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Animal Genetics

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https://www.readbyqxmd.com/read/28597956/a-post-gwas-confirming-gpat3-gene-associated-with-pig-growth-and-a-significant-snp-influencing-its-promoter-activity
#1
Kejun Wang, Yufang Liu, Qiao Xu, Chengkun Liu, Jve Wang, Cui Ding, Meiying Fang
Our previous genome-wide association study revealed that a SNP, ASGA0040372, located upstream of glycerol-3-phosphate acyltransferase 3 (GPAT3), is related to growth traits in Duroc pigs. In this study, we aimed to extensively investigate the genetic variation of GPAT3 and to further verify the contribution of ASGA0040372 to growth traits and its effect on promoter activity. Our data, obtained based on gene cloning and rapid amplification of cDNA ends experiments, showed that there are 14 exons and three alternative splicing variants...
June 9, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28568904/mitochondrial-dna-analysis-of-ancient-sheep-from-altai
#2
M A Dymova, A V Zadorozhny, O V Mishukova, E A Khrapov, A S Druzhkova, V A Trifonov, I G Kichigin, A A Tishkin, S P Grushin, M L Filipenko
A comparative analysis of the genetic diversity of ancient and modern sheep can shed light on the origin of these animals and their distribution as well as help to evaluate the role of humans at each formation stage of different sheep breeds. Here we isolated ancient DNA and performed sequencing of the mitochondrial DNA D-loop from 17 sheep bone remains (~4000-1000 years old) found in the archaeological complexes in the south of Altai (Western Siberia). The length of the sequences obtained ranged between 318 and 586 bp...
May 31, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28568840/characterization-of-a-deletion-in-the-hsp70-cluster-in-the-bovine-reference-genome
#3
M F Suqueli García, M A Castellote, S E Feingold, P M Corva
The 70 kilodalton heat shock proteins (Hsp70) are highly conserved molecular chaperones which have a crucial role in the stress response of the cell. In mammals, the Hsp70 proteins are encoded by a cluster of three genes: HSPA1A, HSPA1B and HSPA1L. In bovines, this cluster is located on chromosome 23 downstream of the major histocompatibility complex (BoLA). We detected inconsistencies in the location of markers on the Hsp70 genes reported in the literature that pointed to a potential deletion in the bovine reference genome UMD 3...
May 31, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28568646/genetic-diversity-of-syrian-arabian-horses
#4
S Almarzook, M Reissmann, D Arends, G A Brockmann
Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added...
May 31, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28568505/bola-drb3-gene-polymorphisms-influence-bovine-leukaemia-virus-infection-levels-in-holstein-and-holstein%C3%A2-%C3%A3-%C3%A2-jersey-crossbreed-dairy-cattle
#5
H A Carignano, M J Beribe, M E Caffaro, A Amadio, J P Nani, G Gutierrez, I Alvarez, K Trono, M M Miretti, M A Poli
Bovine leukemia virus (BLV) infections, causing persistent lymphocytosis and lethal lymphosarcoma in cattle, have reached high endemicity on dairy farms. We observed extensive inter-individual variation in the level of infection (LI) by assessing differences in proviral load in peripheral blood. This phenotypic variation appears to be determined by host genetics variants, especially those located in the BoLA-DRB3 MHCII molecule. We performed an association study using sequencing-based typed BOLA-DRB3 alleles from over 800 Holstein and Holstein × Jersey cows considering LI in vivo and accounting for filial relationships...
May 31, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28568315/relationships-between-the-genes-expressed-in-the-mesenteric-adipose-tissue-of-beef-cattle-and-feed-intake-and-gain
#6
A K Lindholm-Perry, H C Cunningham, L A Kuehn, J L Vallet, J W Keele, A P Foote, K M Cammack, H C Freetly
Mesenteric fat, a depot within the visceral fat, accumulates in cattle during maturation and finishing and may be a potential source of production inefficiency. The aim of this study was to determine whether the genes expressed in the mesenteric fat of steers were associated with body weight gain and feed intake. Sixteen steers chosen by their rank of distance from the bivariate mean for gain and feed intake were used for this study. Mesenteric fat was obtained and evaluated for differences in gene expression...
May 31, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28543827/estimations-of-linkage-disequilibrium-effective-population-size-and-roh-based-inbreeding-coefficients-in-spanish-churra-sheep-using-imputed-high-density-snp-genotypes
#7
P K Chitneedi, J J Arranz, A Suarez-Vega, E García-Gámez, B Gutiérrez-Gil
In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4...
May 22, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28543043/genetic-variation-and-genetic-structure-of-five-chinese-indigenous-pig-populations-in-jiangsu-province-revealed-by-sequencing-data
#8
Q Xiao, Z Zhang, H Sun, H Yang, M Xue, X Liu, W Zhang, Y Zhen, M Zhu, Q Wang, Y Pan
In this study, we investigated the genetic variants, including SNPs and indels (short insertions or deletions, less than 50 bp in length), in the genomes and genetic structures of five pig populations (in the northern Taihu Lake region, Jiangsu Province) using the genotyping by genome reducing and sequencing (GGRS) approach. A total of 581 million good reads with an average depth of 11× and an average coverage of 2.16% were used to call variants. In general, 202 106 SNPs and 34 415 indels were obtained, of which 2690 SNPs and 224 indels were capable of inducing protein-coding changes...
May 22, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28508551/first-study-of-mtdna-d-loop-in-brazilian-caipira-chickens
#9
M E Herkenhoff, F M Salzano, C A V Lima-Rosa
No abstract text is available yet for this article.
May 16, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28508507/detecting-selection-signatures-between-duroc-and-duroc-synthetic-pig-populations-using-high-density-snp-chip
#10
Z Edea, J-K Hong, J-H Jung, D-W Kim, Y-M Kim, E-S Kim, S S Shin, Y C Jung, K-S Kim
The development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs. The detection of genomic selection signals in a population subjected to differential selection pressures may provide insights into the genes associated with economically and biologically important traits. To identify genomic regions under selection, we genotyped 488 Duroc (D) pigs and 155 D × Korean native pigs (DKNPs) using the Porcine SNP70K BeadChip. By applying the FST and extended haplotype homozygosity (EHH-Rsb) methods, we detected genes under directional selection associated with growth/stature (DOCK7, PLCB4, HS2ST1, FBP2 and TG), carcass and meat quality (TG, COL14A1, FBXO5, NR3C1, SNX7, ARHGAP26 and DPYD), number of teats (LOC100153159 and LRRC1), pigmentation (MME) and ear morphology (SOX5), which are all mostly near or at fixation...
May 16, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28508416/frame-shift-variant-in-the-chrne-gene-in-a-juvenile-dog-with-suspected-myasthenia-gravis-like-disease
#11
Vanessa Herder, Malgorzata Ciurkiewicz, Wolfgang Baumgärtner, Vidhya Jagannathan, Tosso Leeb
No abstract text is available yet for this article.
May 16, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28497851/a-novel-mutation-in-the-tyrp1-gene-associated-with-brown-coat-colour-in-the-australian-shepherd-dog-breed
#12
Evelina Hrckova Turnova, Zuzana Majchrakova, Marcela Bielikova, Katarina Soltys, Jan Turna, Andrej Dudas
No abstract text is available yet for this article.
May 12, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28497848/isolation-of-subtelomeric-sequences-of-porcine-chromosomes-for-translocation-screening-reveals-errors-in-the-pig-genome-assembly
#13
R E O'Connor, G Fonseka, R Frodsham, A L Archibald, M Lawrie, G A Walling, D K Griffin
Balanced chromosomal aberrations have been shown to affect fertility in most species studied, often leading to hypoprolificacy (reduced litter size) in domestic animals such as pigs. With an increasing emphasis in modern food production on the use of a small population of high quality males for artificial insemination, the potential economic and environmental costs of hypoprolific boars, bulls, rams etc. are considerable. There is therefore a need for novel tools to facilitate rapid, cost-effective chromosome translocation screening...
May 12, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28485055/a-survey-of-single-nucleotide-polymorphisms-identified-from-whole-genome-sequencing-and-their-functional-effect-in-the-porcine-genome
#14
B N Keel, D J Nonneman, G A Rohrer
Genetic variants detected from sequence have been used to successfully identify causal variants and map complex traits in several organisms. High and moderate impact variants, those expected to alter or disrupt the protein coded by a gene and those that regulate protein production, likely have a more significant effect on phenotypic variation than do other types of genetic variants. Hence, a comprehensive list of these functional variants would be of considerable interest in swine genomic studies, particularly those targeting fertility and production traits...
May 8, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28449233/an-evaluation-of-the-international-society-for-animal-genetics-recommended-parentage-and-identification-panel-for-the-domestic-pigeon-columba-livia-domestica
#15
M de Groot, W A van Haeringen
In this study, the International Society for Animal Genetics (ISAG) recommended panel for the identification of the domestic pigeon (Columba livia domestica) is characterized based on commonly used statistical parameters. The marker panel is based on 16 short tandem repeat (STR) loci (PIGN15, PIGN10, PIGN57, PIGN26, CliμD16, CliμD19, PIGN12, CliμD17, CliμT17, PIGN04, CliμD01, CliμD11, CliμD35, CliμT02, CliμT13, CliμT43). The alleles of the 16 loci consist of a mixture of tri-, tetra-, penta- and hexameric repeat patterns...
April 27, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28444912/whole-genome-sequencing-reveals-a-novel-deletion-variant-in-the-kit-gene-in-horses-with-white-spotted-coat-colour-phenotypes
#16
N Dürig, R Jude, H Holl, S A Brooks, C Lafayette, V Jagannathan, T Leeb
White spotting phenotypes in horses can range in severity from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for such phenotypes in horses. For the present study, we re-investigated a large horse family segregating a variable white spotting phenotype, for which conventional Sanger sequencing of the candidate genes' individual exons had failed to reveal the causative variant. We obtained whole genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes...
April 26, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28378952/haplotype-structure-and-copy-number-polymorphism-of-the-beta-defensin-7-genes-in-diverse-chicken-breeds
#17
M O Lee, M N Romanov, K V Plemyashov, N V Dementieva, O V Mitrofanova, O Y Barkova, J E Womack
Beta-defensins is a family of avian peptides related to the innate immune system. Copy number variation was recently reported for the avian beta-defensin 7 gene (AvBD7) between the highly inbred Leghorn and Fayoumi lines. Here, we examined copy number variants in 35 different chicken breeds and found that 31 of them have at least the same representation of the duplicated AvBD7 allele. We also found haplotypes upstream of the AvBD6 regions that are strongly linked to the AvBD7 duplication. We observed a strong linkage disequilibrium spanning of the upstream region of the AvBD6 gene, with two SNPs being flanking markers to detect duplication of the AvBD7...
April 5, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28378943/exclusion-of-known-progressive-retinal-atrophy-genes-for-blindness-in-the-hungarian-puli
#18
Tracy Chew, Bianca Haase, Cali E Willet, Claire M Wade
No abstract text is available yet for this article.
April 5, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28378922/a-novel-splice-mutation-within-equine-kit-and-the-w15-allele-in-the-homozygous-state-lead-to-all-white-coat-color-phenotypes
#19
Heather M Holl, Samantha A Brooks, Meredith L Carpenter, Carlos D Bustamante, Christa Lafayette
No abstract text is available yet for this article.
April 5, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28370091/genotyping-by-sequencing-reveals-a-new-locus-for-pig-teat-number
#20
L Wang, Y Zhang, T Zhang, L Zhang, H Yan, X Liu, L Wang
Teat number is an extremely valuable trait for sow reproduction performance and piglet survival. Here, we used genotyping-by-sequencing and a general liner model to carry out genome-wide analysis of sow total teat number in an Erhualian population. The results indicated that eight SNPs on chromosomes 4, 5, 9 and 10 were significant genome wide (Bonferroni method, P < 2.85E-7) for sow total teat number. Validation analyses were performed in 298 Erhualian and 904 Large White sows using these significant SNPs and the general liner model procedure in sas...
April 3, 2017: Animal Genetics
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