Animal genetics最新文献

Split paw pad disease is a scarcely defined phenotype characterized by skin lesions on the paw pads of dogs. We studied a family of German Shepherd dogs, in which four dogs developed intermittent paw pad lesions and lameness. The paw pads of two of the affected dogs were biopsied and demonstrated cleft formation in the stratum spinosum and stratum corneum, the outermost layers of the epidermis. Whole genome sequencing data from an affected dog revealed a private heterozygous 18 bp in frame deletion in the KRT5 gene. The deletion NM_001346035.1:c.988_1005del or NP_001332964.1:p.(Asn330_Asp335del) is predicted to lead to a loss of six amino acids in the L12 linker domain of the encoded keratin 5. KRT5 variants in human patients lead to various subtypes of epidermolysis bullosa simplex (EBS). Localized EBS is the mildest of the KRT5-related human diseases and may be caused by variants affecting the L12 linker domain of keratin 5. We therefore think that the detected KRT5 deletion in dogs represents a candidate causal variant for the observed skin lesions in dogs. However, while the clinical phenotype of KRT5-mutant dogs of this study closely resembles human patients with localized EBS, there are differences in the histopathology. EBS is defined by cleft formation within the basal layer of the epidermis while the cleft formation in the dogs described herein occurred in the outermost layers, a hallmark of split paw pad disease. Our study provides a basis for further studies into the exact relation of split paw pad disease and EBS.

Classical Ehlers–Danlos syndrome (cEDS) represents one of 14 subtypes of EDS, hereditary connective tissue disorders characterized by skin hyperextensibility, poor wound healing and, especially in human patients, joint hypermobility (Bowen et al., 2017; Malfait et al., 2020). cEDS is frequently inherited as an autosomal dominant trait and caused by pathogenic variants in the COL5A1 gene encoding the α-1 subunit of collagen type V (Mak et al., 2016; Symoens et al., 2012). Collagen type V represents only a small percentage of the total collagen content in most tissues but plays a key role in regulating collagen fibrillogenesis (Malfait et al., 2020). In cats, five different causative variants for cEDS have been reported in the COL5A1 gene so far (Kiener et al., 2022; McElroy et al., 2023; Spycher et al., 2018; OMIA:002165-9685). In this study, we investigated a female Maine Coon cat with suspected EDS due to complications in wound healing.

The 10-month-old female Maine Coon was presented to a specialty dermatology practice for referral and consultation regarding a nonhealing spay incision. The wound had shown minimal bleeding but had not resolved after multiple attempts at corrective surgery. On initial physical examination, the cat showed bilateral alopecia of the concave and multiple small wounds at the base of the pinnae from self-trauma. Scarring was present on the base of neck and the preauricular region. The wound associated with the spay incision was healed at the time of presentation, but a white scar persisted. Skin elasticity index was determined to be 23% (Figure 1a). The remaining physical examination was unremarkable.

Histopathological examination of a skin biopsy from the cat revealed mildly decreased dermal thickness. Collagen fibers were of variable size and width and increased numbers of fibroblasts were present in some regions (Figure 1b). The epidermis was of normal thickness and the hair follicles and adnexa present in adequate number.

Genomic DNA of the cat was isolated from an EDTA-blood sample. A PCR-free library was prepared and sequenced with 2 × 150-bp reads at 22× coverage. The sequencing reads were aligned to the F.catus_Fcat126_mat1.0 reference assembly and variant calling was performed as described (Jagannathan et al., 2019). Comparison to 87 control genomes (Table S1) yielded three homozygous and 182 heterozygous private protein changing variants (Table S2). However, none of these variants were located in any of the 20 known functional candidate genes for EDS that were analyzed (Table S3).

Therefore, the short-read alignments of the affected cat were visually inspected for structural variants in the same 20 candidate genes using the Integrative Genomics Viewer (Robinson et al., 2011). This led to the discovery of a heterozygous deletion spanning 33 7

Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed.

The Yarkand hare (Lepus yarkandensis) inhabits arid desert areas and is endemic to China. It has evolved various adaptations to survive in hot arid environments, including stress responses, the ability to maintain water homeostasis and heat tolerance. Here, we performed a selective sweep analysis to identify the candidate genes for adaptation to hot arid environments in the Yarkand hare. A total of 397 237 single-nucleotide polymorphisms were obtained from 80 Yarkand hares, which inhabit hot arid environments, and 36 Tolai hares (Lepus tolai), which inhabit environments with a mild climate, via specific-locus amplified fragment sequencing. We identified several candidate genes that were associated with the heat stress response (HSPE1), oxidative stress response (SLC23A and GLRX2), immune response (IL1R1 and IRG1), central nervous system development (FGF13, THOC2, FMR1 and MECP2) and regulation of water homeostasis (CDK1) according to fixation index values and θ_π ratios in the selective sweep analysis, and six of these genes (GLRX2, IRG1, FGF13, FMR1, MECP2 and CDK1) are newly discovered genes. To the best of our knowledge, this is the first study to identify candidate genes for adaptation to hot arid environments in the Yarkand hare. The results of this study enhance our understanding of the adaptation of the Yarkand hare to hot arid environments and will aid future studies aiming to functionally verify these candidate genes.

Cats with a distinctive white hair pattern of unknown molecular cause have been discovered in the Finnish domestic cat population. Based on the unique appearance of these cats, we have named this phenotype salmiak (“salty licorice”). The use of a commercially available panel test to genotype four salmiak-colored cats revealed the absence of all known variants associated with white-haired phenotypic loci: full White (W), Spotting (W^s) and the Birman white Gloves associated (w^g) allele of the KIT proto-oncogene (KIT) gene. Whole-genome sequencing on two salmiak-colored cats was conducted to search for candidate causal variants in the KIT gene. Despite a lack of coding variants, visual inspection of the short read alignments revealed a large ~95 kb deletion located ~65 kb downstream of the KIT gene in the salmiak cats. Additional PCR genotyping of 180 domestic cats and three salmiak-colored cats confirmed the homozygous derived variant genotype fully concordant with the salmiak phenotype. We suggest the newly identified variant be designated as w^sal for “w salmiak”.

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (F_ROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (N_e), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, F_ROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred N_e trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of N_e than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

Neuronal ceroid lipofuscinoses (NCL) are among the most prevalent neurodegenerative disorders of early life in humans. Disease-causing variants have been described for 13 different NCL genes. In this study, a refined pathological characterization of a female rabbit with progressive neurological signs reminiscent of NCL was performed. Cytoplasmic pigment present in neurons was weakly positive with Sudan black B and autofluorescent. Immunohistology revealed astrogliosis, microgliosis and axonal degeneration. During the subsequent genetic investigation, the genome of the affected rabbit was sequenced and examined for private variants in NCL candidate genes. The analysis revealed a homozygous ~10.7 kb genomic duplication on chromosome 15 comprising parts of the MFSD8 gene, NC_013683.1:g.103,727,963_103,738,667dup. The duplication harbors two internal protein coding exons and is predicted to introduce a premature stop codon into the transcript, truncating ~50% of the wild-type MFSD8 open reading frame encoding the major facilitator superfamily domain containing protein 8, XP_002717309.2:p.(Glu235Leufs*23). Biallelic loss-of-function variants in MFSD8 have been described to cause NCL7 in human patients, dogs and a single cat. The available clinical and pathological data, together with current knowledge about MFSD8 variants and their functional impact in other species, point to the MFSD8 duplication as a likely causative defect for the observed phenotype in the affected rabbit.

Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix–partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with ‘regulation of neurotransmitter secretion’ and ‘chromatin formation’. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes—KDM5C, LRRK2, and PME—was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.

Renal dysplasia (RD) is a complex congenital disease characterised by abnormal differentiation of renal tissue (Greco, 2001). Several forms of inherited RD have been reported in various animal species, including dogs (OMIA:001135-9615). The canine RD phenotype can range from asymptomatic to severe chronic kidney disease and the genetic etiology remains unclear (Cavalera et al., 2021; Dillard et al., 2018; Safra et al., 2015). Similar secondary kidney damage can also result from recessive metabolic disorders such as xanthinuria, known in dogs (OMIA:001283-9615) or cattle (OMIA:001283-9913). Leonbergers globally suffer from various diseases, with cancer, orthopedic and neurological conditions being the most frequent (Letko et al., 2020). However, in the owner-reported health survey, 0.44% of dogs were diagnosed with ‘renal system issues’ (Letko et al., 2020). The underlying cause of RD has not yet been described in this breed.

In a litter of eight purebred Leonbergers, one puppy was diagnosed with a congenital form of RD and euthanised at 11 weeks of age owing to worsening clinical signs. For diagnosis confirmation and histopathological examination, the kidneys were collected and fixed in 10% buffered formalin and embedded in paraffin. Sections of 1.5 μm were cut and compared with a kidney sample of a control dog (Figure 1a). Histological lesions were present in both kidneys. The cortex and medulla had areas of fetal glomeruli featuring small glomeruli with peripheral nuclei and inapparent capillaries. Some tubuli appeared small and immature and were lined by closely packed cuboidal epithelial cells while others were ectatic and sometimes contained birefringent greenish crystals and occasional mineralisation. Additionally, some tubuli contained intraluminal eosinophilic droplet material. The interstitium showed multifocal areas with mild fibrosis and aggregates of lymphocytes, plasma cells, a few neutrophils and macrophages, some of which were laden with hemosiderin (Figure 1b).

Samples for genome sequencing of the affected dog or his littermates were not available. Therefore, parental whole-genome sequencing (WGS) data were utilised to gain insights into the genetic basis of RD. Blood samples and the DNA of the unaffected dam and sire of the case were previously donated to the Vetsuisse Biobank for diagnostic purposes. Whole-genome sequencing was performed at ~20× read depth using Illumina NovaSeq6000 and variants were called as described previously (Letko et al., 2023). The pedigree records supported a recessive mode of inheritance (Figure S1). Therefore, the WGS data were queried for variants heterozygous in both parents with respect to canine reference UU_Cfam_GSD_1.0. A global cohort of 1541 dogs, including 85 unrelated adult Leonbergers not known to be RD affected (Table S1), was used to evaluate allele frequency of the 1 090 859 shared v

Dermal mosaicism can result in skin disorders with specific distribution patterns of the lesions. The most common example is X-chromosomal functional mosaicism, in which the distribution pattern results from random X-chromosome inactivation (Lyonization) (Vreeburg & van Steensel, 2012). Three different skin patterns have been described, namely Blaschko lines, the checkerboard pattern and lateralization (Happle, 2006). Verrucous epidermal keratinocytic nevi (OMIA 002117) caused by variants in the X-chromosomal NSDHL gene may present with any of these patterns. The encoded NAD(P)H steroid dehydrogenase-like protein is a C4 demethylase involved in post-squalene cholesterol biosynthesis. Pathogenic NSDHL variants result in disruption of an essential step in cholesterol biosynthesis with a subsequent aggregation of toxic intermediates and a lack of cholesterol in the skin (Caldas & Herman, 2003; König et al., 2000). In heterozygous female dogs, this presents as a cornification disorder and is inherited as an X-linked semidominant trait (Bauer et al., 2017; Christen et al., 2020; Leuthard et al., 2019). NSDHL-associated disorders in humans cause a more severe phenotype involving congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD syndrome; König et al., 2000). In hemizygous males, such variants have been described as embryonic lethal (Happle et al., 1980).

A 10-month-old female intact Appenzeller Mountain Dog was presented with an 8 month history of severe, progressive hyperkeratosis of the paw pads causing lameness and a primarily left-sided multifocal hyperkeratosis of the haired skin, causing alopecia and mild pruritus. The lesions began on the left inner pinna and hind paw pads and slowly progressed to involve all four paws, although the right front was only mildly affected. Stripes of alopecia with hyperkeratosis were present on the lateral and caudal left thigh, with multiple smaller areas on the left tarsus, left lateral neck and left hip. Complete blood count, serum biochemistry and skin cytology were within normal limits and a fungal culture was negative. Multiple skin punch biopsies were taken under sedation to further pursue a diagnosis. Based on these results the paw pads were treated topically in an attempt to reduce cholesterol precursors in the skin and therefore hyperkeratosis. Two-percent ketoconazole cream and then 2% simvastatin ointment were tried successively, without improvement. The lesions on the haired skin then cleared completely with oral ketoconazole 5 mg/kg once daily but the paw pads remained quite hyperkeratotic, requiring repeated trimming (Figure 1).

Histopathologically, skin biopsies showed moderate to severe hyperplasia of the epidermis and infundibula of the hair follicles, forming spiked fronds (Figure 2). The infundibula of the hair fo