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Animal Genetics

L Gao, S-S Xu, J-Q Yang, M Shen, M-H Li
Variations in ear size can be observed in livestock such as sheep; however, the genetic basis of variable ear size in sheep is still poorly understood. To investigate causative genes associated with ear size in sheep, a genome-wide association study was performed in 115 adult Duolang sheep with different-sized floppy ears using the Ovine Infinium HD BeadChip. We found 38 significant SNPs at the genome-wide or chromosome-wise 5% significance level after Bonferroni correction. The most significant association (P = 1...
May 18, 2018: Animal Genetics
Sina Reinartz, Christine Weiß, Reinhard Mischke, Ottmar Distl
No abstract text is available yet for this article.
May 18, 2018: Animal Genetics
Yu Zhang, Meng Wang, Jiao Yuan, Xiang Zhou, Sanping Xu, Bang Liu
No abstract text is available yet for this article.
May 18, 2018: Animal Genetics
S Joller, P Ammann, C Flury, C Drögemüller
The crest in chicken consists of elongated and upraised feathers, as seen in various breeds such as the Silkie chicken. Recently, the still unknown causative mutation for the crest phenotype was assigned to chromosome 33 and an ectopic expression of HOXC8 was shown. The aim this study was to evaluate whether the crest phenotype in a local Swiss chicken breed, the Appenzeller Spitzhaubenhuhn, is associated with HOXC8. Three previously reported crest-associated flanking markers at the HOXC8 locus were genotyped in cohorts of this breed and two other local breeds without the crest phenotype...
May 18, 2018: Animal Genetics
S Y Jiang, H Y Xu, Z N Shen, C J Zhao, C Wu
The Tibetan chicken (TBC), an indigenous chicken breed of the Tibetan Plateau, has adapted to its hypoxic, high-altitude environment over hundreds of years. The objective of this study was to identify the polymorphisms and genes associated with adaptation to hypoxia in this chicken breed. In the present study, samples were collected during days 18-21 of the incubation period from both surviving chicks and dead embryos, all of which were hatched under hypoxic conditions. A genome-wide association study was conducted using the Illumina iSelect 60K SNP array with a case-control design, in which the case group consisted of the dead chicken embryos (n = 54) and controls were the surviving chicks (n = 82)...
May 18, 2018: Animal Genetics
Yu Ueda, Ronald Hak Long Li, Fern Tablin, Eric S Ontiveros, Joshua A Stern
No abstract text is available yet for this article.
May 18, 2018: Animal Genetics
Zonggang Luo, Yuhui Wu, Wen-Xiu Zhang, Ling Wang, Fuyuan Zuo, Gong-Wei Zhang
No abstract text is available yet for this article.
May 18, 2018: Animal Genetics
G Schiavo, F Bertolini, V J Utzeri, A Ribani, C Geraci, L Santoro, C Óvilo, A I Fernández, M Gallo, L Fontanesi
Casertana is an endangered autochthonous pig breed (raised in south-central Italy) that is considered to be the descendant of the influential Neapolitan pig population that was used to improve British breeds in the 19th century. Casertana pigs are characterized by a typical, almost complete, hairless phenotype, even though a few Casertana pigs are normal haired. In this work, using Illumina PorcineSNP60 BeadChip data, we carried out a genome-wide association study and an FST analysis with this breed by comparing animals showing the classical hairless phenotype (n = 81) versus pigs classified as haired (n = 15)...
April 19, 2018: Animal Genetics
M Schmid, M Maushammer, S Preuß, J Bennewitz
In this study, genome-wide association study (GWAS) results of porcine F2 crosses were used to map QTL in outcross Piétrain populations. For this purpose, two F2 crosses (Piétrain × Meishan, n = 304; Piétrain × Wild Boar, n = 291) were genotyped with the PorcineSNP60v2 BeadChip and phenotyped for the dressing yield, carcass length, daily gain and drip loss traits. GWASs were conducted in the pooled F2 cross applying single marker mixed linear models. For the investigated traits, between two and five (in total 15) QTL core regions, spanning 250 segregating SNPs around a significant trait-associated peak SNP, were identified...
April 19, 2018: Animal Genetics
Q Wang, J Pi, J Shen, A Pan, L Qu
Rumplessness in Hongshan chickens has been reported as a novel sex-linked characteristic. Re-sequencing data suggest that a pseudogene on the Z chromosome, LOC431648, is affiliated with this phenotype. In this study, we chose 23 rumpless and 25 normal Hongshan chickens to localize the potential variation by means of a genome-wide association study using a high density microarray. A region on the Z chromosome was found to be closely associated with rumplessness in Hongshan chickens. The region, located in gene LINGO2, was approximately 3 Mb away from pseudogene LOC431648...
April 19, 2018: Animal Genetics
H Bai, Y Sun, N Liu, Y Liu, F Xue, Y Li, S Xu, A Ni, J Ye, Y Chen, J Chen
Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing-You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (CNV) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome-wide CNV detection using Affymetrix chicken high-density 600K data on 48 deformed-beak and 48 normal birds using penncnv...
April 11, 2018: Animal Genetics
K Piórkowska, K Żukowski, K Ropka-Molik, M Tyra
Variant calling analysis based on RNA sequencing data provides information about gene variants. RNA-seq is cheaper and faster than is DNA sequencing. However, it requires individual hard filters during data processing due to post-transcriptional modifications such as splicing and RNA editing. In the present study, RNA-seq transcriptome data on two Polish pig breeds (Puławska, PUL, n = 8, and Polish Landrace, PL, n = 8) were included. The pig breeds are significantly different with regard to meat qualities such as texture, water exudation, growth traits and fat content in carcasses...
April 10, 2018: Animal Genetics
T Druml, G Grilz-Seger, M Neuditschko, M Horna, A Ricard, H Pausch, G Brem
Within the framework of genome-wide analyses using the novel Axiom® genotyping array, we investigated the distribution of two previously described coat color patterns, namely sabino1 (SBI), associated with the KIT gene (KI16+1037A), and splashed white, associated with the PAX3 gene (ECA6:g.11429753C>T; PAX3C70Y ), including a total of 899 horses originating from eight different breeds (Achal Theke, Purebred Arabian, Partbred Arabian, Anglo-Arabian, Shagya Arabian, Haflinger, Lipizzan and Noriker). Based on the data we collected we were able to demonstrate that, besides Quarter horses, the PAX3C70Y allele is also present in Noriker (seven out of 189) and Lipizzan (three out of 329) horses...
April 10, 2018: Animal Genetics
F Biscarini, P Cozzi, P Orozco-Ter Wengel
The 'omics revolution has made a large amount of sequence data available to researchers and the industry. This has had a profound impact in the field of bioinformatics, stimulating unprecedented advancements in this discipline. Mostly, this is usually looked at from the perspective of human 'omics, in particular human genomics. Plant and animal genomics, however, have also been deeply influenced by next-generation sequencing technologies, with several genomics applications now popular among researchers and the breeding industry...
April 6, 2018: Animal Genetics
N Chen, J Huang, A Zulfiqar, R Li, Y Xi, M Zhang, R Dang, X Lan, H Chen, Y Ma, C Lei
The aim of this study was to estimate population structure and ancestry of Qinchuan cattle by genotyping 27 individuals using the GeneSeek HD 77k BeadChip, and another 1355 cattle representing breeds distributed worldwide, which had been genotyped using the Illumina Bovine 50k BeadChip. Qinchuan cattle were characterized by a dominant Bos taurus ancestry, accompanied by a considerable proportion of Bos indicus ancestry based on principal components analysis and supervised admixture analysis. A small proportion of Bos javanicus ancestry was detected as well...
April 6, 2018: Animal Genetics
S Naderi, M Bohlouli, T Yin, S König
Holstein Friesian cow training sets were created according to disease incidences. The different datasets were used to investigate the impact of random forest (RF) and genomic BLUP (GBLUP) methodology on genomic prediction accuracies. In addition, for further verifications of some specific scenarios, single-step genomic BLUP was applied. Disease traits included the overall trait categories of (i) claw disorders, (ii) clinical mastitis and (iii) infertility from 80 741 first lactation Holstein cows kept in 58 large-scale herds...
April 6, 2018: Animal Genetics
P Karlskov-Mortensen, H F Proschowsky, F Gao, M Fredholm
Progressive retinal atrophy (PRA) is a common cause of blindness in many dog breeds. It is most often inherited as a simple Mendelian trait, but great genetic heterogeneity has been demonstrated both within and between breeds. In many breeds the genetic cause of the disease is not known, and until now, the Old Danish Pointing Dog (ODP) has been one of those breeds. ODP is one of the oldest dog breeds in Europe. Seventy years ago the breed almost vanished, but today a population still exists, primarily in Denmark but with some dogs in Germany and Sweden...
April 6, 2018: Animal Genetics
Feng Yu, Zhengxi Liu, Shuyu Jiao, Xiaoying Zhang, Chunyan Bai, Jiabao Zhang, Shouqing Yan
No abstract text is available yet for this article.
March 30, 2018: Animal Genetics
J-H Kang, E-A Lee, K-C Hong, J-M Kim
Among swine reproductive traits, sow lifetime productivity (SLP) is considered a profitable trait in commercial pig farming. Notably, longevity and efficiency in SLP can be adopted as the key phenotype representing SLP. In this study, we conducted a co-association network analysis using results from a genome-wide association study for SLP-related traits. A total of 656 purebred Landrace female pigs were genotyped using a 60K SNP array. Significantly associated SNPs identified from the GWAS were annotated for the specific genes...
March 23, 2018: Animal Genetics
A A Malik, R Sharma, S Ahlawat, R Deb, M S Negi, S B Tripathi
Genetic relatedness of 24 animals belonging to seven Indian cattle breeds was studied using high throughput genotyping-by-sequencing (GBS) markers. GBS produced 93.6 million reads with an average of about 3.9 million reads per animal. A total of 107 488 SNPs were identified in these individuals. When only one SNP per read was considered, a total of 60 261 SNPs representing independent reads were identified with an average SNP-to-SNP distance of 45 kb across the bovine reference genome. About 24% of the GBS-SNP markers were more than 100 kb apart...
March 23, 2018: Animal Genetics
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