Integrated analysis of whole genome and transcriptome sequencing reveals a frameshift mutation associated with recessive embryonic lethality in Holstein cattle

Embryo loss is an important factor affecting fertility in dairy production. HH2 on chromosome 1 was identified as a haplotype associated with embryonic lethality in Holstein cattle. In the current study, both short-read and long-read whole genome sequencing were performed on four carriers and four non-carriers of HH2, to screen for variants in concordance with HH2 haplotype status. Sequence variation analysis revealed five putative functional variants of protein-coding genes, including a frameshift mutation (g.107172616delT) in intraflagellar transport protein 80 (IFT80) gene. Transcriptome analysis of whole blood indicated that no gene exhibited significantly differential expression or allele-specific expression (ASE) between carriers and non-carriers in the candidate region. These evidence point to g.107172616delT as the highest priority causative mutation for HH2. Protein prediction reveals that the frameshift mutation results in a premature stop codon to reduce the peptide chain from 760 to 383 amino acids and greatly alters the structure and function of IFT80 protein. Our results demostrate that a combination of multiple high throughput sequencing technoloigies is an efficient strategy to screen for the candidate causative mutations responsible for Mendelian traits, including genetic disorders.