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Selection and management of DNA markers for use in genomic evaluation

lijanan33 添加于 2015-5-23 21:48 | 1545 次阅读 | 0 个评论

作者
Wiggans GR, VanRaden PM, Bacheller LR, Tooker ME, Hutchison JL, Cooper TA, Sonstegard TS
摘要
To facilitate routine genomic evaluation, a database was constructed to store genotypes for 50,972 single nucleotide polymorphisms (SNP) from the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). Multiple samples per animal are allowed. All SNP genotypes for a sample are stored in a single row. An indicator specifies whether the genotype for a sample was selected for use in genomic evaluation. Samples with low call rates or pedigree conflicts are designated as unusable. Among multiple samples that qualify for use in genomic evaluation, the one with the highest call rate is designated as usable. When multiple samples are stored for an animal, a composite is formed during extraction by using SNP genotypes from other samples to replace missing genotypes. To increase the number of SNP available, scanner output for approximately 19,000 samples was reprocessed. Any SNP with a minor allele frequency of > or = 1% for Holsteins, Jerseys, or Brown Swiss was selected, which was the primary reason that the number of SNP used for USDA genomic evaluations increased. Few parent-progeny conflicts (< or = 1%) and a high call rate (> or = 90%) were additional requirements that eliminated 2,378 SNP. Because monomorphic SNP did not degrade convergence during estimation of SNP effects, a single set of 43,385 SNP was adopted for all breeds. The use of a database for genotypes, detection of conflicts as genotypes are stored, online access for problem resolution, and use of a single set of SNP for genomic evaluations have simplified tracking of genotypes and genomic evaluation as a routine and official process.
详细资料
- 关键词: Animals; Cattle/*genetics; Dairying/*methods; *Databases, Genetic; Female; Genetic Markers/*genetics; Genome/*genetics; Genotype; Male; Polymorphism, Single Nucleotide; United States; United States Department of Agriculture
- 文献种类: Journal Article
- 期刊名称: Journal of Dairy Science
- 期刊缩写: J Dairy Sci
- 期卷页: 2010年第93卷第5期 2287-2292页
- 地址: Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350, USA. George.Wiggans@ars.usda.gov
- ISBN: 0022-0302
学科领域生物医药 » 基础医学
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