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ABSTRACT: This study aimed to investigate the genetics of rearing success (RS) in laying hens. Four rearing traits: clutch size (CS), first week mortality (FWM), rearing abnormalities (RA), and natural death (ND), were included as factors determining RS. Pedigree, genotypic, and phenotypic records of 4 purebred genetic lines of White Leghorn layers were available for 23,000 rearing batches obtained between 2010 and 2020. FWM and ND showed little or no variation amongst the 4 genetic lines over the years 2010–2020, whereas an increase was observed for CS and a decrease for RA. To determine whether these traits were heritable, genetic parameters for each trait were estimated, using a Linear Mixed Model. Heritabilities within lines were low (0.05–0.19 for CS, 0.01–0.04 for FWM, 0.02–0.06 for RA, 0.02–0.04 for ND, and 0.01–0.07 for RS). Additionally, genome wide association study was done to scan the genomes of the breeders to reveal single nucleotide polymorphisms (SNPs) associated with these traits. Manhattan plots indicated the existence of 12 different SNPs having a significant effect on RS. Thus, the identified SNPs will increase the understanding of the genetics of RS in laying hens.

Introduction: Since 2010, genomic selection in Swiss cattle breeding has led to significant progress in the two local Braunvieh populations, Brown Swiss and Original Braunvieh. However, it has also contributed to further inbreeding, leading to an increased risk of outbreaks of monogenic recessive defects. Some long-known inherited diseases such as arachnomelia, spinal muscular atrophy, spinal dysmyelination, Weaver syndrome and renal dysplasia are now of little clinical importance, while new haplotypes and gene variants associated with reproductive disorders have recently been described. These include so-called fertility haplotypes and genetic diseases that rarely or never occur homozygous because the affected animals die shortly after birth or early in pregnancy. This work provides an overview of the known recessive genetic defects in Swiss Braunvieh cattle. Data from 56, 000 Swiss breeding cattle on 12 genetic defects show that known inherited diseases in Braunvieh only occur very sporadically (defect allele frequency < 1 %). Only the recently described achromatopsia (Original Braunvieh haplotype 1) has a relevant defect allele frequency of over 7 % and should be taken into account for mating plans in order to avoid calves with day blindness. In addition, the Braunvieh haplotypes 6 and 14 and the Original Braunvieh haplotypes 4 and 9 occur between 2-6 % and the mating of heterozygous carriers should be avoided in order to avoid homozygous offsprings that are presumably not embryonically viable. The further spread of known genetic defects can be prevented through comprehensive genotyping of the breeding populations and the careful selection of breeding animals, recently also with the help of digital apps for mating planning. Thus, genetically caused reproductive losses or the number of affected animals can be reduced, animal health and welfare can be sustainably improved through selective breeding.

Highlights • A novel framework for evaluating the effect of external parameters on rearing success of European lobsters in SBCC systems has been presented. • Current, wave and turbulent measurements from Cornish waters were used to define external parameters, and internal parameters were predicted from external parameters. • Rearing limitations of European lobsters were defined from available literature based on DO consumption and, foraging and mobility behaviours. • The framework assessed and optimised the geographical location of SBCC systems, the vertical position in the water column and the SBCC design. Abstract Sea Based Container Culture (SBCC) is a mariculture technique that relies on the natural maintenance of environmental conditions, such as Dissolved Oxygen (DO) concentration and feed availability. This paper discusses a framework to evaluate the rearing success of European Lobsters (Homarus gammarus) in SBCC based on temporal and spatial variations of external parameters, including current velocity, wave velocity, turbulent fluctuations and dissolved oxygen concentrations. The temporal variations considered annual changes to the environment and the effect of biofouling growth, and the spatial variations considered the geographical location (case study of Falmouth bay, Cornwall) and vertical position in the water column. The internal parameters of the containers were modelled using transfer functions derived from previous experimental data. The internal parameters were compared to rearing limitations selected from available literature, which included foraging and mobility behaviours, and DO consumption. The time that internal parameters exceeded the rearing limitations was quantified, allowing rearing success to be predicted. This paper uses a case study of external parameters measured in Cornish waters, UK, to demonstrate the framework methodology. The framework showed that in situ measurements of current, wave and turbulence could be used to predict the internal parameters of SBCC containers, which can be used to predict theoretical rearing success based on rearing limitations. The framework indicated that DO concentrations within the containers should not affect rearing success; however, the foraging and mobility limits were exceeded by 0 to 30% of the time (depending on vertical position in the water column and assessment method). The paper aims to demonstrate the generic framework methodology and understands its limitations in predicting rearing success. The framework provides a tool to optimise the SBCC design for spatial and temporal varying conditions related to a geographical location or (vice versa) identify suitable mariculture sites based on SBCC design and environmental conditions. Additionally, the framework can optimise the vertical position of the SBCC in the water column and identify, from parameters considered, those that are most likely to affect rearing success. [ABSTRACT FROM AUTHOR]

Background: Renal syndromes are occasionally reported in domestic animals. Two identical twin Tyrolean Grey calves exhibited weight loss, skeletal abnormalities and delayed development associated with kidney abnormalities and formation of uroliths. These signs resembled inherited renal tubular dysplasia found in Japanese Black cattle which is associated with mutations in the claudin 16 gene. Despite demonstrating striking phenotypic similarities, no obvious presence of pathogenic variants of this candidate gene were found. Therefore further analysis was required to decipher the genetic etiology of the condition. Results: The family history of the cases suggested the possibility of an autosomal recessive inheritance. Homozygosity mapping combined with sequencing of the whole genome of one case detected two associated non-synonymous private coding variants: A homozygous missense variant in the uncharacterized KIAA2026 gene (g.39038055C > G; c. 926C > G), located in a 15 Mb sized region of homozygosity on BTA 8; and a homozygous 1 bp deletion in the molybdenum cofactor sulfurase (MOCOS) gene (g.21222030delC; c.1881delG and c.1782delG), located in an 11 Mb region of homozygosity on BTA 24. Pathogenic variants in MOCOS have previously been associated with inherited metabolic syndromes and xanthinuria in different species including Japanese Black cattle. Genotyping of two additional clinically suspicious cases confirmed the association with the MOCOS variant, as both animals had a homozygous mutant genotype and did not show the variant KIAA2026 allele. The identified genomic deletion is predicted to be highly disruptive, creating a frameshift and premature termination of translation, resulting in severely truncated MOCOS proteins that lack two functionally essential domains. The variant MOCOS allele was absent from cattle of other breeds and approximately 4% carriers were detected among more than 1200 genotyped Tyrolean Grey cattle. Biochemical urolith analysis of one case revealed the presence of approximately 95% xanthine. Conclusions: The identified MOCOS loss of function variant is highly likely to cause the renal syndrome in the affected animals. The results suggest that the phenotypic features of the renal syndrome were related to an early onset form of xanthinuria, which is highly likely to lead to the progressive defects. The identification of the candidate causative mutation thus enables selection against this pathogenic variant in Tyrolean Grey cattle. [ABSTRACT FROM AUTHOR]

Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle, has been recently reported to have an influence on the rearing success of calves. The affected animals show unresponsive diarrhea accompanied by hypocholesterolemia and usually die within the first weeks or months of life. Here, we show that whole genome sequencing combined with the knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred male carrying one copy of the critical 2.24-Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the non-affected carrier male. The genetic makeup of this key animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low-density lipoproteins, and therefore, the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia- 1 (FHBL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle. [ABSTRACT FROM AUTHOR]