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Animal Genetics

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https://www.readbyqxmd.com/read/28703336/a-genome-wide-association-study-reveals-candidate-genes-for-the-supernumerary-nipple-phenotype-in-sheep-ovis-aries
#1
W-F Peng, S-S Xu, X Ren, F-H Lv, X-L Xie, Y-X Zhao, M Zhang, Z-Q Shen, Y-L Ren, L Gao, M Shen, J Kantanen, M-H Li
Genome-wide association studies (GWASs) have been widely applied in livestock to identify genes associated with traits of economic interest. Here, we conducted the first GWAS of the supernumerary nipple phenotype in Wadi sheep, a native Chinese sheep breed, based on Ovine Infinium HD SNP BeadChip genotypes in a total of 144 ewes (75 cases with four teats, including two normal and two supernumerary teats, and 69 control cases with two teats). We detected 63 significant SNPs at the chromosome-wise threshold. Additionally, one candidate region (chr1: 170...
July 12, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28703288/a-comparative-proteomic-analysis-of-blood-serum-for-developmental-stages-in-pigs
#2
K Srikanth, E Lee, A Kwon, J Shin, H Chung
This study aimed to differentiate genes at developmental stages of pigs from 0 to 150 days of age, to build up a protein database and to find candidate genetic markers for growth traits. The analysis of two-dimensional electrophoresis and matrix-assisted laser-desorption/ionization mass spectrometry separated 252 protein segments. After successfully blasting the peptide sequences, the analysis confirmed 37 differentially expressed proteins that increased from birth to 150 days of age (type A), whereas the type B proteins presented the inverse pattern...
July 12, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28699279/a-new-dominant-haplotype-of-mc1r-gene-in-chinese-black-plumage-chicken
#3
Gong-Wei Zhang, Yonglan Liao, Wen-Xiu Zhang, Yuhui Wu, Anfang Liu
No abstract text is available yet for this article.
July 11, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28699276/y-chromosome-and-mtdna-variation-confirms-independent-domestications-and-directional-hybridization-in-south-american-camelids
#4
J C Marín, K Romero, R Rivera, W E Johnson, B A González
Investigations of genetic diversity and domestication in South American camelids (SAC) have relied on autosomal microsatellite and maternally-inherited mitochondrial data. We present the first integrated analysis of domestic and wild SAC combining male and female sex-specific markers (male specific Y-chromosome and female-specific mtDNA sequence variation) to assess: (i) hypotheses about the origin of domestic camelids, (ii) directionality of introgression among domestic and/or wild taxa as evidence of hybridization and (iii) currently recognized subspecies patterns...
July 11, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28677334/genome-wide-association-analysis-identifies-the-genetic-basis-of-fat-deposition-in-the-tails-of-sheep-ovis-aries
#5
S-S Xu, X Ren, G-L Yang, X-L Xie, Y-X Zhao, M Zhang, Z-Q Shen, Y-L Ren, L Gao, M Shen, J Kantanen, M-H Li
Fat-tailed sheep (Ovis aries) can survive in harsh environments and satisfy human's intake of dietary fat. However, the animals require more feed, which increases the cost of farming. Thus, most farmers currently prefer thin-tailed, short-tailed or docked sheep. To date, the molecular mechanism of the formation of fat tails in sheep has not been completely elucidated. Here, we conducted a genome-wide association study using phenotypes and genotypes (the Ovine Infinium HD SNP BeadChip genotype data) of two breeds of contrasting tail types (78 Small-tailed and 78 Large-tailed Han sheep breeds) to identify functional genes and variants associated with fat deposition...
July 4, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28639704/genome-wide-association-analysis-identifies-potential-regulatory-genes-for-eumelanin-pigmentation-in-chicken-plumage
#6
L Yang, X Du, S Wei, L Gu, N Li, Y Gong, S Li
Plumage color in chicken is determined by the proportion of eumelanin and pheomelanin pigmentation. As the main ingredient in plumage melanin, eumelanin plays a key role in the dark black, brown and grey coloration. However, very few studies have been performed to identify the related genes and mutations on a genome-wide scale. Herein, a resource family consisting of one backcross population and two F2 cross populations between a black roster and Yukou Brown I parent stockbreed was constructed for identification of genes related to eumelanin pigmentation...
June 22, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28597956/a-post-gwas-confirming-gpat3-gene-associated-with-pig-growth-and-a-significant-snp-influencing-its-promoter-activity
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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