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Proteome-wide Systems Genetics to Identify Functional Regulators of Complex Traits. Cell Syst 2021; 12:5-22. [PMID: 33476553 DOI: 10.1016/j.cels.2020.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 02/08/2023]
Abstract
Proteomic technologies now enable the rapid quantification of thousands of proteins across genetically diverse samples. Integration of these data with systems-genetics analyses is a powerful approach to identify new regulators of economically important or disease-relevant phenotypes in various populations. In this review, we summarize the latest proteomic technologies and discuss technical challenges for their use in population studies. We demonstrate how the analysis of correlation structure and loci mapping can be used to identify genetic factors regulating functional protein networks and complex traits. Finally, we provide an extensive summary of the use of proteome-wide systems genetics throughout fungi, plant, and animal kingdoms and discuss the power of this approach to identify candidate regulators and drug targets in large human consortium studies.
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Park H, Seo KS, Lee M, Seo S. Identification of meat quality-related differentially methylated regions in the DNA of the longissimus dorsi muscle in pig. Anim Biotechnol 2019; 31:189-194. [PMID: 31060422 DOI: 10.1080/10495398.2019.1604378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The objective of this study was to investigate the association of DNA methylation with postmortem energy metabolism and the pH of the porcine longissimus dorsi muscle (LDM). Analysis of the DNA methylome of eight LDM samples (four pairs of the highest and lowest pH among littermates) identified a total of 3468 differentially methylated regions (DMRs) between high and low pH samples (p ≤ 0.001). Of DMRs, 45.3% co-mapped with quantitative trait loci known to be associated with meat pH and postmortem metabolism. Among the DMRs, 203 hyper-methylated regions (HR) and 190 hypo-methylated regions (HO) were identified for the high pH group compared to the low pH. Furthermore, 44 and 21 protein-coding genes contained HR and HO in their gene body, respectively. It was revealed that ENO1, GYS2, SDHC and DERA, which encode core enzymes in postmortem energy metabolism, contained HR or HO in their gene body.
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Affiliation(s)
- Hyesun Park
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Kang-Seok Seo
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Suncheon National University, Suncheon, Republic of Korea
| | - Mingyung Lee
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
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Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10040113] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.
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Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK, Larkin DM. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res 2016; 27:875-884. [PMID: 27903645 PMCID: PMC5411781 DOI: 10.1101/gr.213660.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
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Affiliation(s)
- Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Rebecca O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Vasileios Panagiotis E Lenis
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Henry J Martell
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Anjali Mandawala
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom.,School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Katie Fowler
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
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Jung H, Lyons RE, Li Y, Thanh NM, Dinh H, Hurwood DA, Salin KR, Mather PB. A candidate gene association study for growth performance in an improved giant freshwater prawn (Macrobrachium rosenbergii ) culture line. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:161-180. [PMID: 24122143 DOI: 10.1007/s10126-013-9555-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 08/06/2013] [Indexed: 06/02/2023]
Abstract
A candidate gene approach using type I single nucleotide polymorphism (SNP) markers can provide an effective method for detecting genes and gene regions that underlie phenotypic variation in adaptively significant traits. In the absence of available genomic data resources, transcriptomes were recently generated in Macrobrachium rosenbergii to identify candidate genes and markers potentially associated with growth. The characterisation of 47 candidate loci by ABI re-sequencing of four cultured and eight wild samples revealed 342 putative SNPs. Among these, 28 SNPs were selected in 23 growth-related candidate genes to genotype in 200 animals selected for improved growth performance in an experimental GFP culture line in Vietnam. The associations between SNP markers and individual growth performance were then examined. For additive and dominant effects, a total of three exonic SNPs in glycogen phosphorylase (additive), heat shock protein 90 (additive and dominant) and peroxidasin (additive), and a total of six intronic SNPs in ankyrin repeats-like protein (additive and dominant), rolling pebbles (dominant), transforming growth factor-β induced precursor (dominant), and UTP-glucose-1-phosphate uridylyltransferase 2 (dominant) genes showed significant associations with the estimated breeding values in the experimental animals (P =0.001-0.031). Individually, they explained 2.6-4.8 % of the genetic variance (R²=0.026-0.048). This is the first large set of SNP markers reported for M. rosenbergii and will be useful for confirmation of associations in other samples or culture lines as well as having applications in marker-assisted selection in future breeding programs.
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Fortes MR, DeAtley KL, Lehnert SA, Burns BM, Reverter A, Hawken RJ, Boe-Hansen G, Moore SS, Thomas MG. Genomic regions associated with fertility traits in male and female cattle: Advances from microsatellites to high-density chips and beyond. Anim Reprod Sci 2013; 141:1-19. [DOI: 10.1016/j.anireprosci.2013.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 07/03/2013] [Accepted: 07/07/2013] [Indexed: 01/08/2023]
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Fan R, Xie J, Bai J, Wang H, Tian X, Bai R, Jia X, Yang L, Song Y, Herrid M, Gao W, He X, Yao J, Smith GW, Dong C. Skin transcriptome profiles associated with coat color in sheep. BMC Genomics 2013; 14:389. [PMID: 23758853 PMCID: PMC3689618 DOI: 10.1186/1471-2164-14-389] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/04/2013] [Indexed: 01/06/2023] Open
Abstract
Background Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in coat color regulation, Illumina sequencing technology was used to catalog global gene expression profiles in skin of sheep with white versus black coat color. Results There were 90,006 and 74,533 unigenes assembled from the reads obtained from white and black sheep skin, respectively. Genes encoding for the ribosomal proteins and keratin associated proteins were most highly expressed. A total of 2,235 known genes were differentially expressed in black versus white sheep skin, with 479 genes up-regulated and 1,756 genes down-regulated. A total of 845 novel genes were differentially expressed in black versus white sheep skin, consisting of 107 genes which were up-regulated (including 2 highly expressed genes exclusively expressed in black sheep skin) and 738 genes that were down-regulated. There was also a total of 49 known coat color genes expressed in sheep skin, from which 13 genes showed higher expression in black sheep skin. Many of these up-regulated genes, such as DCT, MATP, TYR and TYRP1, are members of the components of melanosomes and their precursor ontology category. Conclusion The white and black sheep skin transcriptome profiles obtained provide a valuable resource for future research to understand the network of gene expression controlling skin physiology and melanogenesis in sheep.
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Affiliation(s)
- Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
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Lu Y, Chen SR, Liu WB, Hou ZC, Xu GY, Yang N. Polymorphisms in Wnt signaling pathway genes are significantly associated with chicken carcass traits. Poult Sci 2012; 91:1299-307. [PMID: 22582286 DOI: 10.3382/ps.2012-02157] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Wnt signaling pathway plays a crucial role during embryogenesis in vertebrates. In this study, 124 SNP in 31 Wnt signaling pathway genes were selected to genotype 764 individuals in an F(2) resource population by reciprocally crossing Silkie fowls and Cornish broilers, and 102 SNP were polymorphic. Pairwise linkage disequilibrium among the SNP within each gene was calculated. Haplotypes were reconstructed from the SNP in strong linkage disequilibrium. The associations of SNP and haplotypes with carcass traits were analyzed respectively, and the SNP contributions to phenotypic variance were estimated. The present study showed that 58 SNP in 24 genes and 8 haplotype blocks within 7 genes were significantly (P < 0.05) associated with at least one carcass trait. Fourteen SNP (among the 58 SNP) explained >2% phenotypic variance, 12 of which had significantly (P < 0.01) additive or dominant effects. Furthermore, both rs15865526 (Wnt9A) and rs14066777 (MAPK9) as well as their corresponding haplotype blocks were significantly associated with shank circumference and wing weight, respectively. In addition, 5 muscle-weight-related SNP explained >7% phenotypic variance, which was much higher than those of others. It was found that the Wnt signaling pathway was strongly associated with chicken carcass traits, and 7 genes were particularly important, namely RHOA and CHP for breast muscle weight, Wnt3A for breast muscle weight percentage over carcass weight, RAC1 for thigh weight percentage and thigh muscle weight percentage over carcass weight, Wnt11 for thigh weight percentage over carcass weight, Wnt9A for shank length, and MAPK9 for shank circumference. It is evident that Wnt signaling plays a major role in regulating carcass characteristics important for production traits in chickens.
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Affiliation(s)
- Y Lu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Peletto S, Bertuzzi S, Campanella C, Modesto P, Maniaci MG, Bellino C, Ariello D, Quasso A, Caramelli M, Acutis PL. Evaluation of internal reference genes for quantitative expression analysis by real-time PCR in ovine whole blood. Int J Mol Sci 2011; 12:7732-47. [PMID: 22174628 PMCID: PMC3233434 DOI: 10.3390/ijms12117732] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 11/01/2011] [Indexed: 11/16/2022] Open
Abstract
The use of reference genes is commonly accepted as the most reliable approach to normalize qRT-PCR and to reduce possible errors in the quantification of gene expression. The most suitable reference genes in sheep have been identified for a restricted range of tissues, but no specific data on whole blood are available. The aim of this study was to identify a set of reference genes for normalizing qRT-PCR from ovine whole blood. We designed 11 PCR assays for commonly employed reference genes belonging to various functional classes and then determined their expression stability in whole blood samples from control and disease-stressed sheep. SDHA and YWHAZ were considered the most suitable internal controls as they were stably expressed regardless of disease status according to both geNorm and NormFinder software; furthermore, geNorm indicated SDHA/HPRT, YWHAZ/GAPDH and SDHA/YWHAZ as the best reference gene combinations in control, disease-stressed and combined sheep groups, respectively. Our study provides a validated panel of optimal control genes which may be useful for the identification of genes differentially expressed by qRT-PCR in a readily accessible tissue, with potential for discovering new physiological and disease markers and as a tool to improve production traits (e.g., by identifying expression Quantitative Trait Loci). An additional outcome of the study is a set of intron-spanning primer sequences suitable for gene expression experiments employing SYBR Green chemistry on other ovine tissues and cells.
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Affiliation(s)
- Simone Peletto
- Experimental Zooprophylactic Institute of Piemonte, Liguria and Valle d’Aosta, 10154 Turin, Italy; E-Mails: (S.B.); (C.C.); (P.M.); (M.G.M.); (M.C.); (P.L.A.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-011-2686245; Fax: +39-011-2686322
| | - Simone Bertuzzi
- Experimental Zooprophylactic Institute of Piemonte, Liguria and Valle d’Aosta, 10154 Turin, Italy; E-Mails: (S.B.); (C.C.); (P.M.); (M.G.M.); (M.C.); (P.L.A.)
| | - Chiara Campanella
- Experimental Zooprophylactic Institute of Piemonte, Liguria and Valle d’Aosta, 10154 Turin, Italy; E-Mails: (S.B.); (C.C.); (P.M.); (M.G.M.); (M.C.); (P.L.A.)
| | - Paola Modesto
- Experimental Zooprophylactic Institute of Piemonte, Liguria and Valle d’Aosta, 10154 Turin, Italy; E-Mails: (S.B.); (C.C.); (P.M.); (M.G.M.); (M.C.); (P.L.A.)
| | - Maria Grazia Maniaci
- Experimental Zooprophylactic Institute of Piemonte, Liguria and Valle d’Aosta, 10154 Turin, Italy; E-Mails: (S.B.); (C.C.); (P.M.); (M.G.M.); (M.C.); (P.L.A.)
| | - Claudio Bellino
- Department of Animal Pathology, University of Turin, 10095 Grugliasco, Italy; E-Mail:
| | - Dario Ariello
- Azienda Sanitaria Locale TO3, Sanità Animale, 10098 Rivoli, Italy; E-Mail:
| | - Antonio Quasso
- Azienda Sanitaria Locale AT, Sanità Animale, 14100 Asti, Italy; E-Mail:
| | - Maria Caramelli
- Experimental Zooprophylactic Institute of Piemonte, Liguria and Valle d’Aosta, 10154 Turin, Italy; E-Mails: (S.B.); (C.C.); (P.M.); (M.G.M.); (M.C.); (P.L.A.)
| | - Pier Luigi Acutis
- Experimental Zooprophylactic Institute of Piemonte, Liguria and Valle d’Aosta, 10154 Turin, Italy; E-Mails: (S.B.); (C.C.); (P.M.); (M.G.M.); (M.C.); (P.L.A.)
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Waters SM, Berry DP, Mullen MP. Polymorphisms in genes of the somatotrophic axis are independently associated with milk production, udder health, survival and animal size in Holstein-Friesian dairy cattle. J Anim Breed Genet 2011; 129:70-8. [PMID: 22225586 DOI: 10.1111/j.1439-0388.2011.00938.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The somatotrophic axis consisting of pituitary-derived growth hormone and circulating insulin-like growth factor 1 has been well established as key regulators of animal health, metabolism, lactation, fertility, body composition and growth rate. The aim of this study was to simultaneously quantify the associations between SNPs in candidate genes of the somatotrophic axis (i.e., IGF-1, GH1 and GHR) with performance traits in Holstein-Friesian (HF) dairy cattle. Both novel SNPs identified previously by this group alongside other published SNPs within these genes were analysed for associations with performance in dairy cattle. Multiple regression analyses regressing genetic merit of up to 848 HF sires on novel SNPs (n = 76) and published SNPs (n = 33) were undertaken using weighted animal mixed linear models. Twenty-three SNPs were significantly associated with at least one of 18 traits analysed and involved in milk production, udder health, fertility and growth. Eight traits including milk fat composition, carcass conformation, stature, chest width, body depth, rump width, carcass and cull cow weight were independently associated with SNPs in two genes. Furthermore, for several traits including milk fat yield, somatic cell count, survival and carcass fat, SNPs in all three genes were independently associated with performance. Milk fat yield and carcass fat showed the highest number of independent associations across all three genes with five SNPs associated with both traits. The cumulative effects of the favourable alleles of all five SNPs across GH1, GHR and IGF-1 result in an increase of 5.9 kg and 28.6 units of milk fat and carcass fat, respectively. Cow survival was associated with a single SNP in each of the three genes with a cumulative allele effect of 1.5%. Independent effects of polymorphisms in GH1, GHR and IGF-1 reinforce the central role of the somatotrophic axis on animal development and performance.
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Affiliation(s)
- S M Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.
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Berkowicz EW, Magee DA, Berry DP, Sikora KM, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE. Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle. Anim Genet 2011; 43:81-7. [PMID: 22221028 DOI: 10.1111/j.1365-2052.2011.02211.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The regulation of the bioavailability of insulin-like growth factors (IGFs) is critical for normal mammalian growth and development. The imprinted insulin-like growth factor 2 receptor gene (IGF2R) encodes a transmembrane protein receptor that acts to sequester and degrade excess circulating insulin-like growth factor 2 (IGF-II) - a potent foetal mitogen - and is considered an important inhibitor of growth. Consequently, IGF2R may serve as a candidate gene underlying important growth- and body-related quantitative traits in domestic mammalian livestock. In this study, we have quantified genotype-phenotype associations between three previously validated intronic bovine IGF2R single nucleotide polymorphisms (SNPs) (IGF2R:g.64614T>C, IGF2R:g.65037T>C and IGF2R:g.86262C>T) and a range of performance traits in 848 progeny-tested Irish Holstein-Friesian artificial insemination sires. Notably, all three polymorphisms analysed were associated (P ≤ 0.05) with at least one of a number of performance traits related to animal body size: angularity, body depth, chest width, rump width, and animal stature. In addition, the C-to-T transition at the IGF2R:g.65037T>C polymorphism was positively associated with cow carcass weight and angularity. Correction for multiple testing resulted in the retention of two genotype-phenotype associations (animal stature and rump width). None of the SNPs analysed were associated with any of the milk traits examined. Analysis of pairwise r(2) measures of linkage disequilibrium between all three assayed SNPs ranged between 0.41 and 0.79, suggesting that some of the observed SNP associations with performance may be independent. To our knowledge, this is one of the first studies demonstrating associations between IGF2R polymorphisms and growth- and body-related traits in cattle. These results also support the increasing body of evidence that imprinted genes harbour polymorphisms that contribute to heritable variation in phenotypic traits in domestic livestock species.
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Affiliation(s)
- E W Berkowicz
- Animal Genomics Laboratory, UCD School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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Sikora KM, Magee DA, Berkowicz EW, Berry DP, Howard DJ, Mullen MP, Evans RD, Machugh DE, Spillane C. DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsα)-encoding (GNAS) genomic imprinting domain are associated with performance traits. BMC Genet 2011; 12:4. [PMID: 21214909 PMCID: PMC3025900 DOI: 10.1186/1471-2156-12-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 01/07/2011] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Genes which are epigenetically regulated via genomic imprinting can be potential targets for artificial selection during animal breeding. Indeed, imprinted loci have been shown to underlie some important quantitative traits in domestic mammals, most notably muscle mass and fat deposition. In this candidate gene study, we have identified novel associations between six validated single nucleotide polymorphisms (SNPs) spanning a 97.6 kb region within the bovine guanine nucleotide-binding protein Gs subunit alpha gene (GNAS) domain on bovine chromosome 13 and genetic merit for a range of performance traits in 848 progeny-tested Holstein-Friesian sires. The mammalian GNAS domain consists of a number of reciprocally-imprinted, alternatively-spliced genes which can play a major role in growth, development and disease in mice and humans. Based on the current annotation of the bovine GNAS domain, four of the SNPs analysed (rs43101491, rs43101493, rs43101485 and rs43101486) were located upstream of the GNAS gene, while one SNP (rs41694646) was located in the second intron of the GNAS gene. The final SNP (rs41694656) was located in the first exon of transcripts encoding the putative bovine neuroendocrine-specific protein NESP55, resulting in an aspartic acid-to-asparagine amino acid substitution at amino acid position 192. RESULTS 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. CONCLUSIONS 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 an important role for the imprinted GNAS cluster in underlying complex performance traits in cattle such as animal growth, calving, fertility and health. These findings suggest that GNAS domain-associated polymorphisms may serve as important genetic markers for future livestock breeding programs and support previous studies that candidate imprinted loci may act as molecular targets for the genetic improvement of agricultural populations. In addition, we present new evidence that the bovine NESP55 gene is epigenetically regulated as a maternally expressed imprinted gene in placental and intestinal tissues from 8-10 week old bovine foetuses.
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Affiliation(s)
- Klaudia M Sikora
- Genetics and Biotechnology Laboratory, Department of Biochemistry, University College Cork, Cork, Ireland
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Magee DA, Sikora KM, Berkowicz EW, Berry DP, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE. DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle. BMC Genet 2010; 11:93. [PMID: 20942903 PMCID: PMC2965127 DOI: 10.1186/1471-2156-11-93] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 10/13/2010] [Indexed: 12/17/2022] Open
Abstract
Background Studies in mice and humans have shown that imprinted genes, whereby expression from one of the two parentally inherited alleles is attenuated or completely silenced, have a major effect on mammalian growth, metabolism and physiology. More recently, investigations in livestock species indicate that genes subject to this type of epigenetic regulation contribute to, or are associated with, several performance traits, most notably muscle mass and fat deposition. In the present study, a candidate gene approach was adopted to assess 17 validated single nucleotide polymorphisms (SNPs) and their association with a range of performance traits in 848 progeny-tested Irish Holstein-Friesian artificial insemination sires. These SNPs are located proximal to, or within, the bovine orthologs of eight genes (CALCR, GRB10, PEG3, PHLDA2, RASGRF1, TSPAN32, ZIM2 and ZNF215) that have been shown to be imprinted in cattle or in at least one other mammalian species (i.e. human/mouse/pig/sheep). Results 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). Conclusions 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--a genetic disorder characterised by growth abnormalities. Similarly, the data presented here suggest that the ZNF215 gene may have an important role in regulating bovine growth. Collectively, our results support previous work showing that (candidate) imprinted genes/loci contribute to heritable variation in bovine performance traits and suggest that DNA sequence polymorphisms within these genes/loci represents an important reservoir of genomic markers for future genetic improvement of dairy and beef cattle populations.
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Affiliation(s)
- David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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Systems genetics, bioinformatics and eQTL mapping. Genetica 2010; 138:915-24. [DOI: 10.1007/s10709-010-9480-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 07/30/2010] [Indexed: 12/15/2022]
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15
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Localization of 31 porcine transcripts to the pig genome by SSRH radiation hybrid mapping. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0024-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Buske B, Szydlowski M, Gengler N. A robust method for simultaneous estimation of single gene and polygenic effects in dairy cows using externally estimated breeding values as prior information. J Anim Breed Genet 2010; 127:272-9. [PMID: 20646114 DOI: 10.1111/j.1439-0388.2010.00854.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of this study was to develop a robust method to estimate single gene and random polygenic animal effects simultaneously in a small field dataset with limited pedigree information. The new method was based on a Bayesian approach using additional prior information on the distribution of externally estimated breeding values. The field dataset consisted of 40,269 test-day records for milk performance traits for 1455 genotyped dairy cows for the 11 bp-deletion in the coding sequence of the myostatin gene. For all traits, estimated additive effects of the favoured wild-type allele ('+' allele) were smaller when applying the new method in comparison with the application of a conventional mixed inheritance test-day model. Dominance effects of the myostatin gene showed the same behaviour but were generally lower than additive effects. Robustness of methods was tested using a data-splitting technique, based on the correlation of estimated breeding values from two samples, with one-half of the data eliminated randomly from the first sample and the remaining data eliminated from the second sample. Results for 100 replicates showed that the correlation between split datasets when prior information included was higher than the conventional method. The new method led to more robust estimations for genetic effects and therefore has potential for use when only a small number of genotyped animals with field data and limited pedigree information are available.
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Affiliation(s)
- B Buske
- Université de Liège, Gembloux Agro-Bio Tech (GxABT), Gembloux, Belgium.
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Tobe SS, Linacre A. DNA typing in wildlife crime: recent developments in species identification. Forensic Sci Med Pathol 2010; 6:195-206. [PMID: 20526699 DOI: 10.1007/s12024-010-9168-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2010] [Indexed: 11/27/2022]
Abstract
Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.
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Affiliation(s)
- Shanan S Tobe
- Centre for Forensic Science, Strathclyde University, WestCHEM, Glasgow, UK
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Abstract
Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet.
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Affiliation(s)
- William G Hill
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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