Detection of a Frameshift Deletion in the SPTBN4 Gene Leads to Prevention of Severe Myopathy and Postnatal Mortality in Pigs

Rare and population-specific functional variation across pig lines

BACKGROUND

It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in commercial livestock populations, in particular regarding population-specific variation and how it can affect applications such as across-breed genomic prediction.

METHODS

We re-sequenced the whole genome of 7848 individuals from nine commercial pig lines (average sequencing coverage: 4.1×) and imputed whole-genome genotypes for 440,610 pedigree-related individuals. The called variants were categorized according to predicted functional annotation (from LOF to intergenic) and prevalence level (number of lines in which the variant segregated; from private to widespread). Variants in each category were examined in terms of their distribution along the genome, alternative allele frequency, per-site Wright's fixation index (F_ST), individual load, and association to production traits.

RESULTS

Of the 46 million called variants, 28% were private (called in only one line) and 21% were widespread (called in all nine lines). Genomic regions with a low recombination rate were enriched with private variants. Low-prevalence variants (called in one or a few lines only) were enriched for lower allele frequencies, lower F_ST, and putatively functional and regulatory roles (including LOF and deleterious missense variants). On average, individuals carried fewer private deleterious missense alleles than expected compared to alleles with other predicted consequences. Only a small subset of the low-prevalence variants had intermediate allele frequencies and explained small fractions of phenotypic variance (up to 3.2%) of production traits. The significant low-prevalence variants had higher per-site F_ST than the non-significant ones. These associated low-prevalence variants were tagged by other more widespread variants in high linkage disequilibrium, including intergenic variants.

CONCLUSIONS

Most low-prevalence variants have low minor allele frequencies and only a small subset of low-prevalence variants contributed detectable fractions of phenotypic variance of production traits. Accounting for low-prevalence variants is therefore unlikely to noticeably benefit across-breed analyses, such as the prediction of genomic breeding values in a population using reference populations of a different genetic background.

Review: Balancing Selection for Deleterious Alleles in Livestock

Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.

Novel bi-allelic variants expand the SPTBN4-related genetic and phenotypic spectrum

Neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND, OMIM #617519) is an autosomal recessive disease caused by homozygous or compound heterozygous variants in SPTBN4 coding for type 4 βIV-spectrin, a non-erythrocytic member of the β-spectrin family. Variants in SPTBN4 disrupt the cytoskeletal machinery that controls proper localization of ion channels and the function of axonal domains, thereby generating severe neurological dysfunction. We set out to analyze the genetic causes and describe the clinical spectrum of suspected cases of NEDHND. Variant screening was done by whole exome sequencing; clinical phenotypes were described according to the human phenotype ontology, and histochemical analysis was performed with disease-specific antibodies. We report four families with five patients harboring novel homozygous and compound heterozygous SPTBN4 variants, amongst them a multi-exon deletion of SPTBN4. All patients presented with the key features of NEDHND; severe muscular hypotonia, dysphagia, absent speech, gross motor, and mental retardation. Additional symptoms comprised horizontal nystagmus, epileptiform discharges in EEG without manifest seizures, and choreoathetosis. Muscle histology revealed both characteristics of myopathy and of neuropathy. This report expands the SPTBN4 variant spectrum, highlights the spectrum of morphological phenotypes of NEDHND-patients, and reveals clinical similarities between the NEDHND, non-5q SMA, and congenital myopathies.

Is hull cleaning wastewater a potential source of developmental toxicity on coastal non-target organisms?

Chemical contaminants can be discharged by vessel hull cleaning processes, such as scraping, jet spraying, and painting, all of which produce readily transportable contaminants into the marine environment, where they are referred to as 'hotspots' of contamination in coastal areas. However, many countries have not yet established effective evaluation methods for disposal of waste mixtures or management guidelines for areas of hull cleaning. To define the toxic effects of wastewater from vessel hull cleaning in dry docks on resident non-target organisms, we investigated the chemical concentrations and developmental toxicity on embryonic flounder, which is an organism sensitive to chemical contamination. In this study, the dominant inorganic metal discharged was zinc when cleaning Ship A (300 tons) and copper for Ship B (5,000 tons). The wastewater from high-pressure water blasting (WHPB) of Ship A (300 tons) and Ship B (5,000 tons) produced a largely overlapping suite of developmental malformations including pericardial edema, spinal curvature, and tail fin defects. Forty-eight hours after exposure, the frequency percentage of malformation began to increase in embryos exposed to a 500-fold dilution of WHPB from Ships A and B. We performed transcriptome sequencing to characterize the toxicological developmental effects of WHPB exposure at the molecular level. The results of the analysis revealed significantly altered expression of genes associated with muscle cell differentiation, actin-mediated cell contraction, and nervous system development (cutoff P < 0.01) in embryonic flounder exposed to high-pressure cleaning effluent from Ship A. Genes associated with chromatin remodeling, cell cycling, and insulin receptor signaling pathways were significantly altered in embryonic flounder exposed to WHPB of Ship B (cutoff P < 0.01). These findings provide a greater understanding of the developmental toxicity and potential effects of WHPB effluent on coastal embryonic fish. Furthermore, our results could inform WHPB effluent management practices to reduce impacts on non-target coastal organisms.