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Animal Genetics

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https://www.readbyqxmd.com/read/30378694/allelic-diversity-and-locus-duplication-at-the-mhc-class-ii-dq-sub-region-in-the-indian-yak-population
#1
Shailendra K Mishra, Dimpee S Gonge, Jyotsna Behl, Tapas K Biswas, Jayakumar Sivalingam, Ranjit S Kataria, Saket K Niranjan
No abstract text is available yet for this article.
October 31, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30378686/a-col2a1-de-novo-variant-in-a-holstein-bulldog-calf
#2
Irene Monika Häfliger, Holger Behn, Markus Freick, Vidhya Jagannathan, Cord Drögemüller
No abstract text is available yet for this article.
October 31, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30357873/evolution-of-mhc-class-ii-sla-drb1-locus-in-the-croatian-wild-boar-sus-scrofa-implies-duplication-and-weak-signals-of-positive-selection
#3
H Arbanasić, D Konjević, L Vranković, M Bujanić, S Stipoljev, M Balažin, N Šprem, D Škorić, A Galov
The wild boar is an ancestor of the domestic pig and an important game species with the widest geographical range of all ungulates. Although a large amount of data are available on major histocompatibility complex (MHC) variability in domestic pigs, only a few studies have been performed on wild boars. Due to their crucial role in appropriate immune responses and extreme polymorphism, MHC genes represent some of the best candidates for studying the processes of adaptive evolution. Here, we present the results on the variability and evolution of the entire MHC class II SLA-DRB1 locus exon 2 in 133 wild boars from Croatia...
October 24, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30353936/a-new-marker-isolated-by-ddrad-sequencing-detects-siberian-and-russian-sturgeon-in-hybrids
#4
Miloš Havelka, Elisa Boscari, Alexey Sergeev, Nikolai Mugue, Leonardo Congiu, Katsutoshi Arai
No abstract text is available yet for this article.
October 24, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30353927/snp-based-heritability-and-genetic-architecture-of-tarsal-osteochondrosis-in-north-american-standardbred-horses
#5
A M McCoy, E M Norton, A M Kemper, S K Beeson, J R Mickelson, M E McCue
Osteochondrosis is a common developmental orthopedic disease characterized by a failure of endochondral ossification. Standardbred horses are recognized as being predisposed to tarsal osteochondrosis. Prior heritability estimates for tarsal osteochondrosis in European Standardbreds and related trotting breeds have been based on pedigree data and range from 17-29%. Here, we report on genetic architecture and heritability based on high-density genotyping data in a cohort of North American Standardbreds (n = 479) stringently phenotyped for tarsal osteochondrosis...
October 24, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30324759/distribution-of-runs-of-homozygosity-in-chinese-and-western-pig-breeds-evaluated-by-reduced-representation-sequencing-data
#6
Zhe Zhang, Qianqian Zhang, Qian Xiao, Hao Sun, Hongding Gao, Yumei Yang, Jiucheng Chen, Zhengcao Li, Ming Xue, Peipei Ma, Hongjie Yang, Ningying Xu, Qishan Wang, Yuchun Pan
Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reduced-representation sequencing method. After imputation and quality control, 60 850 high-confidence SNPs were retained for ROH detection...
October 16, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30311252/faang-establishing-metadata-standards-validation-and-best-practices-for-the-farmed-and-companion-animal-community
#7
P W Harrison, J Fan, D Richardson, L Clarke, D Zerbino, G Cochrane, A L Archibald, C J Schmidt, P Flicek
The Functional Annotation of ANimal Genomes (FAANG) project aims, through a coordinated international effort, to provide high quality functional annotation of animal genomes with an initial focus on farmed and companion animals. A key goal of the initiative is to ensure high quality and rich supporting metadata to describe the project's animals, specimens, cell cultures and experimental assays. By defining rich sample and experimental metadata standards and promoting best practices in data descriptions, deposition and openness, FAANG champions higher quality and reusability of published datasets...
October 12, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30311245/early-adipose-deposits-in-sheep-comparative-analysis-of-the-perirenal-fat-transcriptome-of-assaf-and-churra-suckling-lambs
#8
A Suárez-Vega, J J Arranz, V Pérez, L F de la Fuente, J Mateo, B Gutiérrez-Gil
Adipose deposits influence the quality of ruminant carcasses, and in suckling lambs, internal types of adipose deposits represent a notable proportion of total fat. The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf, n = 8; Churra, n = 6) was used for the RNA-seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes...
October 12, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30311254/generation-of-an-equine-biobank-to-be-used-for-functional-annotation-of-animal-genomes-project
#9
E N Burns, M H Bordbari, M J Mienaltowski, V K Affolter, M V Barro, F Gianino, G Gianino, E Giulotto, T S Kalbfleisch, S A Katzman, M Lassaline, T Leeb, M Mack, E J Müller, J N MacLeod, B Ming-Whitfield, C R Alanis, T Raudsepp, E Scott, S Vig, H Zhou, J L Petersen, R R Bellone, C J Finno
The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed...
October 11, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30294799/long-non-coding-meg3-is-a-marker-for-skeletal-muscle-development-and-meat-production-traits-in-pigs
#10
X Yu, Z Wang, H Sun, Y Yang, K Li, Z Tang
Long non-coding RNAmaternally expressed gene 3 (lncRNAMEG3) plays an important role in mammalian muscle development. Our previous transcriptome study showed that lncRNAMEG3 is differentially expressed during postnatal skeletal muscle development in pigs. The objective of the present study was to analyse the role of lncRNAMEG3 in prenatal and postnatal skeletal muscle development and investigate the association of MEG3 with meat production traits in pigs. We investigated the sequence conservation and temporal-spatial expression of lncRNAMEG3 and identified its core promoter and single nucleotide polymorphisms (SNPs)...
October 8, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30276844/genome-wide-association-study-and-heritability-estimate-for-ectopic-ureters-in-entlebucher-mountain-dogs
#11
M Gallana, Y T Utsunomiya, G Dolf, R B Pintor Torrecilha, A-K Falbo, V Jagannathan, T Leeb, I Reichler, J Sölkner, C Schelling
An ectopic ureter is a congenital anomaly which may lead to urinary incontinence and without a surgical intervention even to end-stage kidney disease. A genetic component contributes to the development of this anomaly in Entlebucher mountain dogs (EMD); however, its nature remains unclear. Using the Illumina CanineHD bead chip, a case-control genome-wide association study was performed to identify SNPs associated with the trait. Six loci on canine chromosomes 3, 17, 27 and 30 were identified with 16 significantly associated SNPs...
October 2, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30276836/a-frameshift-variant-in-the-eda-gene-in-dachshunds-with-x-linked-hypohidrotic-ectodermal-dysplasia
#12
S Hadji Rasouliha, A Bauer, M Dettwiler, M M Welle, T Leeb
X-linked hypohidrotic ectodermal dysplasia (XLHED) is a genetic disease characterized by hypoplasia or absence of hair, teeth and sweat glands. The EDA gene, located on the X chromosome, encodes the type II transmembrane protein ectodysplasin A. Variants in the EDA gene can lead to XLHED in humans, mice, cattle and dogs. In the present study, we investigated a litter of Dachshund puppies, of which four male puppies showed clinical signs of XLHED. We performed a candidate gene analysis in one affected puppy and several non-affected relatives...
October 2, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30276831/lncrnanet-a-comprehensive-sus-scrofa-lncrna-database
#13
G Liang, Y Yang, H Li, H Yu, X Li, Z Tang, K Li
Long noncoding RNAs (lncRNAs) constitute a large class of functional non-coding RNAs that play important roles in many biological processes. Thousands of lncRNAs have been identified in mammals. Pig is an important farm animal and biomedical model. It is essential to create a Sus scrofa lncRNA database to enable further study of the function and evolution of lncRNAs. In this study, we built a systematic S. scrofa lncRNA database named lncRNAnet that contains 53 468 S. scrofa lncRNAs with their sequence characteristics, genomic locations, conservation, overlapping SNPs and QTLs, and transcript abundance across nine tissues in pigs...
October 2, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30246406/a-frameshift-variant-in-the-col5a1-gene-in-a-cat-with-ehlers-danlos-syndrome
#14
M Spycher, A Bauer, V Jagannathan, M Frizzi, M De Lucia, T Leeb
Ehlers-Danlos syndrome (EDS) is a group of heritable connective tissue disorders caused by defective collagen synthesis or incorrect assembly of the collagen triple helical structure. EDS is characterised by joint hypermobility, skin hyperextensibility, abnormal scarring, poor wound healing and tissue friability. Human EDS may be caused by variants in several different genes including COL5A1, which encodes the collagen type V alpha 1 chain. For the present study we investigated a 1.5-year-old, spayed female, domestic shorthair cat with EDS...
September 23, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30246344/ruling-out-bgn-variants-as-simple-x-linked-causative-mutations-for-bilateral-corneal-stromal-loss-in-friesian-horses
#15
Coral Alberi, Erin Hisey, Mary Lassaline, Alyssa Atilano, Theodore Kalbfleisch, Riccardo Stoppini, Hanneke Hermans, Willem Back, Michael J Mienaltowski, Rebecca R Bellone
No abstract text is available yet for this article.
September 23, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30246258/genome-wide-scan-reveals-divergent-selection-among-taurine-and-zebu-cattle-populations-from-different-regions
#16
Z Edea, H Dadi, T Dessie, M R Uzzaman, M F Rothschild, E-S Kim, T S Sonstegard, K-S Kim
In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (FST ) values across sliding windows were estimated between zebu and reference combined taurine breeds...
September 23, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30229981/identification-and-diversity-of-y-chromosome-haplotypes-in-qinghai-yak-populations
#17
Z J Ma, X T Xia, S M Chen, X C Zhao, L L Zeng, Y L Xie, S Y Chao, J T Xu, Y G Sun, R Z Li, Z X Guanque, J L Han, C Z Lei
The aim of the present study was to perform a preliminary analysis of the characterization and diversity of Y-chromosome haplotypes/haplogroups in yak of Qinghai Province, China. A total of 322 male yaks from nine populations belonging to three officially recognized breeds (Gaoyuan, Huanhu and Datong) were sampled. Animals were genotyped using six previously reported Y-SNPs present in the SRY, USP9Y, UTY, AMELY and OFD1Y genes and four new Y-SNPs in the OFD1Y gene (g.569A>C, g.578A>C, g.608G>T and g...
September 19, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30229969/population-structure-genetic-diversity-and-selection-signatures-within-seven-indigenous-pakistani-goat-populations
#18
C Kumar, S Song, P Dewani, M Kumar, O Parkash, Y Ma, K K Malhi, N Yang, J M Mwacharo, X He, L Jiang
Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments...
September 19, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30229962/gene-set-enrichment-analysis-of-snp-data-in-dairy-and-beef-cattle-with-bovine-respiratory-disease
#19
M Neupane, J N Kiser, H L Neibergs
Bovine respiratory disease (BRD) is a complex disease that is associated with infection by bacterial and viral pathogens when cattle fail to adequately respond to stress. The objective of this study was to use gene set enrichment analysis of SNP data (GSEA-SNP) and a network analysis (ingenuity pathway analysis) to identify gene sets, genes within gene sets (leading-edge genes) and upstream regulators associated with BRD in pre-weaned dairy calves and beef feedlot cattle. BRD cases and controls were diagnosed using the McGuirk health scoring system...
September 19, 2018: Animal Genetics
https://www.readbyqxmd.com/read/30192028/pre-and-post-puberty-expression-of-genes-and-proteins-in-the-uterus-of-bos-indicus-heifers-the-luteal-phase-effect-post-puberty
#20
M R S Fortes, L F Zacchi, L T Nguyen, F Raidan, M M D C A Weller, J J Y Choo, A Reverter, J P A Rego, G B Boe-Hansen, L R Porto-Neto, S A Lehnert, A Cánovas, B L Schulz, A Islas-Trejo, J F Medrano, M G Thomas, S S Moore
Progesterone signaling and uterine function are crucial in terms of pregnancy establishment. To investigate how the uterine tissue and its secretion changes in relation to puberty, we sampled tissue and uterine fluid from six pre- and six post-pubertal Brahman heifers. Post-pubertal heifers were sampled in the luteal phase. Gene expression of the uterine tissue was investigated with RNA-sequencing, whereas the uterine fluid was used for protein profiling with mass spectrometry. A total of 4034 genes were differentially expressed (DE) at a nominal P-value of 0...
September 7, 2018: Animal Genetics
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