Mature body size is genetically correlated with growth rate, an important economic trait in the sheep industry. Mature body size has been studied extensively in humans as well as cattle and other domestic animal populations but not in sheep. Six‐hundred and sixteen ewes, across 22 breeds, were measured for 28 linear measurements representing various skeletal parts. PCA from these measures generated

Intramuscular fat (IMF) is an important meat‐quality trait of pigs, which influences pork’s shearing force, hydraulics, tenderness and juicy flavor. However, to achieve a higher percentage of lean meat, pigs with lower backfat thickness (BF) are intensively selected for, which may lead to a reduction in pork quality. Therefore, the objective of this study was to locate loci that affect IMF without

The study of skin color in cattle holds both economic and scientific interest. Several ocular diseases of cattle have been associated with low pigmentation of the eyelids, including ocular squamous cell carcinoma and infectious keratoconjunctivitis, the two most common ocular diseases affecting cattle production. Although low eyelid pigmentation is a well‐known risk factor for various ocular diseases

Egg‐type ducks and meat‐type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels

A GWAS was performed using the genotypes obtained by PorcineSNP60 v2 BeadChip and 11 phenotypic traits (carcass lean meat percentage; backfat thickness; Longissimus thoracis muscle thickness; lightness; backfat thickness measured with caliper at the midline; meat pH measured at about 1 h post mortem and 24 h post mortem; CIE L*, a* and b* color parameters; and water‐holding capacity). Three markers

The derived feathering phenotype beard in domestic birds is an ideal resource to investigate the genetic mechanisms controlling feather development and differentiation. In the present study, we performed a GWAS and QTL linkage analysis on the trait of beard in Beijing fatty chicken. One major QTL (1.2–1.9 Mb) was identified that could explain 34% of the phenotypic variation. The copy number variation

In this study, we analyzed 93 whole genomes from Chinese spot‐billed ducks (CSB), meat‐type ducks (MET), and egg and dual purpose‐type ducks (EDT) to characterize the genetic material flowing between the CSB and modern ducks. Using a frequency of shared identical‐by‐descent method, approximately 10.9 Mb introgression segments containing 140 genes were identified showing the signatures of introgression

Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific‐ and unspecific‐parent TRD) and genotypic (additive‐ and dominance‐TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243

The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor‐intensive during fish processing. Despite the difficulty in identifying genes related to the

Transmission ratio distortion (TRD) is defined as the observed deviation from the expected Mendelian inheritance of alleles from heterozygous parents. This phenomenon is attributed to various biological mechanisms acting on germ cells, embryos or fetuses, or even in early postnatal life. Current statistical approaches typically use two independent parametrizations assuming that TRD relies on allele‐

The small yellow croaker (Larimichthys polyactis) is one of the most commercially exploited marine fishes along the coast of the Yellow‐Bohai Sea and the East China Sea. In this study, we used next‐generation high‐throughput 2b‐RAD‐seq technology to identify novel SNPs in L. polyactis. We scored a total of 1 374 008 putative SNPs genome‐wide. Further filtration yielded a final dataset of 6457 high‐quality

Mucopolysaccharidosis (MPS) VI is a lysosomal storage disease caused by a deficiency of N‐acetylgalactosamine‐4‐sulfatase, also called arylsulfatase B (ARSB, EC 3.1.6.12). Dogs with MPS VI show progressive predominantly oculoskeletal signs homologous to those in human and feline patients. We report herein two pathogenic ARSB gene variants in Miniature Pinscher and Miniature Schnauzer dogs with MPS

Drip loss is an essential evaluation indicator for pork quality. It is closely related to other meat quality indicators, including water‐holding capacity, water loss rate and pH value at 45 min (pH1) and 24 h post‐mortem (pH2), and is influenced by environmental and genetic factors and their interactions. We previously conducted differentially expressed gene analysis to identify candidate genes affecting

Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two

A recessive sperm defect of Yorkshire boars was detected more than a decade ago. Affected boars produce ejaculates that contain spermatozoa with defective acrosomes, resulting in low fertility. The acrosome defect was mapped to porcine chromosome 15 but the causal mutation has not been identified. We re‐analyzed microarray‐derived genotypes of affected boars and confirmed that the acrosome defect maps

Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species – taurine cattle, zebu and yak – and their genetic interactions

Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree

In humans and mice, melanocortin receptor 4 (MC4R) and melanocortin receptor accessory protein 2 (MRAP2) can form a complex and control energy balance, thus regulating body weight and obesity. In pigs, a missense variant (p.Asp298Asn) of MC4R has been suggested to be associated with growth and fatness; however, the effect of Asp298Asn substitution on MC4R function is controversial, limiting its application

The American Paint Horse Association (APHA) records pedigree and performance information for their breed, a stock‐type horse valued as a working farm or ranch horse and as a pleasure horse. As the name implies, the breed is also valued for its attractive white‐spotting patterns on the coat. The APHA utilizes visual inspections of photographs to determine if coat spotting exceeds threshold anatomical

The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with

In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half‐sib families from five hatches derived from reciprocal crosses between an Arian fast‐growing line and an Urmia indigenous slow‐growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from

The Tibetan chicken is a native Chinese breed that lives at high elevations and has adapted to the extreme environmental conditions of the Tibetan Plateau. However, its hypoxic adaptation at the gene expression level is unclear. Here, we sequenced nine lung transcriptomes of the Tibetan chicken at three developmental stages (5 and 42 weeks and 4.5 years). A total of 1.02 billion clean reads were obtained

The chicken gizzard is the primary digestive and absorptive organ regulating food intake and metabolism. Body weight is a typical complex trait regulated by an interactive polygene network which is under the control of an interacting network of polygenes. To simplify these genotype–phenotype associations, the gizzard is a suitable target organ to preliminarily explore the mechanism underlying the regulation

Cryptorchidism is the most common disorder of sex development in dogs and testosterone plays a crucial role in the inguinal phase of the testes descending into the scrotum. The molecular background of impaired testosterone synthesis in the testes of cryptorchid dogs is poorly elucidated. In this study, we analyzed the expression of four genes involved in testicular steroidogenesis (CYP17A1, CYP19A1

The heterogeneity of climate and different agro‐ecological conditions in Iran have resulted in development of 27 indigenous sheep breeds. Wild Asiatic mouflon (Ovis orientalis) is believed to be the ancestor of Iranian sheep. Evaluation of genetic diversity and population structure within and among domestic breeds has important implications for animal breeding programs and genetic resources management

The more complex 3′ UTR in higher organisms may have the function of increasing post‐transcriptional gene regulation. Recent RNA sequencing technologies have provided us with the possibility to capture the complete 3′ UTR landscape of different species and cells. However, no systematic analysis of sheep‐related 3′ UTR has been performed. Here, we conducted a detailed analysis of the 3′ UTR with the

Feed efficiency (FE) is one of the most economically and environmentally relevant traits in the animal production sector. The objective of this study was to gain knowledge about the genetic control of FE in rabbits. To this end, GWASs were conducted for individual growth under two feeding regimes (full feeding and restricted) and FE traits collected from cage groups, using 114 604 autosome SNPs segregating

Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole‐genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi‐allelic SNPs and 92 229 indels located

A recessive form of arthrogryposis multiplex congenita (AMC) was detected 20 years ago in the Swiss Large White (SLW) pig population. A diagnostic marker test enabled the identification of carrier animals, but the underlying causal mutation remains unknown. To identify the mutation underlying AMC, we collected SNP chip genotyping data for 11 affected piglets and 23 healthy pigs. Association testing

Cranial cruciate ligament rupture (CCLR) is one of the leading causes of pelvic limb lameness in dogs. About 6% of Labrador Retrievers suffer from this orthopedic problem. The aim of this study was to determine the heritability of CCLR in this breed using SNP array genotyping data. DNA samples were collected from CCLR‐affected dogs (n = 190) and unaffected dogs over the age of 8 years (n = 143). All

Epidermolysis bullosa simplex (EBS) is a hereditary blistering disease affecting the skin and mucous membranes. It has been reported in humans, cattle, buffaloes and dogs, but so far not in cats. In humans, EBS is most frequently caused by variants in the KRT5 or KRT14 genes. Here, we report a case of feline epidermolysis bullosa simplex and describe the causative genetic variant. An 11‐month‐old male

MicroRNA resources in sheep are limited compared with those in other domesticated mammalian species. By sequencing small RNAs of sheep corpus luteum and endometrium, we have generated the largest amount of miRNA‐seq data and compiled the most comprehensive list thus far of miRNAs (n = 599) in sheep. Additionally, we observed a highly conserved maternally imprinted cluster of miRNAs on chromosome 18

Lamb weight at 8 months of age is an important trait in the sheep industry in terms of the onset of puberty around this age; however, knowledge of its effective genetic factors is limited. Therefore, a GWAS using the 50K SNP‐Chip was performed on 96 Baluchi sheep to identify the genomic regions associated with 8‐month weight. The results of the present study revealed five SNPs on chromosomes 4, 14

The swamp buffalo (Bubalus carabanensis) is mainly bred for meat, transport and rice cultivation in China and Southeast Asian countries. In the current study, we investigated the genetic diversity, maternal origin and phylogenetic relationship of swamp buffalo by analyzing 1,786 mitochondrial cytochrome b (cytb) sequences from China, Vietnam, Laos, Thailand, India and Bangladesh. Our results indicated

South Africa has a diverse array of phenotypically distinct and locally adapted sheep breeds that have been developed for different production systems ranging from mutton to wool and pelt, and some dual‐purpose and nondescript breeds kept by smallholder farmers. This study investigated genetic diversity, population genetic structure and divergence between South African sheep breeds in order to gain

Meat‐quality traits play an essential role in meat poultry production. To determine the genetic mechanisms of meat quality in Pekin ducks, we performed a large‐scale GWAS to identify quantitative trait loci affecting meat quality in Pekin ducks. We measured 10 traits in 542 Pekin ducks and genotyped each duck using genotyping‐by‐sequencing. The genetic parameters (genomic heritability, genetic correlation)

Ear morphology is an important determinant of sheep breeds. It includes different variable traits such as ear size and erectness, suggesting a polygenic architecture. Here, we performed a comprehensive genome‐wide analysis to identify regions under selection for ear morphology in 515 sheep from 17 breeds fixed for diverse ear phenotypes using 34k SNP genotyping data. GWASs for two ear type traits,

Large phenotypic differences have been observed between Tongcheng and Large White pigs. However, little is known about their genetic basis. This study performed a genome‐wide comparison of CNVs between Tongcheng and Large White pigs using genome sequencing data. By combining the advantages of three different strategies (read depth, paired‐end mapping and split read), we detected in total 18 687 CNVs

Predicting bull fertility prior to breeding is a current challenge for the dairy industry. The use of molecular biomarkers has been previously assessed. However, the integration of this information has not been performed to extract biologically relevant markers. The goal of this study was to integrate DNA methylation data with previously published RNA‐sequencing results in order to identify candidate

Heat stress negatively impacts the reproductive performance of dairy cows. The main objective of this study was to dissect the genetic basis underlying dairy cow fertility under heat stress conditions. Our first goal was to estimate genetic components of cow conception across lactations considering heat stress. Our second goal was to reveal individual genes and functional gene‐sets that explain a cow’s

The cAMP responsive element binding protein (CREB)‐regulated transcription coactivator 3 (CRTC3) is a member of the CRTC protein family and plays an important role in energy metabolism. The aim of this study was to determine if the expression of porcine CRTC3 is related to intramuscular fat (IMF) deposition and meat quality in Heigai pigs (a local fatty breed in China) and Duroc × Landrace × Yorkshire

Pigs are one of the earliest domesticated animals and multiple breeds have been developed to meet the various demands of consumers. EigenGWAS is a novel strategy to identify candidate genes that underlying population genetic differences and to infer candidate regions under selection as well. In this study, EigenGWAS and F st analyses were performed using the public re‐sequencing data of three typical

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed‐specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised

Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa ) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs

Parathyroid hormone (PTH ) is a crucial regulator of calcium homeostasis and bone remodeling, and the parathyroid hormone 1 receptor (PTH1R ) belongs to a class II G‐protein‐coupled receptor. PTH activates PTH1R , which mediates catabolic and anabolic processes in the skeleton. However, the functional mechanism of PTH1R has not been thoroughly elucidated in organisms. This study identified a 51 bp

Heteropaternal superfecundation may be defined as the fertilisation of two or more ova during the same oestrus cycle as a result of more than one coital act from different males; this results in foetuses being born in the same litter of the same age but different paternity. Heteropaternal superfecundation is more likely to occur in poly‐ovulatory species like sheep; moreover, female sheep are often

Mutations in lipase H (LIPH ) and lysophosphatidic acid receptor 6 (LPAR6 ), which are essential for the lysophosphatidic acid (LPA) signalling pathway, are associated with hypotrichosis and wooly hair in humans. Mutations in LPAR6 and keratin 71 (KRT71 ), result in unusual fur growth and hair structure in several cat breeds (Cornish Rex, Devon Rex and Selkirk Rex). Here, we performed target sequencing

Autochthonous cattle breeds are an important part of cultural heritage and reservoir of genetic diversity. Usually, such breeds have been selected over centuries and reflect adaptation to a specific local environment and human demands. However, owing to low effective population size in conjunction with increased inbreeding and genetic drift, many of these lineages are threatened with extinction. The

The number of teats is a morphological trait that influences the mothering ability of the sows and thus their reproduction performances. In this study, we carried out GWASs for the total number of teats and other 12 related parameters in 821 Italian Large White heavy pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip array. For four investigated parameters (total number of teats

We report haplotype‐based GWASs for 33 blood parameters measured in 843 Italian Large White pigs. In the single‐trait analysis, a total of 30 QTL for number of basophils, six erythrocyte traits (haemoglobin, haematocrit, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, mean corpuscular volume and red blood cell count) and two clinical–biochemical traits (alkaline phosphatase

An 11G nucleotide repeat in the 3′ UTR of FAM174A was recently postulated as a risk allele with a dominant mode of inheritance for equine metabolic syndrome (EMS) and laminitis status in Arabian horses. The objective of this project was to evaluate this hypothesis in a large and diverse across‐breed population. A total of 301 ponies, 292 Morgans, 64 Arabians, 49 Tennessee Walking Horses and 59 Quarter

The Nile tilapia (Oreochromis niloticus ) is a prominent farmed fish in aquaculture worldwide. Crossbreeding has recently been carried out between the Red‐Stirling and the wt Chitralada strains of Nile tilapia, producing a heterotic hybrid (7/8 Chitralada and 1/8 Red‐Stirling) that combines the superior growth performance of the Chitralada with the reddish coloration of the Red‐Stirling strain. While

Canine hip dysplasia is characterized by poor hip joint conformation and laxity. The disease is a complex trait influenced by both genetics and environment. Diagnosis and quantification of hip dysplasia are performed by radiographic examination of the hip joint and the diagnosis is used for making breeding decisions in many breeds. A prognostic genetic test (the Dysgen test) based on seven associated

Pakistani camels have been classified socio‐geographically into 20 breeds, but they have not yet been subjected to substantial selective pressures and the genetic basis for these breeds is not understood. However, it should be possible to distinguish them by use of molecular data. This study investigated the genetic diversity and population structure within and between two major Pakistani camel breeds

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge‐regression BLUP and BayesC , were used to identify SNPs in significant association with three milk production traits

In dogs and cats, unusual coat colour phenotypes may result from various phenomena, including chimerism. In the domestic cat, the tortoiseshell coat colour that combines red and non‐red hairs is the most obvious way to identify chimeras in males. Several cases of tortoiseshell males have been reported, some of which were diagnosed as chimeras without any molecular confirmation. Here, we report the