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Animal Genetics

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https://www.readbyqxmd.com/read/28094451/development-of-diversity-arrays-technology-markers-as-a-tool-for-rapid-genomic-assessment-in-nile-tilapia-oreochromis-niloticus
#1
C E Lind, A Kilian, J A H Benzie
The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively...
January 17, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28094449/genetic-diversity-and-patterns-of-population-structure-in-creole-goats-from-the-americas
#2
C Ginja, L T Gama, A Martínez, N Sevane, I Martin-Burriel, M R Lanari, M A Revidatti, J A Aranguren-Méndez, D O Bedotti, M N Ribeiro, P Sponenberg, E L Aguirre, L A Alvarez-Franco, M P C Menezes, E Chacón, A Galarza, N Gómez-Urviola, O R Martínez-López, E C Pimenta-Filho, L L da Rocha, A Stemmer, V Landi, J V Delgado-Bermejo
Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in-depth analysis of the within- and between-breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats...
January 17, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28094447/on-the-origins-and-genetic-diversity-of-south-american-chickens-one-step-closer
#3
A Luzuriaga-Neira, G Villacís-Rivas, F Cueva-Castillo, G Escudero-Sánchez, A Ulloa-Nuñez, M Rubilar-Quezada, R Monteiro, M R Miller, A Beja-Pereira
Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America...
January 17, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28094446/deep-sequencing-of-a-candidate-region-harboring-the-sox9-gene-for-the-canine-xx-disorder-of-sex-development
#4
J Nowacka-Woszuk, I Szczerbal, H Pausch, S Hundi, M K Hytönen, A Grzemski, K Flisikowski, H Lohi, M Switonski, M Szydlowski
A disorder of sex development (DSD) in dogs with female sex chromosomes (78, XX), a lack of the SRY gene and the presence of testes or ovotestes is commonly diagnosed in numerous breeds. The molecular background of DSD is not fully recognized but has been linked to the copy number variation in the region harboring the SOX9 gene. We applied a genome-wide association study and targeted next-generation sequencing techniques to compare DSD and normal female dogs. The genome-wide association study did not indicate a significant chromosome region...
January 17, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28084638/association-analysis-of-kit-mitf-and-pax3-variants-with-white-markings-in-spanish-horses
#5
S Negro, F Imsland, M Valera, A Molina, M Solé, L Andersson
Several variants in the KIT, PAX3 and MITF genes have previously been associated with white markings in horses. In this study, we examined eight variants of these genes in 70 Menorca Purebred horses (PRMe, only black solid-coloured horses) and 70 Spanish Purebred horses (PRE, different coat colour patterns) that were scored for the extent of white markings. A maximum-likelihood chi-square test, logistic regression model and ridge regression analyses showed that a missense mutation (p.Arg682His) in KIT was associated with white facial markings (P < 0...
January 13, 2017: Animal Genetics
https://www.readbyqxmd.com/read/27943331/genomic-investigation-of-piglet-resilience-following-porcine-epidemic-diarrhea-outbreaks
#6
F Bertolini, J C S Harding, B Mote, A Ladinig, G S Plastow, M F Rothschild
Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome-wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks...
December 12, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27928823/identification-of-differentially-expressed-genes-in-longissimus-muscle-of-pigs-with-high-and-low-intramuscular-fat-content-using-rna-sequencing
#7
K S Lim, K T Lee, J E Park, W H Chung, G W Jang, B H Choi, K C Hong, T H Kim
Intramuscular fat (IMF) content in pork is an important element of consumer preference and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate differentially expressed genes (DEGs) closely related to IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements, and significant differences between extremely high (H, n = 3) and low (L, n = 3) IMF content groups were found (P < 0...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27925267/genetic-variation-and-gene-conversions-within-the-bovine-nk-lysin-gene-family
#8
J Chen, M O Lee, J E Womack
In contrast to a single copy of the NK-lysin gene in humans and many other mammals, we previously identified a family of four expressed NK-lysin genes arising by tandem duplications on cattle chromosome 11. Here, we report two genetic variants in the bovine NK-lysin complex with potential importance in the bovine innate immune system. The first one is a 9-bp deletion causing a three-amino-acid deletion in the pro-region of the NK1 gene product. The second is a deletion of NK2B in some Holstein cattle, resulting in copy number variation that is in disequilibrium with a SNP from the bovine 770K HD SNP array...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27925264/three-intronic-lncrnas-with-monoallelic-expression-derived-from-the-meg8-gene-in-cattle
#9
W Yang, D Li, G Wang, C Zhang, M Zhang, W Zhang, S Li
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Antisense lncRNAs, intergenetic lncRNAs and enhancer lncRNAs can regulate genomic imprinting, which leads to parent-origin-specific monoalletic expression of genes. However, the function of intronic ncRNAs in genomic imprinting remains unclear. Previously, we obtained the cDNA sequence of cattle MEG8 gene, which is located in the DLK1-DIO3 imprinted clusters of cattle chromosome 21. In this study, we undertook a systematic search for transcripts mapping to the MEG8 intronic region and identified three novel lncRNAs, named MEG8 intronic RNA 1 (MEG8-IT1), MEG8 intronic RNA 2 (MEG8-IT2) and MEG8 intronic RNA 3 (MEG8-IT3) according to the GENCODE annotated bibliography...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27917507/evidence-of-a-genomic-insertion-in-intron-2-of-sod1-causing-allelic-drop-out-during-routine-diagnostic-testing-for-canine-degenerative-myelopathy
#10
M E Turba, R Loechel, E Rombolà, G Gandini, F Gentilini
Degenerative myelopathy is a severe and progressive neurodegenerative disease and, in the majority of breeds, is associated with the c.118G>A substitution in exon 2 of the canine superoxide dismutase 1 (SOD1) gene. Our laboratories have been engaged in determining the cause of many discordant findings between the parental and the offspring genotypes found by different laboratories. In both cases, the discordant findings refer to actual heterozygous dogs that had been typed as homozygous for the variant allele...
December 4, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#11
REVIEW
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27885693/association-of-single-nucleotide-polymorphism-in-melatonin-receptor-1a-gene-with-egg-production-traits-in-yangzhou-geese
#12
M A Alsiddig, S G Yu, Z X Pan, H Widaa, T M Badri, J Chen, H L Liu
In the present study the melatonin receptor 1A gene (MTNR1A) was proposed to be a candidate gene for egg production in Yangzhou geese. A total of 210 goose blood samples were collected to investigate the association of the MTNR1A gene with the number of eggs produced. Using a direct sequencing method, a single nucleotide polymorphism (SNP; g.177G>C) was detected in the 5' regulatory region of the MTNR1A gene (Genbank ss1985399687). Two alleles (G and C) and three genotypes were identified. Association analysis results showed that the g...
November 24, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27878834/characterization-of-mirnas-involved-in-response-to-poly-i-c-in-porcine-airway-epithelial-cells
#13
L Wang, J K Wang, L X Han, J S Zhuo, X Du, D Liu, X Q Yang
MicroRNAs (miRNA) have been implicated in a variety of pathological conditions including infectious diseases. Knowledge of the miRNAs affected by poly(I:C), a synthetic analog of viral double-stranded RNA, in porcine airway epithelial cells (PAECs) contributes to understanding the mechanisms of swine viral respiratory diseases, which bring enormous economic loss worldwide every year. In this study, we used high throughput sequencing to profile miRNA expression in PAECs treated with poly(I:C) as compared to the untreated control...
November 22, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27878829/genetic-association-of-plag1-scd-cyp7b1-and-fasn-snps-and-their-effects-on-carcass-weight-intramuscular-fat-and-fatty-acid-composition-in-hanwoo-steers-korean-cattle
#14
Hyun Joo Kim, Aditi Sharma, Soo Hyun Lee, Doo Ho Lee, Da Jeong Lim, Yong Min Cho, Boh Suk Yang, Seung Hwan Lee
No abstract text is available yet for this article.
November 22, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27862083/biallelic-%C3%AE-carotene-oxygenase-2-knockout-results-in-yellow-fat-in-sheep-via-crispr-cas9
#15
Y Niu, M Jin, Y Li, P Li, J Zhou, X Wang, B Petersen, X Huang, Q Kou, Y Chen
The recently emerged CRISPR/Cas9 approach represents an efficient and versatile genome editing tool for producing genetically modified animals. Β-carotene oxygenase 2 (BCO2) is a key enzyme in the progress of β-carotene metabolism and is associated with yellow adipose tissue color in sheep. We have recently demonstrated targeted multiplex mutagenesis in sheep and have generated a group of BCO2-disrupted sheep by zygote injection of the CRISPR/Cas9 components. Here, we show that biallelic modification of BCO2 resulted in yellow fat, compared with the fat color in monoallelic individuals and wild types (snow-flower white)...
November 16, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27862128/regulation-of-crucial-lncrnas-in-differentiation-of-chicken-embryonic-stem-cells-to-spermatogonia-stem-cells
#16
D Li, Y Ji, F Wang, Y Wang, M Wang, C Zhang, W Zhang, Z Lu, C Sun, M F Ahmed, N He, K Jin, S Cheng, Y Wang, Y He, J Song, Y Zhang, B Li
Regulation of crucial lncRNAs involved in differentiation of chicken embryonic stem cells (ESCs) to spermatogonia stem cells (SSCs) was explored by sequencing the transcriptome of ESCs, primordial germ cells (PGCs) and SSCs with RNA-Seq; analytical bioinformatic methods were used to excavate candidate lncRNAs. We detected expression of candidate lncRNAs in ESCs, PGCs and SSCs and forecasted related target genes. Utilizing wego, david and string, function and protein-protein interactions of target genes were analyzed...
November 14, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27807880/selection-signature-analysis-reveals-genes-associated-with-tail-type-in-chinese-indigenous-sheep
#17
Z Yuan, E Liu, Z Liu, J W Kijas, C Zhu, S Hu, X Ma, L Zhang, L Du, H Wang, C Wei
Fat-tailed sheep have commercial value because consumers prefer high-protein and low-fat food and producers care about feed conversion rate. However, fat-tailed sheep still have some scientific significance, as the fat tail is commonly regarded as a characteristic of environmental adaptability. Finding the candidate genes associated with fat tail formation is essential for breeding and conservation. To identify these candidate genes, we applied FST and hapFLK approaches in fat- and thin-tailed sheep with available 50K SNP genotype data...
November 3, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27781291/expressed-microrna-associated-with-high-rate-of-egg-production-in-chicken-ovarian-follicles
#18
N Wu, U Gaur, Q Zhu, B Chen, Z Xu, X Zhao, M Yang, D Li
MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing...
October 26, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27646552/single-nucleotide-polymorphisms-in-exomes-of-high-and-low-marbled-meats-in-korean-cattle
#19
Sungchul Shin, Changpyo Hong, Sanghoon Song, Kung Ahn, Euiryong Chung
No abstract text is available yet for this article.
December 2016: Animal Genetics
https://www.readbyqxmd.com/read/27629771/genetic-diversity-and-genomic-signatures-of-selection-among-cattle-breeds-from-siberia-eastern-and-northern-europe
#20
T Iso-Touru, M Tapio, J Vilkki, T Kiseleva, I Ammosov, Z Ivanova, R Popov, M Ozerov, J Kantanen
Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure...
December 2016: Animal Genetics
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