-
Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing Anim. Genet. (IF 2.4) Pub Date : 2024-03-14 Xudong Wei, Shuang Li, Huixuan Yan, Shengmei Chen, Ruizhe Li, Weizhong Zhang, Shengyu Chao, Weixing Guo, Wenhao Li, Zulfiqar Ahmed, Chuzhao Lei, Zhijie Ma
Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low‐oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole‐genome resequencing technology, along with 192 published sets of whole‐genome sequencing data of Indian indicine cattle,
-
Genomic characterization of dryland adaptation in endangered Anxi cattle in China Anim. Genet. (IF 2.4) Pub Date : 2024-03-04 Yang Lyu, Tingting Yao, Zhefu Chen, Ruiyao Huangfu, Haijian Cheng, Weidong Ma, Xingshan Qi, Fuqiang Li, Ningbo Chen, Chuzhao Lei
Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted
-
-
A de novo mutation in CACNA1A is associated with autosomal dominant bovine familial convulsions and ataxia in Angus cattle Anim. Genet. (IF 2.4) Pub Date : 2024-03-01 Rachel R. Reith, Jonathan E. Beever, Joe C. Paschal, Jason Banta, Brian F. Porter, David J. Steffen, Thomas B. Hairgrove, Jessica L. Petersen
Bovine familial convulsions and ataxia (BFCA) is considered an autosomal dominant syndrome with incomplete penetrance. Nine Angus calves from the same herd were diagnosed with BFCA within days of birth. Necropsy revealed cerebellar and spinal cord lesions associated with the condition. Parentage testing confirmed that all affected calves had a common sire. The sire was then bred to 36 cows across two
-
The role of genetic variability of the host on the resistance to Neospora caninum infection in cattle Anim. Genet. (IF 2.4) Pub Date : 2024-02-29 Anabella Dinon, Franco Fiorani, Lucía María Campero, Dadín Prando Moore, Pablo Marcelo Corva
Neospora caninum is one of the most frequently diagnosed abortifacient pathogens in cattle. There is abundant genomic information about the parasite itself, but very little is known about the genetic variability of resistance in the most common intermediate host. The aim of this review was to compile all the available information about the genetic variability associated with the resistance to N. caninum
-
Evaluation of the effectiveness of single nucleotide polymorphisms compared to microsatellite markers for parentage verification in Moroccan horses Anim. Genet. (IF 2.4) Pub Date : 2024-02-22 O. Aminou, B. Badaoui, M. Machmoum, M. Piro
The International Society for Animal Genetics (ISAG) currently advocates for a transition towards single nucleotide polymorphism (SNP) markers as a potential alternative for equine parentage verification. To ascertain the efficacy of this transition, it is imperative to evaluate the performance of parentage testing using SNPs in juxtaposition with short tandem repeats (STRs). As per ISAG's recommendation
-
Phenotypic correlations of carpal gland diverticular number with production traits and its genome‐wide association analysis in multiple pig populations Anim. Genet. (IF 2.4) Pub Date : 2024-02-21 Dengshuai Cui, Longyun Li, Naibiao Yu, Sanya Xiong, Shijun Xiao, Hao Zheng, Zhiyong Huang, Yuanmei Guo, Lusheng Huang
Pig carpal glands play crucial roles in territorial recognition, reproductive behavior, and information exchange; however, their effects on production traits and underlying genetic mechanisms remain unclear. In this study, 1028 pigs from six populations were counted for the carpal gland diverticular numbers (CGDNs) on the left (CGDNL) and right (CGDNR) legs, and their carcass and meat quality traits
-
LncRNAENSGALG00000021686 regulates fat metabolism in chicken hepatocytes via miR‐146b/AGPAT2 pathway Anim. Genet. (IF 2.4) Pub Date : 2024-02-19 Wenhao Xing, Shijie Li
The liver contributes to lipid metabolism as the hub of fat synthesis. Long non‐coding RNAs (lncRNAs) are considered the regulators of cellular processes. Since LncRNA ENSGALG00000021686 (lncRNA 21 686) has been described as a regulator of lipid metabolism, the present study aimed to clarify the role of lncRNA 21 686 in chicken hepatocytes’ lipid metabolism. Thirty‐two chickens were divided into four
-
Comparison of two methods of sperm- and testis-mediated gene transfer in production of transgenic animals: A systematic review Anim. Genet. (IF 2.4) Pub Date : 2024-02-15 Zeinab Dehghan, Gholamhossein Darya, Shayesteh Mehdinejadiani, Amin Derakhshanfar
Transgenic (Tg) animal technology is one of the growing areas in biology. Various Tg technologies, each with its own advantages and disadvantages, are available for generating Tg animals. These include zygote microinjection, electroporation, viral infection, embryonic stem cell or spermatogonial stem cell-mediated production of Tg animals, sperm-mediated gene transfer (SMGT), and testis-mediated gene
-
Towards identification of new genetic determinants for post-weaning diarrhea in piglets Anim. Genet. (IF 2.4) Pub Date : 2024-02-11 Emil Ibragimov, Esben Østergaard Eriksen, Jens Peter Nielsen, Claus B. Jørgensen, Merete Fredholm, Peter Karlskov-Mortensen
Post-weaning diarrhea in pigs is a considerable challenge in the pig farming industry due to its effect on animal welfare and production costs, as well as the large volume of antibiotics, which are used to treat diarrhea in pigs after weaning. Previous studies have revealed loci on SSC6 and SSC13 associated with susceptibility to specific diarrhea causing pathogens. This study aimed to identify new
-
Naturally occurring genetic diseases caused by de novo variants in domestic animals Anim. Genet. (IF 2.4) Pub Date : 2024-02-07 Luísa Azevedo, Andreia P. Amaro, João Niza-Ribeiro, Mónica Lopes-Marques
With the advent of next-generation sequencing, an increasing number of cases of de novo variants in domestic animals have been reported in scientific literature primarily associated with clinically severe phenotypes. The emergence of new variants at each generation is a crucial aspect in understanding the pathology of early-onset diseases in animals and can provide valuable insights into similar diseases
-
Analysis of genetic variants in protein-coding genes of Aoluguya reindeer based on the whole-genome data Anim. Genet. (IF 2.4) Pub Date : 2024-02-06 Wenfeng Yi, Mingyue Hu, Lulu Shi, Ting Li, Hao Sun, Lihong Qin, Shouqing Yan
CONFLICT OF INTEREST STATEMENT The authors declare no conflict of interest.
-
H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig Anim. Genet. (IF 2.4) Pub Date : 2024-01-31 Renzhuo Kuang, Zhixiang Xu, Honghong Zhou, Zhao Zhang, Hao Peng, Daoyuan Wang, Xuewen Xu, Shuhong Zhao, Yunxia Zhao, Mengjin Zhu
The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and excellent meat quality. However, the characteristics of cis-regulatory elements in CX pigs are still unknown. In this study, cis-regulatory elements of muscle
-
Smartphone-based digital phenotyping for genome-wide association study of intramuscular fat traits in longissimus dorsi muscle of pigs Anim. Genet. (IF 2.4) Pub Date : 2024-01-30 Yang Shen, Yuxi Chen, Shufeng Zhang, Ze Wu, Xiaoyu Lu, Weizhen Liu, Bang Liu, Xiang Zhou
Intramuscular fat (IMF) content and distribution significantly contribute to the eating quality of pork. However, the current methods used for measuring these traits are complex, time-consuming and costly. To simplify the measurement process, this study developed a smartphone application (App) called Pork IMF. This App serves as a rapid and portable phenotyping tool for acquiring pork images and extracting
-
Canine coat color E locus updates: Identification of a new MC1R variant causing ‘sable’ coat color in English Cocker Spaniels and a proposed update to the E locus dominance hierarchy Anim. Genet. (IF 2.4) Pub Date : 2024-01-29 Leena Honkanen, Robert Loechel, Stephen Davison, Jonas Donner, Heidi Anderson
The coat color phenotype ‘sable’ occurs in the English Cocker Spaniel dog breed. It closely resembles other canine color patterns known as domino/grizzle/pied (eA allele) and grizzle/domino (eG allele) determined by variants in the melanocortin 1 receptor gene (MC1R; ‘extension’ or E locus), a key multi-allele regulator of coat color. We examined genetic variation in MC1R, and found one new non-synonymous
-
Whole genome resequencing reveals candidate genes for postaxial polydactyly in Large White pigs Anim. Genet. (IF 2.4) Pub Date : 2024-01-29 Yongle Hao, Yunlei Song, Fei Chen, Jianhong Tang
Polydactyly is a genetic abnormality that affects both pig welfare and industry profits. Despite efforts to explore the genetic basis of pig polydactyly, progress remains limited. In this study, we analyzed a group of Large White pigs with postaxial polydactyly, including 29 cases and 79 controls from 24 families. High-depth sequencing was performed on 20 pigs, while low-depth sequencing was improved
-
Identification of genomic regions associated with resistance to gastrointestinal parasites in an indigenous sheep by single- and multiple-locus methods Anim. Genet. (IF 2.4) Pub Date : 2024-01-10 S. A. Rafat, M. Barbato, R. Hajializadeh Valilou, G. H. Moghaddam, A. Nematollahi, K. Periasamy, R. Pichler, P. Ajmone Marsan
We investigated the association between 157 SNPs located in 75 candidate genes involved in the immune system and proxy traits for resistance to gastrointestinal nematodes in sheep. A total of 211 lambs from eight flocks were sampled. Nematode eggs per gram were counted and classified as: (i) Strongyles, (ii) Nematodirus spp., (iii) Trichuris spp. and (iv) Marshallagia marshalli. Single- and multiple-locus
-
Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens Anim. Genet. (IF 2.4) Pub Date : 2024-01-09 Xiaotong Zheng, Jianfei Chen, Ruixue Nie, Huanhuan Miao, Ziwei Chen, Jiaheng He, Yinku Xie, Hao Zhang
The genetic foundation of chicken body plumage color has been extensively studied. However, little attention has been paid to the inheritance patterns and molecular mechanisms underlying the formation of distal feather colors (tail and wingtip). Differences in these colors are common; for example, the Chinese Huiyang Beard chicken has black tail feathers, but yellow body plumage. Here, the hybrid offspring
-
Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs Anim. Genet. (IF 2.4) Pub Date : 2024-01-08 Michao Deng, Zijian Qiu, Chenxi Liu, Lijing Zhong, Xinfeng Fan, Yuquan Han, Ran Wang, Pinghua Li, Ruihua Huang, Qingbo Zhao
Teat number (TNUM) is an important reproductive trait of sows, which affects the weaning survival rate of piglets. In this study, 1166 Dutch Large White pigs with TNUM phenotype were used as the research object. These pigs were genotyped by 50K SNP chip and the chip data were further imputed to the resequencing level. The estimated heritabilities of left teat number (LTN), right teat number (RTN) and
-
Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds Anim. Genet. (IF 2.4) Pub Date : 2024-01-08 Giuseppina Schiavo, Francesca Bertolini, Samuele Bovo, Giuliano Galimberti, María Muñoz, Riccardo Bozzi, Marjeta Čandek-Potokar, Cristina Óvilo, Luca Fontanesi
Large genotyping datasets, obtained from high-density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this study, we applied the Boruta algorithm, a wrapper
-
Evaluating three strategies of genome-wide association analysis for integrating data from multiple populations Anim. Genet. (IF 2.4) Pub Date : 2024-01-07 Zhanming Zhong, Guangzhen Li, Zhiting Xu, Haonan Zeng, Jinyan Teng, Xueyan Feng, Shuqi Diao, Yahui Gao, Jiaqi Li, Zhe Zhang
In livestock, genome-wide association studies (GWAS) are usually conducted in a single population (single-GWAS) with limited sample size and detection power. To enhance the detection power of GWAS, meta-analysis of GWAS (meta-GWAS) and mega-analysis of GWAS (mega-GWAS) have been proposed to integrate data from multiple populations at the level of summary statistics or individual data, respectively
-
Integrated analysis of differently expressed microRNAs and mRNAs at different postnatal stages reveals intramuscular fat deposition regulation in goats (Capra hircus) Anim. Genet. (IF 2.4) Pub Date : 2024-01-04 Wenyang Zhang, Yu Liao, Peng Shao, Yuling Yang, Lian Huang, Zhanyu Du, Changhui Zhang, Yong Wang, Yaqiu Lin, Jiangjiang Zhu
Intramuscular fat refers to the adipose tissue distributed in the muscle. It is an important indicator that affects the quality of goat meat, and can directly affect the tenderness and flavor of goat meat. Our previous study revealed the mRNA that may be crucial for intramuscular fat deposition during goat growth; however, how the microRNAs (miRNAs) are involved in the process is largely unclear. In
-
Genome-wide association studies for the number of piglets born alive and dead in Dongliao black pigs Anim. Genet. (IF 2.4) Pub Date : 2023-12-26 Hao Sun, Yu Cheng, Yu He, Chao Cheng, Hongxia Zhao, Sumei Yang, Meng Wei, Jingxiu Yang, Shuang Liang, Chunyan Bai, Boxing Sun
Litter size (total number born) trait has a great impact on the economic success of pork production. The total number born consists of the number of piglets born alive and dead. To clarify the genetic background of litter size, genome-wide association studies were undertaken in the present study. Samples of DNA were collected and genotyped using the Porcine 50K BeadChip from 723 Dongliao Black sows
-
Single and longitudinal genome-wide association studies for dairy traits available in goats with three recorded lactations Anim. Genet. (IF 2.4) Pub Date : 2023-12-22 Maria Gracia Luigi-Sierra, Amparo Martínez, Martina Macri, Juan Vicente Delgado, Anna Castelló, Javier Fernández Alvarez, Xavier Such, Jordi Jordana, Marcel Amills
Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been
-
Review: Wildlife forensic genetics—Biological evidence, DNA markers, analytical approaches, and challenges Anim. Genet. (IF 2.4) Pub Date : 2023-12-20 Sree Kanthaswamy
Wildlife-related crimes are the second most prevalent lawbreaking offense globally. This illicit trade encompasses hunting, breeding and trafficking. Besides diminishing many species and their habitats and ecosystems, hindering the economic development of local communities that depend on them, undermining the rule of law and financing terrorism, various cross-species transmissions (zoonoses) of pathogens
-
A network-based approach to understanding gene–biological processes affecting economically important traits of Nelore cattle Anim. Genet. (IF 2.4) Pub Date : 2023-12-19 Mariely Simone Lopes Corrêa, Evandro Neves Silva, Thaís Cristina Ferreira dos Santos, Larissa Fernanda Simielli Fonseca, Ana Fabrícia Braga Magalhães, Lucas Lima Verardo, Lucia Galvão de Albuquerque, Danielly Beraldo dos Santos Silva
This study aimed to build gene–biological process networks with differentially expressed genes associated with economically important traits of Nelore cattle from 17 previous studies. The genes were clustered into three groups by evaluated traits: group 1, production traits; group 2, carcass traits; and group 3, meat quality traits. For each group, a gene–biological process network analysis was performed
-
Insights into the influence of diet and genetics on feed efficiency and meat production in sheep Anim. Genet. (IF 2.4) Pub Date : 2023-12-19 Steffimol Rose Chacko Kaitholil, Mark H. Mooney, Aurélie Aubry, Faisal Rezwan, Masoud Shirali
Feed costs and carcass yields affect the profitability and sustainability of sheep production. Therefore, it is crucial to select animals with a higher feed efficiency and high-quality meat production. This study focuses on the impact of dietary and genetic factors on production traits such as feed efficiency, carcass quality, and meat quality. Diets promote optimal sheep growth and development and
-
Genome-wide association studies for loin muscle area, loin muscle depth and backfat thickness in DLY pigs Anim. Genet. (IF 2.4) Pub Date : 2023-12-15 Xiang Zhao, Yibin Qiu, Fanming Meng, Zhanwei Zhuang, Donglin Ruan, Jie Wu, Fucai Ma, Enqin Zheng, Gengyuan Cai, Jie Yang, Ming Yang, Zhenfang Wu
This study aimed at identifying genes associated with loin muscle area (LMA), loin muscle depth (LMD) and backfat thickness (BFT). We performed single-trait and multi-trait genome-wide association studies (GWASs) after genotyping 685 Duroc × (Landrace × Yorkshire) (DLY) pigs using the Geneseek Porcine 50K SNP chip. In the single-trait GWASs, we identified two, eight and two significant SNPs associated
-
Whole-genome resequencing reveals candidate genes associated with milk production trait in Guanzhong dairy goats Anim. Genet. (IF 2.4) Pub Date : 2023-12-13 Jie Ni, Ming Xian, Yijie Ren, Lina Yang, Yu Li, Songmao Guo, Benkang Ran, Jianhong Hu
Milk production is one of the most important economic utility of goats. Guanzhong dairy goat is a local dairy goat in Shaanxi Province of China and has high milk yield and quality. However, there are relatively few studies on molecular markers of milk production traits in Guanzhong dairy goats. In this study, we sequenced the whole genomes of 20 Guanzhong dairy goats, 10 of which had high milk yield
-
Npc1 gene mutation abnormally activates the classical Wnt signalling pathway in mouse kidneys and promotes renal fibrosis Anim. Genet. (IF 2.4) Pub Date : 2023-12-12 Lihong Guan, Zisen Jia, Keli Xu, Minlin Yang, Xiaoying Li, Liang Qiao, Yanli Liu, Juntang Lin
Niemann–Pick disease type C1 (NPC1) is a lysosomal lipid storage disease caused by NPC1 gene mutation. Our previous study found that, compared with wild-type (Npc1+/+) mice, the renal volume and weight of Npc1 gene mutant (Npc1−/−) mice were significantly reduced. We speculate that Npc1 gene mutations may affect the basic structure of the kidneys of Npc1−/− mice, and thus affect their function. Therefore
-
Integrated analysis of whole genome and transcriptome sequencing uncovers genetic differences between Zi goose and Xianghai flying goose Anim. Genet. (IF 2.4) Pub Date : 2023-12-12 Hongyu Ni, Yonghong Zhang, Yuwei Yang, Yijing Yin, Jing Ren, Qingxing Xiao, Puze Zhao, Xiaoqing Hong, Ziyi Zhang, Benhai Cui, Hao Sun, Xueqi Sun, Yumei Li
Zi goose is a famous indigenous breed originating from northeast China with high annual egg production. Xianghai flying goose is a composite breed and is bred by crosses of the wild swan goose and the Zi goose. Our previous study revealed significant differences in muscle fiber characteristics between the two populations. Here, we aimed to reveal the underlying genetic basis of the above phenotype
-
Genome-wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons Anim. Genet. (IF 2.4) Pub Date : 2023-12-08 Haobin Hou, Xiaoliang Wang, Xin Li, Xia Cai, Yingying Tu, Changsuo Yang, Junfeng Yao
Selective breeding of meat pigeons is primarily based on growth traits, especially muscle mass (MM). Identification of functional genes and molecular markers of growth and slaughter traits through a genome-wide association study (GWAS) will help to elucidate the underlying molecular mechanisms and provide a theoretical basis for the selective breeding of meat pigeons. The phenotypic data of body weight
-
Genetic basis of ear length in sheep breeds sampled across the region from the Middle East to the Alps Anim. Genet. (IF 2.4) Pub Date : 2023-12-08 Jürgen Klawatsch, Dimitris Papachristou, Panagiota Koutsouli, Maulik Upadhyay, Doris Seichter, Ingolf Russ, Boro Mioč, Mojca Simčič, Iosif Bizelis, Ivica Medugorac
Ear length in sheep (Ovis aries) shows a wide range of natural variation, from the absence of an outer ear structure (anotia), to small outer ears (microtia), to regular ear length. Up until now, the underlying genetics of this phenotype has been studied in four sheep breeds from China, Jordan and Italy. These studies revealed a broad range of genes significantly associated with ear length, potentially
-
Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data Anim. Genet. (IF 2.4) Pub Date : 2023-11-23 Alessio Longo, Khrystyna Kurta, Tytti Vanhala, Henrik Jeuthe, Dirk-Jan de Koning, Christos Palaiokostas
Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest
-
Genome-wide analyses based on a novel donkey 40K liquid chip reveal the gene responsible for coat color diversity in Chinese Dezhou donkey Anim. Genet. (IF 2.4) Pub Date : 2023-11-23 Shuqin Liu, Jiangtian Su, Qiwen Yang, Minhao Sun, Zhaofei Wang, Jie Yu, Halima Jafari, Chuzhao Lei, Yujiang Sun, Ruihua Dang
Dezhou donkey is one of the representative local breeds in China, which is mainly divided into two strains: Sanfen and Wutou. There are obvious differences in coat color between the two strains. The former shows light points around the eyes, around the muzzle and under the belly, while the latter is completely solid black. In this study, genome-wide association analysis was performed for the differences
-
Relevance of pharmacogenetics and pharmacogenomics in veterinary clinical practice: A review Anim. Genet. (IF 2.4) Pub Date : 2023-11-22 Ayushi Vaidhya, Kanika Ghildiyal, Divya Rajawat, Sonali Sonejita Nayak, Subhashree Parida, Manjit Panigrahi
The recent advances in high-throughput next-generation sequencing technologies have heralded the arrival of the Big Data era. As a result, the use of pharmacogenetics in drug discovery and individualized drug therapy has transformed the field of precision medicine. This paradigm shift in drug development programs has effectively reshaped the old drug development practices, which were primarily concerned
-
Identification of genomic regions associated with differences in fleece type in Huacaya and Suri alpacas (Vicugna pacos) Anim. Genet. (IF 2.4) Pub Date : 2023-11-20 K. Tan, O. O. Adeniyi, A. Letko, G. RuddGarces, E. Manz, H. Wagner, P. Zanolari, C. Drögemüller, G. Lühken
The difference in fleece type is the distinguishing trait between the two types of alpacas (Vicugna pacos), Huacaya and Suri. The Suri fleece type has been found to be inherited dominantly over the Huacaya type, resulting in offspring with the Suri phenotype. The aim of our study was to map genomic regions associated with the two different fleece types. In this study, 91 alpacas (54 Huacayas and 37
-
Effect of selection genotype on immune response to Brucella abortus RB51 in Holstein cattle Anim. Genet. (IF 2.4) Pub Date : 2023-11-09 Kaitlyn M. Sarlo Davila, Paola Boggiatto, Steven Olsen, John D. Lippolis, Brian A. Crooker, Ellie J. Putz
Genetic selection for milk production traits in US Holsteins has affected numerous genes associated with reproduction and immunity. This study compares the transcriptomic response of peripheral blood mononuclear cells to an in vitro Brucella abortus strain RB51 (RB51) bacterial challenge between contemporary Holsteins and Holsteins that have not been selected for milk production traits since the mid-1960s
-
No trade-off between growth and OsHV-1 tolerance in Pacific oysters (Crassostrea gigas) farmed on the West Coast, USA Anim. Genet. (IF 2.4) Pub Date : 2023-11-03 Konstantin Divilov, Blaine Schoolfield, Noah Merz, Chris Langdon
An important pathogen of concern for Pacific oyster growers in the USA is ostreid herpesvirus 1 (OsHV-1). Currently, oyster stocks exist that are tolerant to OsHV-1; however, it is uncertain if a trade-off exists between their tolerance to OsHV-1 and their growth in different environments. To investigate any potential trade-offs, Pacific oyster families with varying levels of OsHV-1 tolerance were
-
MFSD2A frameshift variant in Kerry Hill sheep with microcephaly Anim. Genet. (IF 2.4) Pub Date : 2023-11-03 Gabriela Rudd Garces, Anna Letko, Irene M. Häfliger, Jana Müller, Christiane Herden, Anne Nesseler, Henrik Wagner, Martin J. Schmidt, Cord Drögemüller, Gesine Lühken
Microcephaly is a rare neurodevelopmental disorder characterized by reduced skull circumference and brain volume that occurs sporadically in farm animals. We investigated an early-onset neurodegenerative disorder observed in seven lambs of purebred Kerry Hill sheep. Clinical signs included inability to stand or severe ataxia, convulsions, and early death. Diagnostic imaging and brain necropsy confirmed
-
RNA sequencing analysis reveals that missense mutation in SOX10 is associated with iris color phenotype in quail Anim. Genet. (IF 2.4) Pub Date : 2023-10-31 Shiwei Ren, Xiaohui Zhang, Youzhi Pang, Yanxia Qi, Linke Huo, Fanghu Wu, Yuanyuan Shang, Jinquan Xi
To investigate the molecular mechanisms underlying the differences in iris color in quail, the transcriptome of iris tissue from black quail and Korean quail at day 10 of hatching was RNA sequenced in this study. The differentially expressed genes (DEGs) were screened, functionally annotated and enriched after the quality control and mapping of the raw data. RT-qPCR validation was performed using EIF2S3
-
Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs Anim. Genet. (IF 2.4) Pub Date : 2023-10-25 Wei Lv, Yaxin Peng, Jingjing Hu, Mingfei Zhu, Yangcang Mao, Litong Wang, Guoshui Wang, Zaiyan Xu, Wangjun Wu, Bo Zuo
Our previous studies showed that SYISL is a negative regulator of muscle growth and regeneration in mice, pigs and humans. SYISL knockout resulted in an increase in the density of muscle fibers and muscle growth. However, it is unclear whether there are natural mutations in pig SYNPO2 intron sense-overlapping lncRNA (pSYISL) that affect the expression of pSYISL and muscle growth traits. In this study
-
Rapid genotyping of bovine MC1R gene c.296T>C and c.310delG haplotypes using high-resolution melting analysis Anim. Genet. (IF 2.4) Pub Date : 2023-10-24 Rui Hong, Yi Yan, Changhong Zhu, Fuyuan Zuo, Gong-Wei Zhang
CONFLICT OF INTEREST STATEMENT The authors declare no conflict of interest.
-
The 4 bp deletion mutation in HOXD1 gene determines the polycerate trait in Chinese Sishui fur sheep Anim. Genet. (IF 2.4) Pub Date : 2023-10-17 Cheng Zhang, Huan Zhang, Tenggang Di, Guan Wang, Fengyi Gao, Zhiqiang Li, Ming Li, Guangli Yang
CONFLICT OF INTEREST STATEMENT The authors declare that they have no competing interests.
-
Identification of potential biomarkers associated with meat tenderness in Hanwoo (Korean cattle): An expression quantitative trait loci analysis Anim. Genet. (IF 2.4) Pub Date : 2023-10-12 Yoonji Chung, Sun Sik Jang, Dong Hun Kang, Yeong Kuk Kim, Hyun Joo Kim, Ki Yong Chung, Inchul Choi, Seung Hwan Lee
Meat tenderness is considered the most important trait contributing to beef quality, level of consumer satisfaction, willingness to pay premium prices and industry profit. Genomic selection method would be helpful for genetic improvement of traits with low heritability and that are difficult to measure. The identification of core genes can aid genomic selection for complex traits with low heritability
-
Genome-wide association study using a single-step approach for teat number in Duroc, Landrace and Yorkshire pigs in Korea Anim. Genet. (IF 2.4) Pub Date : 2023-10-09 Jun Park, Kyoung-Tag Do, Kyung-Do Park, Hak-Kyo Lee
We investigated the genetic basis of teat number in sows, which is an important factor in their reproductive performance. We collected genotyping data from 20 353 pigs of three breeds (Duroc, Landrace and Yorkshire) using the Porcine SNP60K Bead Chip, and analyzed phenotypic data from 240 603 pigs. The heritability values of total teat number were 0.33 ± 0.02, 0.51 ± 0.01 and 0.50 ± 0.01 in Duroc,
-
A new method for molecular sex identification in the Japanese quail (Coturnix japonica) Anim. Genet. (IF 2.4) Pub Date : 2023-10-09 Xiaoxu Jia, Wanqiang Chen, Xiujun Tang, Junxian Lu, Yanfeng Fan, Yushi Gao
CONFLICT OF INTEREST STATEMENT The authors declare no conflict of interest.
-
Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig Anim. Genet. (IF 2.4) Pub Date : 2023-10-05 Qingjie Zeng, Zhi-Qiang Du
As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber-type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process
-
A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province Anim. Genet. (IF 2.4) Pub Date : 2023-10-05 Yang Lyu, Xiwen Guan, Xinglong Xu, Pengfei Wang, Qiaoxian Li, Manjit Panigrahi, Jicai Zhang, Ningbo Chen, Bizhi Huang, Chuzhao Lei
Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve
-
Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes Anim. Genet. (IF 2.4) Pub Date : 2023-10-05 María Victoria Borja Lozano, Bianca Vigil Santillán, Manuel J. More Montoya, Jonathan A. Morón Barraza, Aura Liz García-Serquén, Gustavo Gutiérrez Reynoso, Claudia E. Yalta-Macedo
Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite the economic and cultural relevance of guinea pigs, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping of livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of
-
Detection of genomic variations and selection signatures in Wagyu using whole-genome sequencing data Anim. Genet. (IF 2.4) Pub Date : 2023-10-04 Lulu Shi, Mingyue Hu, Weining Lai, Wenfeng Yi, Zhengxi Liu, Hao Sun, Feng Li, Shouqing Yan
Wagyu is recognized for producing marbled beef with high nutritional value and flavor. Reportedly, Wagyu has been widely used to improve the meat quality of local breeds around the world. However, studies on the genetic mechanism of meat quality in Wagyu at the whole-genome level are rarely reported. Here, whole-genome sequencing data of 11 Wagyu and 115 other individuals were used to explore the genomic
-
Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye Anim. Genet. (IF 2.4) Pub Date : 2023-10-03 Eymen Demir, Nina Moravčíková, Sarp Kaya, Radovan Kasarda, Ümit Bilginer, Huriye Doğru, Murat Soner Balcıoğlu, Taki Karslı
Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method. The integrated
-
Whole-genome sequencing of alpaca revealed variants in KIT gene potentially associated with the white coat phenotype Anim. Genet. (IF 2.4) Pub Date : 2023-10-01 Stefano Pallotti, Marco Antonini, Valerio Napolioni, Carlo Renieri
The association between variants on ASIP, KIT and MC1R genes and fleece color has been described for alpaca (Chandramohan et al., 2015; Feeley et al., 2016; Jones et al., 2019; Pallotti et al., 2020; Tan et al., 2022). However, the genetics behind the white coat phenotype in this species is still unknown. In this regard, variants on KIT were associated in alpaca with gray- and blue-eyed white phenotypes
-
A purebred South American breed showing high effective population size and independent breed ancestry: The Chilean Terrier Anim. Genet. (IF 2.4) Pub Date : 2023-10-01 Paola C. Mujica, Víctor Martinez
The Chilean Terrier is a known breed in Chile that has not been genetically assessed despite its distinctive color patterns, agility, and hardiness across the diversity of climates encountered within the Chilean landscape. The population structure and its relatedness with other breeds, as well as the actual origin of the breed, remain unknown. We estimated several population parameters using samples
-
Using genetics to trace the ancestry and ‘breed-type’ of rescued horses Anim. Genet. (IF 2.4) Pub Date : 2023-09-30 Daniel Lee Clifton, Jamie A. Boyd, Laura Patterson Rosa
CONFLICT OF INTEREST STATEMENT Laura Patterson Rosa serves as unaffiliated scientific consultant for Etalon Diagnostics, but received no payment compensation or funding for the current article. All other authors have no conflicts of interest to disclose.
-
Genomic signatures reveal selection in Chinese and European domesticated geese Anim. Genet. (IF 2.4) Pub Date : 2023-09-19 Lihua Zhang, Haiying Li, Bihui Tang, Xiaoyu Zhao, Yingping Wu, Teng Jiang, Yingying Yao, Jiahui Li, Yang Yao, Lin Wang
The Swan goose and Greylag goose are species of geese native to East Asia and Europe, respectively, and are widely believed to be the ancestors of Chinese and European domesticated geese. The Yili goose (YL) and European domestic geese originated from the Greylag goose, but the history of domestication is unclear. In this study, we sequenced and analyzed the genome of the YL goose and the Hortobagy
-
Landmarks in the history of selective sweeps Anim. Genet. (IF 2.4) Pub Date : 2023-09-14 Manjit Panigrahi, Divya Rajawat, Sonali Sonejita Nayak, Kanika Ghildiyal, Anurodh Sharma, Karan Jain, Chuzhao Lei, Bharat Bhushan, Bishnu Prasad Mishra, Triveni Dutt
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed
-
Genome-wide association study identifies variants associated with semen volume in white-feathered broilers Anim. Genet. (IF 2.4) Pub Date : 2023-09-13 G. M. Zhang, P. H. Liu, L. Chen, J. M. Zheng, G. P. Zhao, W. H. Xing, J. Wen, Q. H. Li
Semen is a measure of the reproductive efficiency of roosters, which affects the economic benefits of white-feathered broilers. Over the years, research in this field has mainly focused on hens, while there have been fewer studies on the reproductive traits of roosters. To identify the genes related to the semen traits of roosters, we used a chicken 55 K SNP chip to genetically type the white-feathered
-
Searching for new signals for susceptibility to umbilical hernia through genome-wide association analysis in three pig breeds Anim. Genet. (IF 2.4) Pub Date : 2023-09-13 Hui Yang, Lei Wang, Lilin Yin, Zhenshuang Tang, Zhangxu Wang, Xiangdong Liu, Tao Xiang, Mei Yu, Xiaolei Liu, Changchun Li
Umbilical hernia (UH) is a prevalent congenital disorder in pigs, resulting in considerable economic losses and severe animal welfare issues. In the present study, we conducted a genome-wide association study (GWAS) using the GeneSeek 50K Chip in 2777 pigs (Duroc, n = 1267; Landrace, n = 696; and Yorkshire, n = 814) to explore the candidate genes underlying the risk of umbilical hernia in pigs. After
-
A de novo 2.3 kb structural variant in MITF explains a novel splashed white phenotype in a Thoroughbred family Anim. Genet. (IF 2.4) Pub Date : 2023-09-12 R. R. Bellone, J. Tanaka, E. Esdaile, R. B. Sutton, F. Payette, L. Leduc, B. J. Till, A. K. Abdel-Ghaffar, M. Hammond, K. G. Magdesian
Splashed white in horses is characterized by extensive white patterning on the legs, face and abdomen and may be accompanied by deafness. To date, seven variants in microphthalmia-associated transcription factor (MITF) and two variants in Paired Box 3 (PAX3) have been identified to explain this phenotype. A splashed white Thoroughbred stallion, whose sire and dam were not patterned, was hypothesized