Introduction

1. Source Combined With Source Suspect Area Carrier Possible Introduction Figure 1. CR loss during gestation. Sequencing and Discovery of HH1 Tracking Known Recessives • Large numbers of genotyped animals and affordable DNA sequencing now allow rapid discovery of new recessive defects. • Breeders can use haplotype tests or gene tests in selection and mating programs. • Located the source haplotype for 3 BS and 3 HO known recessives (Table 2). • HH1 fine mapped to 3.2 Mb suspect region. • Founder bull (Chief) and 3 sons (Mark,Ivanhoe Chief, and Valiant) were sequenced by U. Illinois. • Sequence analysis found 12 candidate SNPs but only 3 exonic. The suspect allele for a SNP in gene APAF1 produces a stopgain mutation in its homozygous recessive state. • APAF1 knockout also causes embryonic loss in mice. • 758 animals, including 486 HH1 carriers, were selected for APAF1 validation genotyping. • Concordance was 100% between HH1 carrier status and APAF1 mutation carrier status. Table 2. Using SNP haplotypes to track known recessives. Objectives • Locate haplotypes with significant expected homozygous animals but none observed. • Narrow down suspect region using fine mapping. • Use sequence data to locate the causative mutation within the fine mapped region. • Explore ways to use causative mutation test results in the future. Fine Mapping the Haplotypes Imputing Causative Mutations • Source haplotype is ~75 markers or ~ 5 Mb. • Only used crossovers between a 50K animal and a 50K parent. • Animals that have the source haplotype and a crossover of the source haplotype were used for fine mapping. • Interval that never becomes homozygous in live animals is the suspect region. • Haplotypes narrowed down to a suspect region ranging from 4.5 Mb for BH1to 0.8 Mb for JH1(Figure 2). • Carriers can be determined by haplotypes, gene tests, or combining and imputing. • For JH1730 causative mutation test results were used to impute test results for 6,784 50K animals. • Causative mutation test results were also imputed for the HO known recessives CVM, BLAD and DUMPS; 84,713, 83,694 and 92,234 tests were imputed respectively. • New carrier animals were discovered through imputation; 2,176 for CVM , 332 for BLAD and 3 for DUMPS. Finding Haplotypes Affecting Fertility Sequencing and Discovery of JH1 • 50K genotypes were used for haplotype discovery. Methods tested on Brachyspina. • Numbers of expected homozygous animals were calculated using real matings and ranged from 7 to 90 for haplotypes examined further. • Fertility records were used to confirm lethality, the number of carrier x carrier matings ranged from 936 to 52,449. • 5haplotypes, named by breed and number within breed, (Table 1) were confirmed to be lethal with affects on conception rate (CR) ranging from 3.0% to 3.7%. • CR loss occurs <60 days HH3 and JH1, <100 days for HH2, and throughout gestation for HH1 (Figure 1). • JH1 fine mapped to 0.8 Mb suspect region. • Founder bull (Soldier) and 10 other carriers sequenced at 30X coverage by BFGL with funding from American Jersey Cattle Association. • 15 candidate SNPs found but only 1 exonic. • Causative mutation (stopgain) was found in CWC15 gene. • 758 animals, including 486 JH1 carriers, were selected for CWC15 validation genotyping. • Concordance was 99.3% between JH1 carrier status and CWC15 mutation carrier status. Figure 2. Fine Mapping of JH1. Conclusions • 5 haplotypes affecting fertility have been reported to breeders since August 2011. • Suspect regions narrowed using crossovers. • Sequence data revealed the causative mutations for 2 of the 5, located in APAF1 for HH1 and CWC15 for JH1. • Imputation can combine information from both SNPs and QTLs to determine status. • Mating of heterozygotes should be avoided. Table 1. Haplotypes affecting fertility. HH2, HH3, BH1 Sequencing • Sequenced exome (expressed DNA) for 8 carriers of each defect. • Causative mutations are not obvious yet. • BH1 includes 2 consecutive SNPs that never become homozygous. Some genomic evaluations may exclude these because of Hardy-Weinberg edits, but could indicate location of defect. Acknowledgments • These methods were automated to update the suspect region and report haplotypes monthly. • Breeders receive official haplotype status for all genotyped animals (3K are unofficial). • Sequencing and analysis of HH1 conducted by H. Lewin, D. Larkin, A. Beavers, M. McClure, and Geneseek. • Fertility analyses conducted by J. Hutchison.