lu Y (2006). Historical events and allelic polymorphism at the gametophytic self-incompatibility locus in Solanaceae. Heredity, 96: 22-28

[29] Margison G P, Heighway J, Pearson S, McGown G, Thorncroft M R, Watson A J, Harrison K L, Lewis S J, Rohde K, Barber P V, O’Donnell P, Povey A C, Santibáñez-Koref M F (2005). Quantitative trait locus analysis reveals two intragenic sites that influence O6-alkylguanine-DNA alkyltransferase activity in peripheral blood mononuclear cells. Carcinogenesis, 26: 1473-1480

[30] Milinski M (2006). The major histocompatibility complex, sexual selection, and mate choice. Annu Rev Ecol Evol Syst, 37: 159-186

[31] Miller M R, Dunham J P, Amores A, Cresko W A, Johnson E A (2007). Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res, 17: 240-248

[32] Mockler T C, Ecker J R (2005). Applications of DNA tiling arrays for whole-genome analysis. Genomics, 85: 1-15

[33] Morozova O, Marra M A (2008). Applications of next-generation sequencing technologies in functional genomics. Genomics, 92: 255-264

[34] Nelson T, Dengler N G (1992). Photosynthetic tissue differentiation in C4 plants. Int J Plant Sci, 153: S93-S105

[35] Obbard D J, Jiggins F M, Halligan D L, Little T J (2006). Natural selection drives extremely rapid evolution in antiviral RNAi genes. Curr Biol, 16: 580-585

[36] Paape T, Igic B, Smith S D, Olmstead R, Bohs L, Kohn J R (2008). A 15-myr-old genetic bottleneck. Mol Biol Evol, 25: 655-663

[37] Pecsenye K, Komlósi I, Saura A (2004). Heritabilities and additive genetic variances of the activities of some enzymes in Drosophila melanogaster populations living in different habitats. Heredity, 93: 215-221

[38] Ragoussis J, Elvidge G P, Kaur K, Colella S (2006). Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research. PloS Genet, 2: e100

[39] Rausher M D, Lu Y, Meyer K (2008). Variation in constraint versus positive selection as an explanation for evolutionary rate variation among anthocyanin genes. J Mol Evol, 67: 137-144

[40] Richman A (2000). Evolution of balanced genetic polymorphism. Mol Ecol, 9: 1953-1963

[41] Richman A D, Kao T H, Schaeffer S W, Uyenoyama M K (1995). S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle). Heredity, 75: 405-415

[42] Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyren P (1996). Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem, 242: 84-89

[43] Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Bruedigam C, Kopka J, Willmitzer L, Zamir D, Fernie A R (2006). Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol, 24: 447-454

[44] Smith N G C, Eyre-Walker A (2002). Adaptive protein evolution in Drosophila. Nature, 415: 1022-1024

[45] Solberg O D, Mack S J, Lancaster A K, Single R M, Tsai Y, Sanchez-Mazas A, Thomson G (2008). Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies. Human Immun, 69: 443-464

[46] Tatar M, Bartke A, Antebi A (2003). The endocrine regulation of aging by insulin-like signals. Science, 299: 1346-1351

[47] Traherne J A (2008). Human MHC architecture and evolution: implications for disease association studies. Int J Immunogenet, 35: 179-192

[48] Trauger S A, Kalisak E, Kalisiak J, Morita H, Weinberg M V, Menon AL, Poole F L 2nd, Adams M W, Siuzdak G (2008). Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile. J Proteome Res, 7: 1027-1035

[49] Wegner K M, Kalbe M, Milinski M, Reusch T B (2008). Mortality selection during the 2003 European heat wave in three-spined sticklebacks: effects of parasites and MHC genotype. BMC Evol Biol, 8: 124

[50] Whitt S R, Wilson L M, Tenaillon M I, Gaut B S, Buckler E S 4th (2002). Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci USA, 99: 12959-12962

[51] Wishart D S (2008). Metabolomics: applications to food science and nutrition research. Trends Food Sci & Tech, 19: 482-493

[52] Zhang X, Shiu S, Cal A, Borevitz J O (2008). Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana. PloS Genet, 4: e100032

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