Fine-mapping of QTL using high-density SNP genotypes - PowerPoint PPT Presentation

Fine-mapping of QTL using high-density SNP genotypes. Illumina genotyping arrays. BovineSNP50 54,001

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Fine-mapping of QTL using high-density SNP genotypes

Illumina genotyping arrays


54,001 SNPs (version 1)

54,609 SNPs (version 2)


777,962 SNPs


6,909 SNPs

Allows for additional SNPs (e.g.,GeneSeek Genomic Profiler)

BovineSNP50 v2



Bovine High-Density Bead Chip (HD)
  • 778K SNP chosen to
    • Be evenly spaced
    • Include some Y-specific SNP
    • Include mitochondrial SNP
  • Utilize across-breed information
  • Fine mapping of QTL
  • Enhanced performance in Zebu cattle
Estimation of marker effects
  • Predict traditional PTA using phenotypes and pedigree
  • Compute SNP effects using deregressed PTA weighted by reliability
    • Bayes A-type model
    • Regress small effects to mean
    • Allow large effects to grow
We got right to the point…

Cole, J.B. et al. 2009. Distribution and location of genetic effects for dairy traits. ICAR Tech Ser. 13:355–360.

…and found some interesting things


Cole, J.B., VanRaden, P.M., O'Connell, J.R., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., and Wiggans, G.R. 2009/ Distribution and location of genetic effects for dairy traits. J. Dairy Sci. 92(6):2931–2946.

Is luck better than skill?
  • ARS-BFGL-NGS-109285 at 57,895,121 Mb on BTA18
    • Signal consistent in HD data
  • Intronic to a putative CD33-related Siglec gene
    • This region is gene-rich
    • Many Siglecs involved in leptin signaling
  • Also affects gestation length

Maltecca, C., Gray, K. A., Weigel, K. A., Cassady, J. P., Ashwell, M. 2011. A genome-wide association study of direct gestation length in US Holstein and Italian Brown populations. Animal Genetics 42:1365-2052.

50k SNP are good for regions, not genes

Cole et al. 2009. J. Dairy Sci. 92(6):2931–2946.

Simple strategy
  • Compute SNP effects for trait of interest
  • Look for peaks
  • Perform bioinformatics on regions under interesting peaks
    • NCBI/Ensembl
    • Bovine Gene Atlas
    • Bovine QTLdb
Can we look at every peak?Are 777k SNP better than 50k?

VanRaden, P.M., Null, D.J., Sargolzaei, M., Wiggans, G.R., Tooker, M.E., Cole, J.B., Sonstegard, T.S., Connor, E.E., Winters, M., van Kaam, J.B.C.H.M., Van Doormaal, B.J., Faust, M.A., and Doak, G.A. Genomic imputation and evaluation using high density Holstein genotypes. J. Dairy Sci. (Submitted).

Case studies
  • Identification of causal variants associated with two haplotypes related to fertility
    • Discovery and validation of HH1 in U.S. Holstein cattle
    • Discovery and validation of JH1 in U.S. Jersey cattle
  • Fine-mapping of the Weaver locus
Recessive defect discovery
  • Check for homozygous haplotypes
    • 7 to 90 expected but none observed
    • 5 of top 11 are potentially lethal
    • 3.1% to 3.7% lower conception rates
    • Some slightly higher stillbirth rates
  • Confirmed Brachyspina same way
Novel haplotypes affecting fertility

VanRaden, P.M., Olson, K.M., Null, D.J., and Hutchison, J.L. 2011. Harmful recessive effects on fertility detected by absence of homozygous haplotypes. J. Dairy Sci. 94(12):6153–6161.

Economics of Next Generation Sequencing

Bovine genome = 2.85 billion bases

30X Coverage = about 90 billion bases

1 run on HiSeq2000 = 600 billion bases

20 animals sequenced to 30X coverage in 9 days (2 x 100 bp reads)

Cost about €19,600

HH1 in Holstein cattle
  • 75 SNPs spanning 7 Mbp on Bostaurus chromosome 5
  • Traced to Pawnee Farm ArlindaChief
  • Very popular bull
    • >16,000 daughters
    • >500,000 granddaughters
    • >2 millionrecorded great-granddaughters

Sequencing and haplotype reconstruction


  • Chief
  • Elevation




  • Valiant
  • Mark
  • Ivanhoe
  • Chief
  • Pat Son Elevation Chris
  • Royal Cedar Oak Hanna
  • Starbuck
  • To Mar Wayne Hay
  • Chairman
  • Ked Mark Justine
  • Blackstar
  • Juror


= Four bulls used to identify

mutation causative for HH1

= Eight bulls in study derived from purchased semen- ~30X seq. coverage

= Previously sequenced-6X on 454 Roche

Locating HH1 causal variant

Original75 SNP HH1 haplotype

Refined 38 SNP haplotype




Sequence analysis of HH1 SNPAnnotation of mutated gene
  • APAF1 - Bos taurus apoptotic peptidase activating factor 1
    • ATP binding factor
  • Gene expression for APAF1 in murine development begins between 7 and 9 d in heart, mesenchyme, periderm, and primitive intestine (Muller et al., 2005)
  • Gene knockout of APAF1 in mice leads to embryonic lethality (Muller et al., 2005)
    • Proteins required for thispathway/cascade are importantfor neural tube closure in vivo
SNP validation in HH1 interval
  • Designed Sequenome 24 assays for 12 SNP in the HH1 interval
  • Encompasses all SNP for coding, 3’ UTR, and downstream regions – and 5 other SNP covering all other genes in the interval
  • Tested wide diversity of haplotypes for HH1 region– use SNP50 DNA archive
Concordance of genotype to HH1 status

Exonic SNP

1.2% false positives at intron SNP

Concordance to HH1 haplotypes (12, 32)

One Mbp Interval

Genome Coordinates UMD3.1

HH1 - Conclusions
  • HH1 Haplotype 12 100% concordant with heterozygosity at one exonic SNP location (N=486)
  • HH1 Haplotype 32 100% concordant with het status at same exonic SNP location (N=11)
  • Other 256 non-carrier animals for HH1 interval were homozygous normal at this exonic SNP
  • One intronic SNP was 98.8% concordant to HH1 carrier status
  • No other individual SNP were viable candidates
  • Based on collaborative work with Harris Lewin
NGS sequencing of JH1 carrier animals
  • Sequencing run included Chocolate Soldier (JH1 founder) and Oman (for HH3)
  • 30X coverage of whole genome per animal
  • Funded by American Jersey Cattle Association
  • Found 38 candidate SNP in 492 kbpinterval
SNP Validation in JH1 Interval
  • Designed 30 Sequenomassays for 15 unique SNP in the JH1 interval
    • Only 1 SNP in a gene
      • Stopgain mutation in CWC15spliceosome-associated protein
      • Not expressed in every bovine tissue
  • Test all JH1 carriers in the SNP50 repository
    • 185 normal, 546 carriers
Spliceosome structure and CWC15

Will and Lührmann. 2011.

Spliceosome structure and

Function. Cold Spring


JH1 - SNP Validation Results
  • JH1 Haplotype 99.3% concordant with CWC15stopgain mutation
  • 5 non-concordant samples
    • False negative JH1 haplotypes (2 cases)
    • DNA misplating? Retest samples
  • 2 other SNP in complete LD with JH1-CWC15stopgain
  • Working with Jersey to complete an independent validation
Annotation is a big problem
  • Function of CWC15 in the bovine is unknown
    • CWC15ortholog in mice, mED1, expressed in early embryos (Duan et al., 2010)
  • No analagous studies in large mammals
    • Funding
    • Time
    • Perceived impact
Preliminary fine-mapping of Weavers
  • 35,353 SNP on BTA4
  • 69 Brown Swiss bulls with HD genotypes
  • 20 cases and 49 controls
    • No affected animals!
  • Microsatellite-mapped to the interval 43.2–51.2 cM
  • Phenotype based on name
Preliminary sliding-window analysisHD analysis and NGS
  • GWAS with Bovine HD
    • 20 carrier and 50 controls
    • Collaboration with Italian consortium
    • Refined historic intervalfrom 46-56Mb to 48-53Mb on BTA4
  • Weaver similar to ALS in humans
    • 18 annotated genes in interval
      • 7 of them interact with major gene responsible for heritable ALS
  • NGS performed on a pool of 10 Normal and 10 Carriers resulting in ~30x coverage
    • 117 SNV in the Weaver locus,
      • 1 synonymous, 3 non-synonymous
      • Test all SNP
Validation of Weavers
  • 5 Sequenom multiplexes tested 114 SNV
    • 715 Brown Swiss, 26 Carora, 4 Angus, 4 Holstein, 4 Jersey, 3 Senepol, 3 Herefords
  • Phenotype mapping refined locus to 35 SNP
  • The test is accurate
    • 5 Carora carriers based upon the 35 SNP
    • Multiple ‘assumed normal’ BS are carriers/affected
    • A few BS diagnosed normals were carriers
    • Found 1 Holstein heterozygous for the right 30 SNP and homozygous normal for the left 5 SNP
      • Related (6.25%) to BSUSA000000183023 (MEADOW VIEW MATT ALEX) who is a confirmed Weaver carrier
Future application of NGS sequencing

Researchers Catalog Loss-of-Function Variants in Human Protein-Coding Genes

NEW YORK (GenomeWeb News) – A Wellcome Trust Sanger Institute and Yale University-led team has sifted through data from three 1000 Genomes Project pilot efforts to find a set of authentic loss-of-function variants in the human genome.

"Each of us can be walking around with at least 20 genes basically inactivated," the study's first author, Daniel MacArthur, told GenomeWeb Daily News.

If this is true for humans, then is it true for cattle???

  • Targeted resequencing is effective
    • Genotyping-by-sequencing can identify loss-of-function mutations
  • Functional studies of protein function in vivo are needed
  • New precision mating strategies should be developed
  • AIPL, Beltsville, MD (USDA-ARS)
    • George Wiggans and Tabatha Cooper
  • BFGL, Beltsville, MD(USDA-ARS)
    • Larry Shade
    • George Liu, Derek Bickhart. Rueben Anderson, Sasho A.
    • Steve Schroeder
    • Alicia Beavers
  • University of Illinois, Urbana-Champaign
    • Denis Larkin
  • Meat Animal Research Center, Clay Center, NE (USDA-ARS)
    • Tim Smith, Tara McDaneld, John Keele

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