Identification of small and large genomic candidate variants in bovine pulmonary hypoplasia and anasarca syndrome

Abstract

SummaryThe pulmonary hypoplasia and anasarca syndrome (PHA) is a congenital lethal disorder, which until now has been reported in cattle and sheep. PHA is characterized by extensive subcutaneous fetal edema combined with hypoplasia or aplasia of the lungs and dysplasia of the lymphatic system. PHA is assumed to be of genetic etiology. This study presents the occurrence of PHA in two different cattle breeds and their genetic causation. Two PHA cases from one sire were observed in Slovenian Cika cattle. Under the assumption of monogenic inheritance, genome‐wide homozygosity mapping scaled down the critical regions to 3% of the bovine genome including a 43.6 Mb‐sized segment on chromosome 6. Whole‐genome sequencing of one case, variant filtering against controls and genotyping of a larger cohort of Cika cattle led to the detection of a likely pathogenic protein‐changing variant perfectly associated with the disease: a missense variant on chromosome 6 in ADAMTS3 (NM_001192797.1: c.1222C>T), which affects an evolutionary conserved residue (NP_001179726.1: p.(His408Tyr)). A single PHA case was found in Danish Holstein cattle and was whole‐genome sequenced along with its parents. However, as there was no plausible private protein‐changing variant, mining for structural variation revealed a likely pathogenic trisomy of the entire chromosome 20. The identified ADAMTS3 associated missense variant and the trisomy 20 are two different genetic causes, which shows a compelling genetic heterogeneity for bovine PHA.

Constitutional trisomy 20 in an aborted Holstein fetus with pulmonary hypoplasia and anasarca syndrome

“…The absence of reports of most chromosomal aberrations indicates their lethality, most probably during early gestation 11 . This further case of chromosome 20 trisomy shared important features with a previously described association of trisomy 20 with PHA in cattle 3 . Therefore, it presents a recurrent mutation event apparently leading to bovine PHA, a disorder that was for a long time assumed to be recessively inherited.…”

“…Genomic DNA extracted from a sample from the ear was whole‐genome sequenced as described before and deposited publicly (http://www.ebi.ac.uk/ena, sample accession no. SAMEA6528903) 3 . Variant calling revealed no evidence for the presence of protein‐changing variants in the ADAMTS3 gene; neither the previously described missense variant causing PHA in Cika cattle was found nor any other.…”

“…As there had not been reported any other PHA case in this Holstein family, the constitutional trisomy probably arose through non‐disjunction during early cell division in the fertilized egg. Rare cases of chromosomal aberrations in cattle are described for a small number of chromosomes (18, 20, 21, 22, 28 and 29) and are associated with brachygnathia, blindness, reduced growth, aplasia of various organs and other malformations 3 , 6–13 . Whereas most of them are associated with severe body malformations and are lethal, 3 , 6–8 , 11 , 13 a few trisomies have been observed in living animals 9 , 10 , 12 .…”

“…The extensive accumulation of fluid in the subcutaneous tissue and formation of large subcutaneous cysts deteriorate the body conformation, thus potentially causing dystocia. In cattle, PHA was recently described as either a recessive disorder owing to a missense variant in ADAMTS3 in Cika cattle or as a dominant disorder caused by a trisomy of chromosome 20 in a single PHA‐affected Holstein calf 3 …”

A de novo mutation in KRT5 in a crossbred calf with epidermolysis bullosa simplex

“…Skin biopsies from this area and from other representative cutaneous lesions were taken immediately after euthanasia for histological analysis, whereas the necropsy was completed at the university a few 30 except for the trimming, which was performed using fastp. 31 Further preparation of the genomic data had been done according to Häfliger et al 32 In order to find private variants, we compared the genotypes of the affected calf with 493 cattle genomes of various breeds that had been sequenced in the course of other ongoing studies and that are publicly available (Table S2) (Table S3) To confirm that the c.534_536delCAA variant in KRT5 was a de novo mutation, the affected genomic region was amplified by polymerase chain reaction (PCR) and Sanger sequenced in the affected calf, its Belgian Blue sire and Holstein dam based on DNA extracted from EDTA blood of the dam, and from both EDTA blood and semen of the sire. PCR products were amplified using flanking primers for the KRT5 exon 1 deletion with 5 0 -AGGCATCCAAGAGGTCACCG-3 0 (forward primer) and 5 0 -TAGCACATATCCCACACTCATGG-3 0 (reverse primer).…”