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Search Results: 1 - 10 of 201269 matches for " Donagh P Berry "
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Purging of inbreeding depression within the Irish Holstein-Friesian population
Sinéad Mc Parland, Francis Kearney, Donagh P Berry
Genetics Selection Evolution , 2009, DOI: 10.1186/1297-9686-41-16
Abstract: Inbreeding is defined as the probability that two alleles at any locus are 'identical by descent' [1] and occurs when related individuals are mated. Inbreeding results in an increase in the number of homozygous loci [2], which may lead to an increase in the accumulation of recessive alleles. Mendelian factors unfavourable to fitness are more frequently recessive than dominant for two reasons: firstly, mutations tend to have negative effects on fitness and secondly, because dominant mutations will be quickly selected out of populations. This will lead to an accumulation of deleterious recessive alleles [2]. The loss in performance and vitality associated with inbreeding is termed "inbreeding depression" [3] and has generally been shown to be unfavourable [4].It has been considered for different traits that dominance [3], overdominance [5], and epistatic effects [6] influences inbreeding depression. Where the genes are governed by dominance, inbreeding depression is caused by an increase in the number of genes with homozygous deleterious recessive genotypes and the decline in performance is expected to be linear with respect to the inbreeding coefficient [6]. Where traits are governed by overdominance, heterozygotes perform better than either homozygote, thus as inbreeding increases the number of homozygous loci, the proportion of advantageous heterozygous loci decreases. Epistasis occurs when an allele at one locus has an effect on an allele at another locus. Where epistatic interactions exist, a non-linear effect on performance is expected with respect to inbreeding [7]. The non-linear interactions are explained by the interaction deviation of double or multiple heterozygotes [8].Regardless of the mechanisms underlying inbreeding depression, the effects of inbreeding are not consistent across populations or even sub-populations. Thus the level of inbreeding depression experienced is dependent, amongst other factors, on the genetic load of individuals [9].Purging of
A Genome Wide Association Scan of Bovine Tuberculosis Susceptibility in Holstein-Friesian Dairy Cattle
Emma K. Finlay, Donagh P. Berry, Brian Wickham, Eamonn P. Gormley, Daniel G. Bradley
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030545
Abstract: Background Bovine tuberculosis is a significant veterinary and financial problem in many parts of the world. Although many factors influence infection and progression of the disease, there is a host genetic component and dissection of this may enlighten on the wider biology of host response to tuberculosis. However, a binary phenotype of presence/absence of infection presents a noisy signal for genomewide association study. Methodology/Principal Findings We calculated a composite phenotype of genetic merit for TB susceptibility based on disease incidence in daughters of elite sires used for artificial insemination in the Irish dairy herd. This robust measure was compared with 44,426 SNP genotypes in the most informative 307 subjects in a genome wide association analysis. Three SNPs in a 65 kb genomic region on BTA 22 were associated (i.e. p<10?5, peaking at position 59588069, p = 4.02×10?6) with tuberculosis susceptibility. Conclusions/Significance A genomic region on BTA 22 was suggestively associated with tuberculosis susceptibility; it contains the taurine transporter gene SLC6A6, or TauT, which is known to function in the immune system but has not previously been investigated for its role in tuberculosis infection.
Genetics of animal health and disease in cattle
Donagh P Berry, Mairead L Bermingham, Margaret Good, Simon J More
Irish Veterinary Journal , 2011, DOI: 10.1186/2046-0481-64-5
Abstract: There continues to be very significant advances in efforts to control disease in cattle, with the potential for significant improvements to both performance and welfare. These advances have included improved understanding of disease pathophysiology and epidemiology, as well as the development of products such as antibiotics and anthelmintics for improved disease control.Concurrently, there have been considerable advances in animal breeding and genetics, relevant to animal disease control. These advances are of considerable veterinary interest, noting that observed animal performance is the outcome of the interaction between the animal's genetic makeup and the specific environment it was exposed to. Logically, therefore, improved genetics has the potential to complement current approaches to animal disease control. Improvement in animal health through genetic selection is advantageous, because genetic gain is cumulative and permanent, as the genes introduced into a population can persist for many generations. Unravelling the genetic architecture of health and disease resistance not only facilitates knowledge development on potential for breeding for improved health status but also generates knowledge for biomedical research in animals and humans including applications such as vaccine development.The objective of this review is to summarise research studies on the genetics of animal health and disease resistance in cattle, with particular reference to studies undertaken in Irish cattle. The implications of these results in breeding for improved animal health and disease resistance are discussed.Prior to discussing the genetics of animal health and disease resistance, the terms commonly used by animal breeders to describe the characteristics of a population need to be explained:The phenotype is simply the observed performance of an animal "in the field" (e.g., dystocia in cows or the presence or absence of infection as measured by a positive or negative diagnostic test
Runs of homozygosity and population history in cattle
Purfield Deirdre C,Berry Donagh P,McParland Sinead,Bradley Daniel G
BMC Genetics , 2012, DOI: 10.1186/1471-2156-13-70
Abstract: Background Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that are present in an individual due to parents transmitting identical haplotypes to their offspring. The extent and frequency of ROHs may inform on the ancestry of an individual and its population. Here we use high density (n = 777,962) bi-allelic SNPs in a range of cattle breed samples to correlate ROH with the pedigree-based inbreeding coefficients and to validate subsequent analyses using 54,001 SNP genotypes. This study provides a first testing of the inference drawn from ROH through comparison with estimates of inbreeding from calculations based on the detailed pedigree data available for several breeds. Results All animals genotyped on the HD panel displayed at least one ROH that was between 1–5 Mb in length with certain regions of the genome more likely to be involved in a ROH than others. Strong correlations (r = 0.75, p < 0.0001) existed between the pedigree-based inbreeding coefficient and a statistic based on sum of ROH of length > 0.5 KB and suggests that in the absence of an animal’s pedigree data, the extent of a genome under ROH may be used to infer aspects of recent population history even from relatively few samples. Conclusions Our findings suggest that ROH are frequent across all breeds but differing patterns of ROH length and burden illustrate variations in breed origins and recent management.
Single Nucleotide Polymorphisms in the Insulin-Like Growth Factor 1 (IGF-1) Gene are Associated with Performance in Holstein-Friesian Dairy Cattle
Michael Paul Mullen,Donagh P. Berry,Ciaran O. Lynch,David A. Magee
Frontiers in Genetics , 2011, DOI: 10.3389/fgene.2011.00003
Abstract: Insulin-like growth factor 1 (IGF-1) has been shown to be associated with fertility, growth, and development in cattle. The aim of this study was to (1) identify novel single nucleotide polymorphisms (SNPs) in the bovine IGF-1 gene and alongside previously identified SNPs (2) determine their association with traits of economic importance in Holstein-Friesian dairy cattle. Nine novel SNPs were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5′ promoter, intronic, and 3′ regulatory regions, encompassing ~5 kb of IGF-1. Genotyping and associations with daughter performance for milk production, fertility, survival, and measures of body size were undertaken on 848 Holstein-Friesian AI sires. Using multiple regression analysis nominal associations (P < 0.05) were identified between six SNPs (four novel and two previously identified) and milk composition, survival, body condition score, and body size. The C allele of AF017143 a previously published SNP (C-512T) in the promoter region of IGF-1 predicted to introduce binding sites for transcription factors HSF1 and ZNF217 was associated (P < 0.05) with increased cow carcass weight (i.e., an indicator of mature cow size). Novel SNPs were identified in the 3′ region of IGF-1 were associated (P < 0.05) with functional survival and chest width. The remaining four SNPs, all located within introns of IGF-1 were associated (P < 0.05) with milk protein yield, milk fat yield, milk fat concentration, somatic cell score, carcass conformation, and carcass fat. Results of this study further demonstrate the multifaceted influences of IGF-1 on milk production and growth related traits in cattle.
Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires
Linda Giblin, Stephen T Butler, Breda M Kearney, Sinead M Waters, Michael J Callanan, Donagh P Berry
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-73
Abstract: All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05).Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.Leptin is a 16 kD non-gly
Polymorphisms in bovine immune genes and their associations with somatic cell count and milk production in dairy cattle
Christine Beecher, Mairead Daly, Stuart Childs, Donagh P Berry, David A Magee, Tommie V McCarthy, Linda Giblin
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-99
Abstract: TLR4-2021 associated (P < 0.05) with both milk protein and fat percentage in late lactation (P < 0.01) within the cow cohort. No association was observed between this polymorphism and either yield or composition of milk within the bull population. CXCR1-777 significantly associated (P < 0.05) with fat yield in the bull population and tended to associate (P < 0.1) with somatic cell score (SCS) in the cows genotyped. CD14-1908 A allele was found to associate with increased (P < 0.05) milk fat and protein yield and also tended to associate with increased (P < 0.1) milk yield. A SERPINA1 haplotype with superior genetic merit for milk protein yield and milk fat percentage (P < 0.05) was also identified.Of the sixteen polymorphisms in seven immune genes genotyped, just CXCR1-777 tended to associate with SCS, albeit only in the on-farm study. The lack of an association between the polymorphisms with SCS in the Holstein-Friesian data set would question the potential importance of these variants in selection for improved mastitis resistance in the Holstein-Friesian cow.Mastitis, an inflammation of the mammary gland, is a major source of economic loss on dairy farms. The disease cost to the EU dairy industry was €1.5 billion in 2005 [1]. This is due to increased involuntary culling [2], therapeutic costs [3], reduced milk yield and changes in milk composition [4]. Although farm management practices play a major role in mastitis incidence and control [5], modern day breeding programmes aim to incorporate increased mastitis resistance in the dairy herd without compromising milk production [6]. With the exception of the Nordic countries [7], most countries are limited to select for animals with low somatic cell count (SCC) due to the lack of routinely available phenotypic data on clinical mastitis. Indeed it has been shown in sheep that animals bred for low somatic cell score (SCS; natural logarithm of SCC) possess a better ability to limit and eliminate mastitis infections than
DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle
David A Magee, Klaudia M Sikora, Erik W Berkowicz, Donagh P Berry, Dawn J Howard, Michael P Mullen, Ross D Evans, Charles Spillane, David E MacHugh
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-93
Abstract: Heterozygosities for all SNPs analysed ranged from 0.09 to 0.46 and significant deviations from Hardy-Weinberg proportions (P ≤ 0.01) were observed at four loci. Phenotypic associations (P ≤ 0.05) were observed between nine SNPs proximal to, or within, six of the eight analysed genes and a number of performance traits evaluated, including milk protein percentage, somatic cell count, culled cow and progeny carcass weight, angularity, body conditioning score, progeny carcass conformation, body depth, rump angle, rump width, animal stature, calving difficulty, gestation length and calf perinatal mortality. Notably, SNPs within the imprinted paternally expressed gene 3 (PEG3) gene cluster were associated (P ≤ 0.05) with calving, calf performance and fertility traits, while a single SNP in the zinc finger protein 215 gene (ZNF215) was associated with milk protein percentage (P ≤ 0.05), progeny carcass weight (P ≤ 0.05), culled cow carcass weight (P ≤ 0.01), angularity (P ≤ 0.01), body depth (P ≤ 0.01), rump width (P ≤ 0.01) and animal stature (P ≤ 0.01).Of the eight candidate bovine imprinted genes assessed, DNA sequence polymorphisms in six of these genes (CALCR, GRB10, PEG3, RASGRF1, ZIM2 and ZNF215) displayed associations with several of the phenotypes included for analyses. The genotype-phenotype associations detected here are further supported by the biological function of these six genes, each of which plays important roles in mammalian growth, development and physiology. The associations between SNPs within the imprinted PEG3 gene cluster and traits related to calving, calf performance and gestation length suggest that this domain on chromosome 18 may play a role regulating pre-natal growth and development and fertility. SNPs within the bovine ZNF215 gene were associated with bovine growth and body conformation traits and studies in humans have revealed that the human ZNF215 ortholog belongs to the imprinted gene cluster associated with Beckwith-Wiedemann syndrome
DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsα)-encoding (GNAS) genomic imprinting domain are associated with performance traits
Klaudia M Sikora, David A Magee, Erik W Berkowicz, Donagh P Berry, Dawn J Howard, Michael P Mullen, Ross D Evans, David E MacHugh, Charles Spillane
BMC Genetics , 2011, DOI: 10.1186/1471-2156-12-4
Abstract: SNP genotype-phenotype association analyses indicate that the single intronic GNAS SNP (rs41694646) is associated (P ≤ 0.05) with a range of performance traits including milk yield, milk protein yield, the content of fat and protein in milk, culled cow carcass weight and progeny carcass conformation, measures of animal body size, direct calving difficulty (i.e. difficulty in calving due to the size of the calf) and gestation length. Association (P ≤ 0.01) with direct calving difficulty (i.e. due to calf size) and maternal calving difficulty (i.e. due to the maternal pelvic width size) was also observed at the rs43101491 SNP. Following adjustment for multiple-testing, significant association (q ≤ 0.05) remained between the rs41694646 SNP and four traits (animal stature, body depth, direct calving difficulty and milk yield) only. Notably, the single SNP in the bovine NESP55 gene (rs41694656) was associated (P ≤ 0.01) with somatic cell count--an often-cited indicator of resistance to mastitis and overall health status of the mammary system--and previous studies have demonstrated that the chromosomal region to where the GNAS domain maps underlies an important quantitative trait locus for this trait. This association, however, was not significant after adjustment for multiple testing. The three remaining SNPs assayed were not associated with any of the performance traits analysed in this study. Analysis of all pairwise linkage disequilibrium (r2) values suggests that most allele substitution effects for the assayed SNPs observed are independent. Finally, the polymorphic coding SNP in the putative bovine NESP55 gene was used to test the imprinting status of this gene across a range of foetal bovine tissues.Previous studies in other mammalian species have shown that DNA sequence variation within the imprinted GNAS gene cluster contributes to several physiological and metabolic disorders, including obesity in humans and mice. Similarly, the results presented here indicate a
Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland
Brian K Meredith, Francis J Kearney, Emma K Finlay, Daniel G Bradley, Alan G Fahey, Donagh P Berry, David J Lynn
BMC Genetics , 2012, DOI: 10.1186/1471-2156-13-21
Abstract: Significant associations were detected for milk yield, fat yield, protein yield, fat percentage, protein percentage and somatic cell score using separate single-locus, frequentist and multi-locus, Bayesian approaches. These associations were detected using two separate populations of Holstein-Friesian sires and cows. In total, 1,529 and 37 associations were detected in the sires using a single SNP regression and a Bayesian method, respectively. There were 103 associations in common between the sires and cows across all the traits. As well as detecting associations within known QTL regions, a number of novel associations were detected; the most notable of these was a region of chromosome 13 associated with milk yield in the population of Holstein-Friesian sires.A total of 276 of novel SNPs were detected in the sires using a single SNP regression approach. Although obvious candidate genes may not be initially forthcoming, this study provides a preliminary framework upon which to identify the causal mechanisms underlying the various milk production traits and somatic cell score. Consequently this will deepen our understanding of how these traits are expressed.Dairy production is an economically important sector of global agriculture with the top 10 leading dairy companies turning over in excess of $114 billion in 2009 [1]. Dairy cows account for 84% of global dairy output [1] so consequently there is great interest placed upon the production potential and health of these animals. Until recently, the majority of international dairy breeding programmes selected solely for increased milk production, however, breeding goals have diversified to include health and functional traits in an effort to minimise and reverse the decline in these traits [2]. Prominent among these health-related traits is mastitis (commonly measured using somatic cell score (SCS) as an indicator trait), which is one of the most important and costly production diseases in the dairy industry. Selection
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