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Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole‐genome genotyping assay
Author(s) -
HARA Kazuhiro,
KON Yukari,
SASAZAKI Shinji,
MUKAI Fumio,
MANNEN Hideyuki
Publication year - 2010
Publication title -
animal science journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.606
H-Index - 38
eISSN - 1740-0929
pISSN - 1344-3941
DOI - 10.1111/j.1740-0929.2010.00766.x
Subject(s) - snp , genotyping , single nucleotide polymorphism , snp genotyping , genetics , biology , genotype , restriction fragment length polymorphism , population , allele frequency , tag snp , gene , medicine , environmental health
Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers. The allelic frequencies for each SNP were estimated using additional individuals by PCR‐RFLP (restriction fragment length polymorphism). A total of 87 SNP markers added in conjunction with previously developed 27 SNPs were evaluated to assess the utility of the test. The estimated identity power was 2.01 × 10 −34 . Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.7 and 0.99998010, respectively. This developed SNP panel was quite powerful and could successfully exclude false sires with a probability of >0.9999 even if the dam's genotype information was not obtained. The SNP system would contribute to management of the beef industry in Japan.