MilkProtChip - a microarray of SNPs in candidate genes associated with milk protein biosynthesis - development and validation

• Autorzy: Kaminski S , Ahman A , Rusc A , Wojcik E , Malewski T
• Języki publikacji: EN

Abstrakty

EN

MilkProtChip is an oligonucleotide microarray based on the arrayed primer extension (APEX) technique, allowing genotyping of single nucleotide polymorphisms (SNPs) in genes of interest for bovine milk protein biosynthesis. APEX consists of a sequencing reaction primed by an oligonucleotide anchored with its 5’end to a glass slide and terminating one nucleotide before the polymorphic site. The extension with one fluorescently labeled dideoxy nucleotide complementary to the template reveals the polymorphism. A total of 75 SNPs were selected among those associated directly or potentially with milk protein content. Among the 75 SNPs, 4 did not produce a positive signal. Most of the remaining SNPs produced a signal for both strands, except for 4 (one strand). In the validation step, 12 Polish Holstein bulls, 1 Polish Red bull, 1 bison (Bison bonasus), 11 Jersey cows and 25 Polish Holstein cows were screened to validate SNPs. Among the 71 selected SNPs - 26 were found monoallelic, the rest showing at least two genotypes for the entire population under study. All the animals were earlier genotyped for 2-5 SNPs by PCR-RFLP and PCR sequencing and all showed complete concordance with APEX genotyping. APEX reactions showed relatively high signal frequencies: more than 0.9, 0.9-0.8 and below 0.8, for 65,4 and 2 DNA samples, respectively. The primary application of the MilkProtChip is the simultaneous genotyping of dozens of SNPs to reveal and clarify the genetic background of milk protein biosynthesis. The chip may possibly be used for dairy cattle identification and paternity analysis, evolutionary studies, the evaluation of genetic distances between wild and domestic cattle breeds and the domestication history of bovine species.

Słowa kluczowe

EN

MilkProtChip preparation; animal genetics; arrayed primer extension technique; milk protein; validation; oligonucleotide microarray; development; candidate gene; biosynthesis; single nucleotide polymorphism; gene; ruminant milk; protein content

• Wydawca: -
• Czasopismo: Journal of Applied Genetics
• Rocznik: 2005
• Tom: 46
• Numer: 1
• Opis fizyczny: p.45-58,fig.,ref.

Twórcy

autor

Kaminski S

• Department of Animal Genetics, University of Warmia and Mazury in Olsztyn, Michala Oczapowskiego 5, 10-719 Olsztyn, Poland

autor

Ahman A

• Asper Biotech Ltd., Oru 3, Tartu, Estonia

autor

Rusc A

• Department of Animal Genetics, University of Warmia and Mazury in Olsztyn, Michala Oczapowskiego 5, 10-719 Olsztyn, Poland

autor

Wojcik E

• Department of Animal Genetics, University of Warmia and Mazury in Olsztyn, Michala Oczapowskiego 5, 10-719 Olsztyn, Poland

autor

Malewski T

• Institute of Animal Genetics and Breeding, Polish Academy of Sciences, Jastrzębiec, Poland

Bibliografia

• Altschul LSF, Gish W, Miller W, Myers EW, Lipman DJ, 1990. Basic local alignment search tool. J Mol Biol 215: 403—410.
• Antoniou E, Grosz M, Skidmore JC, 1998. Cloning, analysis and SSCP characterization of the SH2 domain of the bovine gene STAT5. J Anim Sci 76, Supplement 1: 379.
• Aschaffenburg R, Drewry J, 1955. Occurrence of different beta-lactoglobulin in cow’s milk. Nature 176: 219.
• Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J, et al. 2000. An ordered comparative map of the cattle and human genomes. Genome Res 10: 1359-1368.
• Bleck TG, Bremel DR, 1993a. Sequence and single-base polymorphisms of the bovine alfa-lactalbumin 5’-flanking region. Gene 126: 213-218.
• Bleck TG, Bremel DR, 1993b. Correlation of the alfa-lactalbumin (+15) polymorphism to milk production and milk composition of Holsteins. J Dairy Sci 76: 2292-2298.
• Blott S, Kim JJ, Moisio S, Schmidt-Küntzel A, Cornet A, Berzi P, et al. 2003. Molecular dissection of a quantitative trait locus : A phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 163: 253-266.
• Boichard D, Grohs C, Bourgeois F, Cerquiera F, Faugeras R, Neau A, et al. 2003. Detection of genes influencing economic traits in three French dairy cattle breeds. Genet Sel Evol 35: 77-101.
• Cheung VG, Spielman RS, 2002. The genetics of variation in gene expression. Nature Genet 32: 522-525.
• Coronini R, De Looze MA, Puget P, Bley G, Ramani SV, 2003. Decoding the literature on genetic variation. Nature Biotechnol 21: 21-29.
• Ehrmann S, Bartenschlager H, Geldermann H, 1997. Quantification of gene effects on single milk proteins in selected groups of dairy cows. J Anim Breed Genet 114: 121-132.
• Eigel NW, Butler EJ, Emstrom AC, Farrel Jr.MH, Harwalkar RV, Jenness R, Whitney MR, 1984. Nomenclature of proteins of cow’s milk: fifth revision. J Dairy Sci 67: 1599-1631.
• Falaki M, Gengler N, Sneyers M, Prandi A, Massart S, Formigoni A, Burny and growth hormone receptor genes with milk production traits for Italian Holstein-Friesian bulls. J Dairy Sci 79: 1446-1453.
• Farber CR, Medrano JF, 2003. Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences. Anim Genet 34: 11-18.
• Flisikowski K, Zwierzchowski L, 2002. Single-strand conformation polymorphism within exon 7 of the bovine STAT5A gene. Anim Sci Pap Rep 20: 133-137.
• Fries R, Durstewitz G, 2001. Digital DNA signatures: SNPs for animal tagging. Nature Biotechnology 19: 508.
• Geldermann H, Gogol J, Kock M, Tacea G, 1996. DNA variants within the 5’ flanking region of bovine milk protein encoding genes. J Anim Breed Genet 113: 261-267.
• Gorodetsky IS, Kershulyte DR, Korobko VG, 1983. Nucleotide sequence of cDNA of κ-casein macropeptide of Bos taurus. Bioorganischeskaya Khimia 9: 1693-1695.
• Heaton MP, Harhay GP, Bennett GL, Stone RT, Grosse WM, Casas C, et al. 2002. Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle. Mamm Genome 13: 272-281.
• Jacob E, Puhan Z, 1992. Technological properties of milk as influenced by genetic polymorphism of milk proteins (a review). Inter Dairy J 2: 157-178.
• Kaminski S, 1999. Simultaneous SSCP genotyping of two bovine casein loci. Anim Sci Pap Rep 17: 29-33.
• Kaminski S, 2000. Associations between polymorphism within regulatory and coding fragments of bovine kappa-casein gene and milk performance traits. J Anim Feed Sci 9: 435-446.
• Kaminski S, Zabolewicz T, 1998. SSCP polymorphism within 5’ region of bovine beta-lactoglobulin (LGB) gene. J Appl Genet 39: 97-102.
• Kaminski S, Zabolewicz T, 2000. Association between bovine beta-lactoglobulin polymorphism within coding and regulatory sequences and milk performance traits. J Appl Genet 41: 91-99.
• Kamiński S, Ruść A, Malewski T, 2004. Single nucleotide polymorphism database of candidate genes associated with cow milk protein biosynthesis. J Anim Feed Sci 13: 53-66.
• Kurg A, Tonisson N, Georgiou I, Shumaker J, Tollett J, Metspalu A, 2000. Arrayed primer extension: solid-phase four-color DN A resequencing and mutation detection technology. Genet Test 4: 1-7.
• Lageziel A, Lipkin E, Soller M, 1996. Associations between SSCP haplotypes at the bovine growth hormone gene and milk protein percentage. Genetics 142: 945-951.
• Leveziel H, Metenier L, Mahe FM, Choplain J, Furet PJ, Pabeuf G, Mercier CJ, Grosclaude F, 1988. Identification of the two common alleles of the bovine kappa-casein locus by the RFLP technique, using the enzyme Hind III. Genet Sci Evol 20: 247-254.
• Lien S, Alestrom P, Steine T, Langsrud T, Vegarud G, Rogne S, 1990. A method for-lactoglobulin genotyping of cattle. Livestock Prod Sci 25: 173-176.
• Lien S, Kaminski S, Alestrom P, Rogne S, 1993. A simple and powerful method for linkage analysis by amplification of DNA from single sperm cells. Genomics 16: 41-44.
• Lindersson M, Lunden A, Andersson L, 1995. Genotyping bovine milk proteins using allele discrimination by primer length and automated DNA sizing technology. Anim Genet 26: 67-72.
• Looft C, ReinschN, Karali-Albrecht C, Paul S, Brink M, Thomsen H, et al. 2001. A mammary gland EST showing linkage disequilibrium to a milk production QTL on bovine chromosome 14. Mamm Genome 12: 646-650.
• Mao LI, Buttazzoni GL, Aleandri R, 1992. Effects of polymorphic milk protein genes on milk yield and composition traits in Holstein Cattle. Acta Agric Scand, Anim Sci 42: 1-8.
• Martin P, Szymanowska M, Zwierzchowski L, Leroux C, 2002. The impact of genetic polymorphisms on the protein composition of ruminant milks. Reprod Nutr Dev 42: 433-459.
• Mosig MO, Lipkin E, Khutoreskaya G, Tchourzyna E, Soller M, Friedmann A, 2001. A whole genome scan for quantitative trait loci affecting milk protein percentage in Israeli-Holstein cattle, by means of selective milk DNA pooling in a daughter design, using an adjusted false discovery rate criterion. Genetics 157 : 1683-1698.
• Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M, 1999. Mining SNPs from EST databases. Genome Res 9(2): 167-174.
• Prinzenberg EM, Weimann C, Brandt H, Bennewitz J, Kaim E, Schwerin M, Erhardt G, 2003. Polymorphism of the bovine CSN1S1 promoter: linkage mapping, intragenic haplotypes, and effects on milk production traits. J Dairy Sci 86: 2696-2705.
• Rando A, Di Gregorio P, Masina P, 1988. Identification of bovine kappa-casein genotypes at the DNA level. Anim Genet 19: 51-54.
• Schild AT, Wagner V, Geldermann H, 1994. Variants within the 5’-flanking regions of bovine milk protein genes: I. kappa-casein-encoding gene. Theor Appl Genet 89: 116-120.
• Schild AT, Geldermann H, 1996. Variants within the 5’-flanking regions of bovine milk-protein-en- coding genes. III. Genes encoding the Ca-sensitive caseins αsl, αs2 and β. Theor Appl Genet 93: 887-893.
• Schwerin M, Maak S, Fuerbass R, 2002. Interacting phenotypic effects of co-existing variants within a single gene - cellular stress response is significantly affected by interactions between promoter and 3 ’-UTR variants of the porcine hsp70.2 gene. Papers of 28th Conference of the ISAG, 11-15 August, Gettingen - Germany: 64.
• Shumaker JM, Metspalu A, Caskey CT, 1996. Mutation detection by solid phase primer extension. Hum Mutat 7(4): 346-354.
• Sonstegard TS, Garrett WM, Ashwell MS, Bennett GL, Kappes SM, Van Tassell CP, 2000. Comparative map alignment of BTA27 andHSA4 and 8 to identify conserved segments of genome containing fat deposition QTL. Mamm Genome 11: 682-688.
• Sorensen P, Grochowska R, Holm L, Henryon M, Lovedahl P, 2002. Polymorphism in the bovine growth hormone gene affects endocrine release in dairy calves. J Dairy Sci 85: 1887-1893.
• Stone RT, Grosse WM, Casas E, Smith TPL, Keele JW, Bennet GL, 2002. Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mamm Genome 13: 211-215.
• Voelker RG, BleckTG, Wheeler BM, 1997. Single-base polymorphisms within the 5 ’ flanking region of the bovine alfa-lactalbumin gene. J Dairy Sci 80: 194-197.
• Wagner JS, Schild AT, Geldermann H, 1994. DNA variants within the 5’-flanking region of milk-protein- encoding genes. II The β-lactoglobulin-encoding gene. Theor Appl Genet 89: 121-126.