Properties of different density genotypes used in dairy cattle evaluation Topics


НазваProperties of different density genotypes used in dairy cattle evaluation Topics
Дата конвертації26.04.2013
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Properties of different density genotypes used in dairy cattle evaluation


Topics

  • Chips available

    • 3K, 50K_v1, 50K_v2, HD, others
  • Selection of SNPs from each chip

    • Edits for conflict and missing rates
    • Properties of chosen SNPs
  • Corrections to map locations

  • Accuracy of imputation



Why Multiple Chips?

  • More SNPs can increase accuracy

  • Fewer SNPs can decrease cost

  • Different animals are worth more

  • Full sequence = 3 billion bases

  • More laboratories may read DNA

    • Perhaps similar to milk meters


Illumina chips are [mostly] nested



How do we deal with other chips?

  • Impute to highest density

  • Account for loss of accuracy due to imputation error

  • Store only observed genotypes

  • Label evaluations with source of genotype



SNP Edits

  • SNPs from each chip kept if:

    • > 1% minor allele frequency (MAF) in any breed (polymorphic)
    • < 10% missing genotypes
    • < 2% parent-progeny conflicts
  • A SNP is excluded:

    • if it has a high call rate, but also has a high parent-progeny conflict



Good Clustering



Not-So-Good Clustering



Hardy-Weinberg-Chetverikov

  • AA p2 AB 2pq BB q2

    • Random mating, no selection, unlimited population size, no random genetic drift, no gene flow, etc.
    • Compute ratios within breed, then combine ratios
  • SNP deleted: (observed/expected)

    • Heterozygous < .3 or > 1.3
    • Homozygous < .1 or > 10


SNPs Selected



Properties of Selected SNP



Correction of Map Locations

  • Some misplaced SNP on UMD3.0 (Zimin, 2009)

  • 50K SNP locations fixed by cooperation between:

    • AIPL / BFGL
    • Univ of Maryland
    • Univ of Missouri
    • Univ of Guelph


Correction of Map Locations

  • For 777K chip, misplaced SNP are simply deleted

  • Count haplotypes per 50 marker segment

  • Get SNP correlations with segment

  • Remove least correlated SNP blocks (140 markers deleted)



SNP Correlation Matrix



Heat Map Correlations



3K vs. 50K Reliability

  • Compare 319 regenotyped animals

    • 3K chip in December 2010
    • 50K chip in April 2011
  • Correct imputation = 96.3% of SNP

  • Correlations of PTAs = .94 to .97

  • Reliability of NM$ = 32% for PA, 60% for 3K, and 65% for 50K



Other Chips

  • Affymetrix

    • 650K, 25K, 10K
  • Illumina

    • Bovine LD 6.5K (replacing 3K)
  • Parentage Only



Summary / Conclusions

  • Many chips are now available

    • More choices in the future
  • Different chips must be comparable

    • In the past year, three new chips added, and SNP edits are automated.
  • Increase reliabilities for less cost



Questions about Chips or Maps?



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