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QTL analysis for early growth in an intercross between native Japanese Nagoya and White Plymouth Rock chicken breeds using RAD sequencing‐based SNP markers Anim. Genet. (IF 2.841) Pub Date : 2021-01-18 B. H. Essa; S. Suzuki; A. J. Nagano; S. Z. Elkholya; A. Ishikawa
An F2 population of 239 chickens was obtained by an intercross between Nagoya (NAG), a native Japanese breed with low growth, and White Plymouth Rock (WPR), a Western breed with high growth. Using SNP markers obtained by restriction site‐associated DNA sequencing, genome‐wide QTL analysis was performed and it revealed three QTL for early postnatal growth in the F2 population at genome‐wide 5% significance
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Positive selection signatures in Anqing six‐end‐white pig population based on reduced‐representation genome sequencing data Anim. Genet. (IF 2.841) Pub Date : 2021-01-17 L. Guo; H. Sun; Q. Zhao; Z. Xu; Z. Zhang; D. Liu; Q. R. Qadri; P. Ma; Q. Wang; Y. Pan
Anqing six‐end‐white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore
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Genomic characteristics of four different geese populations in China Anim. Genet. (IF 2.841) Pub Date : 2021-01-15 H. Liu; C. Zhu; W. Song; W. Xu; Z. Tao; S. Zhang; H. Li
It is well known that many Chinese goose breeds differ substantially in economic performance, but the genetic changes involved are still poorly understood. This study sequenced 35 individuals from four goose breeds namely Shitou, Zhedong White, Taihu, and Zi with an average sequencing depth of 10× for each individual. Among these populations, SNPs were identified, which clustered the individuals into
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Online Mendelian Inheritance in Animals (OMIA): a record of advances in animal genetics, freely available on the Internet for 25 years Anim. Genet. (IF 2.841) Pub Date : 2020-11-06 F. W. Nicholas
For the last 25 years, Online Mendelian Inheritance in Animals (OMIA) has been providing free global access to an ever‐increasing record of discoveries made by animal geneticists around the world. To mark this 25‐year milestone, this document provides a brief account (including some pre‐history) of how OMIA came to be; some timelines of important discoveries and advances in the genetics of the animal
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Rabbits – their domestication and molecular genetics of hair coat development and quality Anim. Genet. (IF 2.841) Pub Date : 2020-11-20 K. Dorożyńska; D. Maj
The European rabbit (Oryctolagus cuniculus) is the only representative of its genus living in present‐day Europe and North Africa, and all domestic rabbits are descendants of this one species, which is native to the Iberian Peninsula. There are over 300 breeds of rabbits that differ in size, coat color, length of ears and type of fur. Rabbits are bred for various reasons, such as for laboratory animals
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Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations Anim. Genet. (IF 2.841) Pub Date : 2020-11-11 A. Moscarelli; M. T. Sardina; M. Cassandro; E. Ciani; F. Pilla; G. Senczuk; B. Portolano; S. Mastrangelo
Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity
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Genome‐enabled prediction of reproductive traits in Nellore cattle using parametric models and machine learning methods Anim. Genet. (IF 2.841) Pub Date : 2020-11-16 A. A. C. Alves; R. Espigolan; T. Bresolin; R. M. Costa; G. A. Fernandes Júnior; R. V. Ventura; R. Carvalheiro; L. G. Albuquerque
This study aimed to assess the predictive ability of different machine learning (ML) methods for genomic prediction of reproductive traits in Nellore cattle. The studied traits were age at first calving (AFC), scrotal circumference (SC), early pregnancy (EP) and stayability (STAY). The numbers of genotyped animals and SNP markers available were 2342 and 321 419 (AFC), 4671 and 309 486 (SC), 2681 and
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Brain‐specific monoallelic expression of bovine UBE3A is associated with genomic position Anim. Genet. (IF 2.841) Pub Date : 2020-11-17 J. Li; C. Zhang; H. Si; S. Gu; X. Liu; D. Li; S. Meng; X. Yang; S. Li
Genomic imprinting is a rare epigenetic process in mammalian cells that leads to monoallelic expression of a gene with a parent‐specific pattern. The UBE3A (ubiquitin protein ligase E3A) gene is imprinted with maternal allelic expression in the brain but biallelically expressed in all other tissues in humans. The silencing of the paternal UBE3A allele is thought to be caused by the paternally expressed
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Unraveling molecular mechanisms involved in the development of leptin resistance using the pig as a model Anim. Genet. (IF 2.841) Pub Date : 2020-12-02 E. Mármol‐Sánchez; J. S. Artman; M. Fredholm; S. Cirera
The increase in obesity worldwide underlines the need for research concerning its metabolic and genetic determinants. One of the most intriguing mechanisms regarding obesity involves leptin and its signaling cascade. Leptin is a key regulator contributing to the fine‐tuned crosstalk between nutrient availability and appetite signaling in the central nervous system. Owing to ethical concerns, many human
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Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene Anim. Genet. (IF 2.841) Pub Date : 2020-12-14 V. A. Bâlteanu; T. F. Cardoso; M. Amills; M. G. Luigi‐Sierra; I. Egerszegi; I. Anton; A. Zsolnai
The Mangalitza lard‐type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow‐Belly Mangalitza and Red Mangalitza. The Swallow‐Belly line has a black coat combined with yellow‐blond throat and underbelly. In the current
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Comparative genome‐wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs Anim. Genet. (IF 2.841) Pub Date : 2020-12-10 X.‐J. Li; L.‐Q. Liu; H. Dong; J.‐J. Yang; W.‐W. Wang; Q. Zhang; C.‐L. Wang; J. Zhou; H.‐Q. Chen
DNA methylation was one of the earliest discovered epigenetic modifications in vertebrates, and is an important epigenetic mechanism involved in the expression of genes in many biological processes, including muscle growth and development. Its effects on economically important traits are evidenced in reported differences in meat quality traits between Chinese indigenous pig breeds (Wannanhua pig) and
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Characterisation of sperm piRNAs and their correlation with semen quality traits in swine Anim. Genet. (IF 2.841) Pub Date : 2020-11-23 M. Ablondi; M. Gòdia; J.E. Rodriguez‐Gil; A. Sánchez; A. Clop
Piwi‐interacting RNAs (piRNAs) are a class of non‐coding RNAs that are essential in the transcriptional silencing of transposable elements and warrant genome stability in the mammalian germline. In this study, we have identified piRNAs in porcine sperm using male germline and zygote datasets from human, mice, cow and pig, and evaluated the relation between their abundances and sperm quality traits
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A functional mutation in the AMPD1 promoter region affects promoter activity and breast meat freshness in chicken Anim. Genet. (IF 2.841) Pub Date : 2020-11-23 S. Yu; G. Wang; J. Liao; X. Chen
Freshness is an important index to determine the quality deterioration (protein degradation and changes in appearance) of chilled chicken meat and is a primary consideration of consumers. Adenosine monophosphate deaminase 1 (AMPD1) catalyzes the deamination of adenosine monophosphate to inosine monophosphate in skeletal muscle and is the rate‐limiting step in the purine nucleotide cycle. Inosine monophosphate
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Identification of new genes and quantitative trait locis associated with growth curve parameters in F2 chicken population using genome‐wide association study Anim. Genet. (IF 2.841) Pub Date : 2021-01-11 R. Seifi Moroudi; S. Ansari Mahyari; R. Vaez Torshizi; H. Lanjanian; A. Masoudi‐Nejad
The markers which are correlated with the growth curve parameters help in understanding the characteristics of individual growth during the rearing of livestock. This study aimed to identify a set of biomarkers through a GWAS for growth curve parameters in crossbred chickens using the Illumnia 60K chicken SNP Beadchip. Growth data were collected from a total of 301 birds from cross of a broiler line
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A genome‐wide association study for the number of teats in European rabbits (Oryctolagus cuniculus) identifies several candidate genes affecting this trait Anim. Genet. (IF 2.841) Pub Date : 2021-01-11 S. Bovo; G. Schiavo; V. J. Utzeri; A. Ribani; M. Schiavitto; L. Buttazzoni; R. Negrini; L. Fontanesi
In the European rabbit (Oryctolagus cuniculus), a polytocous livestock species, the number of teats indirectly impacts the doe reproduction efficiency and, in turn, the sustainable production of rabbit meat. In this study, we carried out a genome‐wide association study (GWAS) for the total number of teats in 247 Italian White does included in the Italian White rabbit breed selection program, by applying
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Genome‐wide association studies for growth‐related traits in a crossbreed pig population Anim. Genet. (IF 2.841) Pub Date : 2020-12-29 Y. Xue; C. Li; D. Duan; M. Wang; X. Han; K. Wang; R. Qiao; X.‐J. Li; X.‐L. Li
Growth‐related traits are important economic traits in the pig industry that directly influence pork production efficiency. To detect quantitative trait loci and candidate genes affecting growth traits, genome‐wide association studies were performed for backfat thickness (BF) and loin muscle depth (LMD) in 370 Chuying‐black pigs using Illumina PorcineSNP50 BeadChip array. We totally identified 14 BF‐associated
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Discriminating between allele‐ and genotype‐specific transmission ratio distortion Anim. Genet. (IF 2.841) Pub Date : 2020-09-30 J. Casellas; S. Id‐Lahoucine; A. Cánovas
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‐
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Weighted gene co‐expression network analysis reveals potential candidate genes affecting drip loss in pork Anim. Genet. (IF 2.841) Pub Date : 2020-09-28 X. Zhao; C. Wang; Y. Wang; L. Zhou; H. Hu; L. Bai; J. Wang
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
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Genetic signature of hybridization between Chinese spot‐billed ducks and domesticated ducks Anim. Genet. (IF 2.841) Pub Date : 2020-10-05 X. Guo; Z.‐C. Wang; S. Wang; H.‐F. Li; C. Suwannapoom; J.‐X. Wang; C. Zhang; Y. Shao; M.‐S. Wang; R.‐S. Jiang
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
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Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach Anim. Genet. (IF 2.841) Pub Date : 2020-10-01 E. A. Abdalla; S. Id‐Lahoucine; A. Cánovas; J. Casellas; F. S. Schenkel; B. J. Wood; C. F. Baes
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
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A joint analysis strategy reveals genetic changes associated with artificial selection between egg‐type and meat‐type ducks Anim. Genet. (IF 2.841) Pub Date : 2020-10-15 H. Gu; T. Zhu; X. Li; Y. Chen; L. Wang; X. Lv; W. Yang; Y. Jia; Z. Jiang; L. Qu
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
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Genome‐wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum) Anim. Genet. (IF 2.841) Pub Date : 2020-10-01 J. R. S. Nunes; F. Pértille; S. C. S. Andrade; C. A. Perazza; P. M. S. Villela; V. M. F. Almeida‐Val; Z.‐X. Gao; L. L. Coutinho; A. W. S. Hilsdorf
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
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The genomic architecture of South African mutton, pelt, dual-purpose and nondescript sheep breeds relative to global sheep populations. Anim. Genet. (IF 2.841) Pub Date : 2020-09-07 E F Dzomba,M Chimonyo,M A Snyman,F C Muchadeyi
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
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Combined approaches to reveal genes associated with litter size in Yunshang black goats Anim. Genet. (IF 2.841) Pub Date : 2020-09-28 L. Tao; X. Y. He; Y. T. Jiang; R. Lan; M. Li; Z. M. Li; W. F. Yang; Q. H. Hong; M. X. Chu
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
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Transcriptomic analysis of eyelid pigmentation in Hereford cattle Anim. Genet. (IF 2.841) Pub Date : 2020-10-15 E. Jara; F. Peñagaricano; C. Menezes; L. Tardiz; G. Rodons; A. Iriarte; E. Armstrong
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
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Deletion of porcine BOLL is associated with defective acrosomes and subfertility in Yorkshire boars Anim. Genet. (IF 2.841) Pub Date : 2020-09-25 A. Nosková; C. Wurmser; D. Crysnanto; A. Sironen; P. Uimari; R. Fries; M. Andersson; H. Pausch
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
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Genome‐wide association study identifies markers associated with carcass and meat quality traits in Italian Large White pigs Anim. Genet. (IF 2.841) Pub Date : 2020-10-14 M. C. Fabbri; M. Zappaterra; R. Davoli; P. Zambonelli
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
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Genome-wide association study reveals novel loci associated with fat-deposition and meat-quality traits in Pekin ducks. Anim. Genet. (IF 2.841) Pub Date : 2020-08-26 M-T Deng,F Zhang,F Zhu,Y-Z Yang,F-X Yang,J-P Hao,Z-C Hou
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)
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Copy number variation in HOXB7 and HOXB8 involves in the formation of beard trait in chickens Anim. Genet. (IF 2.841) Pub Date : 2020-10-14 K. X. Yang; H. Zhou; J. M. Ding; C. He; Q. Niu; C. J. Gu; Z. X. Zhou; H. Meng; Q. Z. Huang
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
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Identification of a large dataset of SNPs in Larimichthys polyactis using high‐throughput 2b‐RAD sequencing Anim. Genet. (IF 2.841) Pub Date : 2020-09-29 Y. Chen; J. Mao; W. Senanan; W. Wang
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
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A genome-wide association study revealed five SNPs affecting 8-month weight in sheep. Anim. Genet. (IF 2.841) Pub Date : 2020-09-10 M Pasandideh,M Gholizadeh,G Rahimi-Mianji
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
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Genetic diversity of mitochondrial cytochrome b gene in swamp buffalo. Anim. Genet. (IF 2.841) Pub Date : 2020-09-10 T Sun,S Wang,Q Hanif,N Chen,H Chen,C Lei
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
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ARSB gene variants causing Mucopolysaccharidosis VI in Miniature Pinscher and Miniature Schnauzer dogs Anim. Genet. (IF 2.841) Pub Date : 2020-09-28 K. Raj; L. Berman‐Booty; P. Foureman; U. Giger
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
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Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica) Anim. Genet. (IF 2.841) Pub Date : 2020-11-02 S. Vollmar; V. Haas; M. Schmid; S. Preuß; R. Joshi; M. Rodehutscord; J. Bennewitz
A large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome‐wide
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Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits Anim. Genet. (IF 2.841) Pub Date : 2020-10-27 J. Sweet‐Jones; A. A. Yurchenko; A. V. Igoshin; N. S. Yudin; M. T. Swain; D. M. Larkin
Russian sheep breeds represent an important economic asset by providing meat and wool, whilst being adapted to extreme climates. By resequencing two Russian breeds from Siberia: Tuva (n = 20) and Baikal (n = 20); and comparing them with a European (UK) sheep outgroup (n = 14), 41 million variants were called, and signatures of selection were identified. High‐frequency missense mutations on top of selection
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All sheeps and sizes: a genetic investigation of mature body size across sheep breeds reveals a polygenic nature Anim. Genet. (IF 2.841) Pub Date : 2020-10-21 C. J. Posbergh; H. J. Huson
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
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Identification of genes related to intramuscular fat independent of backfat thickness in Duroc pigs using single‐step genome‐wide association Anim. Genet. (IF 2.841) Pub Date : 2020-10-18 Z. Zhang; Z. Zhang; F. O. Oyelami; H. Sun; Z. xu; P. Ma; Q. Wang; Y. Pan
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
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Evolution and domestication of the Bovini species. Anim. Genet. (IF 2.841) Pub Date : 2020-07-27 K Zhang,J A Lenstra,S Zhang,W Liu,J Liu
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
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Genomics to accelerate genetic improvement in tilapia. Anim. Genet. (IF 2.841) Pub Date : 2020-08-05 J M Yáñez,R Joshi,G M Yoshida
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
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The Asp298Asn polymorphism of melanocortin-4 receptor (MC4R) in pigs: evidence for its potential effects on MC4R constitutive activity and cell surface expression. Anim. Genet. (IF 2.841) Pub Date : 2020-08-01 J Zhang,J Li,C Wu,Z Hu,L An,Y Wan,C Fang,X Zhang,J Li,Y Wang
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
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Impact of white-spotting alleles, including W20, on phenotype in the American Paint Horse. Anim. Genet. (IF 2.841) Pub Date : 2020-07-20 S A Brooks,K M Palermo,A Kahn,J Hein
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
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Exome analysis and functional classification of identified variants in racing Quarter Horses. Anim. Genet. (IF 2.841) Pub Date : 2020-07-21 R A Curi,G L Pereira,M V N Alvarez,W A Baldassini,O R Machado Neto,L A L Chardulo
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
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Genome-wide association study of shank length and diameter at different developmental stages in chicken F2 resource population. Anim. Genet. (IF 2.841) Pub Date : 2020-07-13 H Emrani,A A Masoudi,R Vaez Torshizi,A Ehsani
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
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Comprehensive analysis of lncRNA and mRNA expression changes in Tibetan chicken lung tissue between three developmental stages. Anim. Genet. (IF 2.841) Pub Date : 2020-08-07 Ruixiang Tang,Jiao Wang,Min Zhou,Yue Lan,Lan Jiang,Megan Price,Bisong Yue,Diyan Li,Zhenxin Fan
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
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Food intake-related genes in chicken determined through combinatorial genome-wide association study and transcriptome analysis. Anim. Genet. (IF 2.841) Pub Date : 2020-07-28 Xuemin Cao,Yuzhe Wang,Dingming Shu,Hao Qu,Chenglong Luo,Xiaoxiang Hu
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
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Altered expression of CYP17A1 and CYP19A1 in undescended testes of dogs with unilateral cryptorchidism. Anim. Genet. (IF 2.841) Pub Date : 2020-07-13 P Krzeminska,M Stachowiak,M Skrzypski,T Nowak,A Maslak,M Switonski
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
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Genetic diversity in Iranian indigenous sheep vis-à-vis selected exogenous sheep breeds and wild mouflon. Anim. Genet. (IF 2.841) Pub Date : 2020-07-29 S Eydivandi,G Sahana,M Momen,M H Moradi,A A Schönherz
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
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Reinterpreting sheep muscle strand-specific RNA sequencing data showing extensive 3'UTR extensions. Anim. Genet. (IF 2.841) Pub Date : 2020-07-22 Caifang Ren,Kaiping Deng,Zhibo Wang,Mingtian Deng,Yixuan Fan,Yanli Zhang,Jianyu Ma,Shuting Wang,Zifei Liu,Feng Wang
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
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Genome-wide association study for feed efficiency in collective cage-raised rabbits under full and restricted feeding. Anim. Genet. (IF 2.841) Pub Date : 2020-07-22 J P Sánchez,A Legarra,M Velasco-Galilea,M Piles,A Sánchez,O Rafel,O González-Rodríguez,M Ballester
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
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Detection of selection signatures in Limousin cattle using whole-genome resequencing. Anim. Genet. (IF 2.841) Pub Date : 2020-07-20 M Mariadassou,Y Ramayo-Caldas,M Charles,M Féménia,G Renand,D Rocha
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
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A 63-bp insertion in exon 2 of the porcine KIF21A gene is associated with arthrogryposis multiplex congenita. Anim. Genet. (IF 2.841) Pub Date : 2020-07-20 Z-H Fang,A Nosková,D Crysnanto,S Neuenschwander,P Vögeli,H Pausch
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
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SNP-based heritability and genetic architecture of cranial cruciate ligament rupture in Labrador Retrievers. Anim. Genet. (IF 2.841) Pub Date : 2020-07-22 S R Cook,M G Conzemius,M E McCue,K J Ekenstedt
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
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A nonsense variant in the KRT14 gene in a domestic shorthair cat with epidermolysis bullosa simplex. Anim. Genet. (IF 2.841) Pub Date : 2020-07-13 M Dettwiler,F Leuthard,A Bauer,V Jagannathan,A M Lourenço,H Pereira,T Leeb,M M Welle
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
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Identification and characterization of miRNAs during early pregnancy in domestic sheep. Anim. Genet. (IF 2.841) Pub Date : 2020-08-13 Kisun Pokharel,Jaana Peippo,Meng-Hua Li,Juha Kantanen
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
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The three missense mutations of EPAS1, IL37 and EEF1D genes associated with high-altitude adaptation in Chinese cattle. Anim. Genet. (IF 2.841) Pub Date : 2020-09-03 Xiwen Guan,Quratulain Hanif,Fang Yu Li,Jianyong Liu,Kaixing Qu,Jicai Zhang,Ningbo Chen,Hong Chen,Bi-Zhi Huang,Chu-Zhao Lei
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Ear type in sheep is associated with the MSRB3 locus. Anim. Genet. (IF 2.841) Pub Date : 2020-08-17 J M Paris,A Letko,I M Häfliger,P Ammann,C Drögemüller
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,
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Whole-genome sequencing reveals breed-differential CNVs between Tongcheng and Large White pigs. Anim. Genet. (IF 2.841) Pub Date : 2020-08-17 Q Wu,Y Zhou,Y Wang,Y Zhang,Y Shen,Q Su,G Gao,H Xu,X Zhou,B Liu
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
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Evidence supports white spotting in donkeys as a homozygous lethal condition. Anim. Genet. (IF 2.841) Pub Date : 2020-07-13 Jocelyn Tanaka,Robert Grahn,Rebecca R Bellone
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Haplotypes of three missense mutations in Melanocortin 1 receptor serve as genetic markers for black plumage in Chinese chicken. Anim. Genet. (IF 2.841) Pub Date : 2020-07-05 Yonglin Deng,Baisen Li,Huiyou Chen,Jianmin Zhang,Yi Yan,Jialin Xiang,Anfang Liu,Gong-Wei Zhang
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Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility. Anim. Genet. (IF 2.841) Pub Date : 2020-04-23 Nicole Gross,Francisco Peñagaricano,Hasan Khatib
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
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