Chromosomal imbalance in pigs showing a syndromic form of cleft palate

Abstract

Background Palatoschisis or cleft palate is a known anomaly in pigs resulting in their death. However, little is known about its aetiology. A detailed description of the phenotype was derived from necropsy and by computed tomography revealing that all 20 cases also exhibited hypodontia and renal cysts. Furthermore, a genetic origin was assumed due to dominant inheritance as all 20 recorded cases were confirmed offspring of a single boar. Results Single nucleotide variant (SNV) genotyping data were used to map the defect in the porcine genome and led to the detection of a chromosomal imbalance in the affected offspring. Whole genome sequencing of an affected piglet and a normal full sib was used to identify a chromosomal translocation and to fine map the breakpoints in the genome. Finally, we proved that the boar, which sired the malformed piglets, carried a balanced translocation. The detected translocation of Mb-sized segments of chromosome 8 and 14 had not been previously observed during karyotyping. All affected offspring were shown to be carriers of a partial trisomy of chromosome 14 including the FGFR2 gene, which is associated with various dominant inherited craniofacial dysostosis syndromes in man, and partial monosomy of chromosome 8 containing MSX1 known to be associated with tooth agenesis and orofacial clefts in other species. Conclusions This study illustrates the usefulness of recently established genomic resources in pigs. In this study, the application of genome-wide genotyping and sequencing methods allowed the identification of the responsible boar and the genetic cause of the observed defect. By implementing systematic surveillance, it is possible to identify genetic defects at an early stage and avoid further distribution of congenital disorders. Electronic supplementary material The online version of this article (10.1186/s12864-019-5711-4) contains supplementary material, which is available to authorized users.

Using short read sequencing to characterise balanced reciprocal translocations in pigs

“…It is certainly easier to obtain DNA material for sequencing than to perform chromosome staining with laborious analysis of lymphocyte cultures. Furthermore, sequence data provides an enormous amount of additional genomic information besides large karyotype defects, because it is possible to detect recessive lethal alleles (23), de novo events and smaller structural variation events (5), as well as SNP and InDels.…”

“…In general, sequence reads will not only enable detection of RTs, but also enhance re nement of the location of the breakpoints and detailed description of the breaks and junctions. In pigs, Grahofer et al (5) have successfully re ned the breakpoint location of an segregating RT causing malformed piglets using sequence data of an unbalanced and balanced sib. Donaldson et al (18) showed that translocation breakpoints are nonrandomly distributed across cytogenetic bands, they are more prevalent on longer cytogenetic bands, gram negative bands, and common fragile sites.…”

Using Short Read Sequencing to Characterise Balanced Reciprocal Translocations in Pigs

“…3 one of the lter criteria for the detected inter-chromosomal translocations was the presence of a matching pair, hence between brackets are the number of reciprocal pairs, i.e. the actual number of possible RTs Strict ltering: Basic ltering: Pass DELLY quality lter and precise position; nal ltering: mapping quality = 60, at least 10 split reads supporting the translocation, ≤ 60 discordant paired end reads, consensus alignment quality > 0.9, and matching second translocation with matching connection type present 2 Relaxed ltering: Translocations that failed the quality lter of DELLY (LowQual instead of PASS; basic ltering) and with 5 or more split reads supporting the translocation ( nal ltering) were retained. 3 one of the lter criteria for the detected inter-chromosomal translocations was the presence of a matching pair, hence between brackets are the number of reciprocal pairs, i.e.…”

“…Heterozygous individuals carrying a balanced RT produce three type of gametes: unbalanced gametes, balanced RT carrying gametes, and normal gametes. The unbalanced gametes give rise to embryos carrying partial monosomy and trisomy, which are mostly lethal or result in severely malformed piglets (1)(2)(3). Carriers of balanced RTs tend to be hypoproli c individuals with a reduction in litter size of approximately 36-39% (1,4).…”

“…An important limitation of current routine chromosome staining is the fact that not all chromosomal rearrangement can be detected. For instance, translocations smaller than the band size (~ 3-10 Mb) or exchange of parts similar in size and banding pattern remain undetected (2). In addition, chromosome staining does not indicate the exact breakpoint position, and does not allow further investigation of the breakpoint area.…”