Matthew McClure October 18, 2013
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1 Matthew McClure October 18, 2013
2 Microsatellite Imputation Infer MS from SNP Haplotype Genotyped ONCE
3 Initial Study 347 cattle -ISAG bovine MS parentage panel -Illumina HDSNP -Phased using BEAGLE Brown Swiss= 33 Guernsey= 16 Holstein= 250 Jersey= 48
4 SNP haplotype - MS allele Associations BM1824 Imputated Allele Haplotype Brown Swiss Guernesy Holstein Jersey Overall BABBAABBAAAABBBAABABABBBABBBAAAB BAABAABBAAAABBBAABABABBBABBBAAAB BBBBAABBAAAABBBAABABABBBABBBAAAB BABBAABBAAAABBBAABABABBBAABBBBAB BABBAABBAAAABBBAABABABBBABBBAABA BAABBAABBAAABBBAABABABABABBBAAAB BAABABABBAAABBAABAABABBBABAAAABA BAABABABBAAABBAABAABABBBABBBAAAB AABBAABBBAAABBAABAABABBBABBBAAAB AAAABAAABBABBAAABAABABABABAAAAAB AAAABAAABBABBAAABAABABABABAAAABA AAAABAAABBABBAAABAABABABABAAAAAA BAABBAABBBABBBAABBABABABABABAAAA AAAABAAABBABBAAABAABABABABABAAAA BABBAABBAABAABBBBBBABAAABABBBBAB BAAABABBAABAABBBBBBABAAABABBBBAB BAABAABBAABAABBBBBBABAAABABBBBAB _188 AABBAABBAABAABBBBBBABAAABABBBBAB AAAABABBAABAABBBBBBABAAABABBBBAB _ _ _190 17% MS-SNP haplotypes identical across >2 breeds
5 Beef Application 8 beef breeds: 116 animals Beagle phased Vlookup for MS Belgian Blue Charolais Maine-Anjou Texas Longhorn Ankole-Watusi Angus Devon Dexter ~77% had imputed alleles ~86% Concordance
6 Microsatellite Imputation Initial reference population: SNP + ISAG MS genotypes 7,076 Bos taurus 1,008 B. indicus 39 pure breeds B. taurus: 1,463 to 7,069 animals per MS Breed SNP SNP+MS Abondance Angus Aubrac Ayshire Bazadaise Beefmaster Belmont Red 40 Belgian Blue Blonde D'Aquitain Brahman Brangus Braunvieh Bretonne Pie Noire Brown Swiss Brune Des Alpes Charolais Chiangus 19 0 Crossbred Devon Dexter Fresian Gasconne Gelbvieh 44 0 Gir Guernsey Hereford Holstein Jersey Kerry 1 0 Limousin Longhorn Maine Anjou Montbeliarde Murray Grey 22 N'Dama 24 0 Nelore Normande Parthenaise Pie Rouge Des Plaines Piedmontese Red Angus Red Pie (italial) 2 0 Romagnola Rouge Flamande Salers Santa Gertrudis 99 0 Sheko 18 0 Shorthorn Simmental Swedish Red 12 9 Tarentaise Tropical Composite 336 Vosgienne Watusi TOTAL
7 Haplotype Selection: 1: Haplotypes centered on MS 2: >4 SNP-MS haplotype count 3: Haplotype is associated with 1 MS >90% 4: Maximize # animals selected A: Increase haplotype if >1% animals selected
8 Per MS: ~780 haplotypes, ~70 SNP per haplotype (1,088 total)
9 Microsatellite Imputation Initial reference population: SNP + ISAG MS genotypes 7,076 Bos taurus 1,008 B. indicus 39 pure breeds Initial validation population: SNP genotypes 8,622 Bos taurus & B. indicus animals 45 pure breeds, some crossbreds Breed SNP SNP+MS Abondance Angus Aubrac Ayshire Bazadaise Beefmaster Belmont Red 40 Belgian Blue Blonde D'Aquitain Brahman Brangus Braunvieh Bretonne Pie Noire Brown Swiss Brune Des Alpes Charolais Chiangus 19 0 Crossbred Devon Dexter Fresian Gasconne Gelbvieh 44 0 Gir Guernsey Hereford Holstein Jersey Kerry 1 0 Limousin Longhorn Maine Anjou Montbeliarde Murray Grey 22 N'Dama 24 0 Nelore Normande Parthenaise Pie Rouge Des Plaines Piedmontese Red Angus Red Pie (italial) 2 0 Romagnola Rouge Flamande Salers Santa Gertrudis 99 0 Sheko 18 0 Shorthorn Simmental Swedish Red 12 9 Tarentaise Tropical Composite 336 Vosgienne Watusi TOTAL
10 MS Accuracy: Parental Validation 1 MS conflict allowed Validation Population (N=1287) 90.55% Discovery Population (N=3470) 96.47%
11 Microsatellite Imputation -Beagle used PHASE + Haplotype. Angus Ayshire BelgianBlue Charolais Guernsey Hereford Holstein Jersey Limousin RedAngus Shorthorn Simmental Overall AAABABBAABBAABABBBBBAABBAAABBAAAABBABAAABAABBBBBAABBBBABABBBBBBBBBABAAAABBABAAAA BBBBBAAAABBAABABBBBAABAABAABAAABABBABAABABBAAAAABBAAAABABBBAAAAAAABBAAAABBABAAAA. 262 AABBBABBAAABBABAAABAABAABAABAAABABBABAABABBAAAAABBAAAABAABBAAAAAAABABBBBBBBABBBB BBBBBAAAABBAABABBBBAABAABAABBAAAABBABAABBABAAAAABBAAAABAABBAAAAABBABAAAABBABAAAA AABBABAAABBAABABBBBBAABBAABABABAAABBAABABABBBBBBAABBBBABAABBBABBBBAAAAAAAAABABAB AABBBABBABABBABAAABBAAABAAABBAAAABBABAAABAABBBBBAABBBBABBBBAAAABAABAABAAAABAABBB. 286 AABBBABBABABBABAAABBAABBAAABBAAAABBABAAABAABBBBBAABBBBABAAABBBBBBBAAAAAAABBAABBA AABBABBAABBAABABBBBBAABBAABABABAABBBBAAABABBBBBBAAABBBABAABBBBBBBAAAAAAABBBABBAB AABBABBAABBAABABBBBBBABBAABBAABAABBBAAAABABBBBBBAAABBBABAABBBBBBBAAAAAAABBBAABAB. 268 BBBBBAAAABBAABABBBBBAABBBAABBAABABBABBABABABBBBBAABBBBABBBBAAAAAAABABBBBBBBABAAA AABBABBAABBAABABBBBBAABBAAABBAAAABBABAAABAABBBBBAABBBBABAAABBBBBBBAAAAAAABBABBBB AABBBABBABABBABAAABBABAABAABBAAAABBABAAABAABAABBAABBBAABBABABBBBBBBAAAAAABBABBBB AAABABBAABBAABABBBBBAABBAAABBAAAABBABAAABAABBBBBAABBBBABAAABBBBBBBAAAAAAABBAABBA AAABBABBABABBABAAAAAABAABAABABBAAAABAAAABAABBBBBAABBBBABABBBBBBBBBABAAAABBABAAAA AABBABBAABBAABABBBBBAABBAAABBAAAABBABAAABAABBBBBAABBBBABAAABBBBBBBAAAAAAABBABBBB AAABABAAABBAABABBBBBAABBAAABBAAAABBABAAABAABBBBBAABBBBABABBBBBBBBBABAAAABBABAAAA AAABABBAABBAABABBBBBAABBAAABBAAAABBABAAABAABBBBBAABBBBABAAABBBBBBBAAAAAAABBAABBA AAABABBAABBAABABBBABABAABAABABBAAAABAAAABAABBBBBAABBBBABBBBAAAAAAABABBBBBBBABAAA AABBBABBAAABBABAAABAABBABAABBAABABBABAABABBAAAAABBAAAAABBBBAAAABAABBAAAABBABAAAA AABBBABBABABBABAAAABAABBAABABAABABBABBABABBAAAAABBAAAABABAABBBBBBBAAAAAAABBABBBB BM /258
12 Irish Parent Verification Process Certificate Issued Herdbook Rules Applied Failed Verified 2000 SNP shared: 3K, LD, 50K, HD, IDB Verified ISAG 120 SNP ICBF Database Weatherbys Hair Roots
13 Irish Parent Verification Process Certificate Issued Rules Applied Failed Failed Verified Verified Herdbook 1088 SNP + BEAGLE + 7,699 reference Imputed MS ICBF Database Weatherbys Hair Roots
14 Irish Parent Verification Process Report Generated Certificate Issued Herdbook Rules Applied Failed Verified Verified Wrong Sire Verify Result No Sire MS Verified Failed Verified Imputed MS ICBF Database Weatherbys Hair Roots
15 Genotyping Irish status for 2013 ~16,680 Animals genotyped ~5,600 Beef Animals ~750 failed genotyped: Call Rate <0.90 Sire Verification within breed By SNP: 48% to 10% By Microsatellite: 60% to 20% Remaining are Typed
16 Imputation Accuracy for Parentage Verification TGLA53= ~20% TGLA53= ~16% Applied: ICBF imputed MS genotypes. Reference: McClure et al s imputed MS genotype. Validation: McClure et al s traditional MS genotype Passed: no marker conflicts. Passed -1 off: 1 marker conflict occurred. Fail: >2 marker conflicts exist.
17 Impact of Microsatellite Imputation 4,952 Irish animals have had microsatellite genotypes imputed (October, 2013) as: SNP parentage failed (small #) Embryo transfer animal No SNP genotype on sire (most of them) >96% accuracy with imputed microsatellites Accuracy will increase for new runs >97% accuracy without TGLA53 Microsatellite imputation has saved Irish cattle farmers ~ 95,000, as cost of MS genotyping is ~ 20/animal.
18 Thank you <1990 s Present Future
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