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1.
  • Anderung, C, et al. (author)
  • Investigation of X- and Y-specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle
  • 2007
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 38:6, s. 595-600
  • Journal article (peer-reviewed)abstract
    • Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni; and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.
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2.
  • Andersson-Eklund, Lena (author)
  • Fine mapping of quantitative trait loci for mastitis resistance on bovine chromosome 11
  • 2009
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 40, s. 509-515
  • Journal article (peer-reviewed)abstract
    • P>Quantitative trait loci (QTL) affecting clinical mastitis (CM) and somatic cell score (SCS) were mapped on bovine chromosome 11. The mapping population consisted of 14 grandsire families belonging to three Nordic red cattle breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB) and Danish Red. The families had previously been shown to segregate for udder health QTL. A total of 524 progeny tested bulls were included in the analysis. A linkage map including 33 microsatellite and five SNP markers was constructed. We performed combined linkage disequilibrium and linkage analysis (LDLA) using the whole data set. Further analyses were performed for FA and SRB separately to study the origin of the identified QTL/haplotype and to examine if it was common in both populations. Finally, different two-trait models were fitted. These postulated either a pleiotropic QTL affecting both traits; two linked QTL, each affecting one trait; or one QTL affecting a single trait. A QTL affecting CM was fine-mapped. In FA, a haplotype having a strong association with a high negative effect on mastitis resistance was identified. The mapping precision of an earlier detected SCS-QTL was not improved by the LDLA analysis because of lack of linkage disequilibrium between the markers used and the QTL in the region.
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4.
  • De Koning, Dirk-Jan (author)
  • Genome-wide associations for investigating time-dependent genetic effects for milk production traits in dairy cattle
  • 2012
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 43, s. 375-382
  • Journal article (peer-reviewed)abstract
    • Phenotypic variation in milk production traits has been described over the course of a lactation as well as between different parities. The objective of this study was to investigate whether variation in production is affected by different loci across lactations. A genome-wide association study (GWAS) using a 50-k SNP chip was conducted in 152 divergent German Holstein Friesian cows to test for association with milk production traits over different lactations. The first four lactations were analysed regarding milk yield, fat, protein, lactose, milk urea nitrogen yield and content as well as somatic cell score. Two approaches were used: (i) Wilmink curve parameters were used to assess the genetic effects over the course of a lactation and (ii) test-day yield deviations (YD) were used as a normative approach for a GWAS. The significant effects were largest for markers affecting curve parameters for which there was a statistical power <0.8 of detection even in this small design. While significant markers for YDs were detected in this study, the power to detect effects of a similar magnitude was only 0.11, suggesting that many loci may have been missed with this approach in the present design. Furthermore, all significant effects were specific for a single lactation, leading to the conclusion that the variance explained by a certain locus changes from lactation to lactation. We confirm the common evidence that most production traits vary in the degree of persistency after the peak as a result of genetic influence.
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5.
  • Fang, M., et al. (author)
  • Mitochondrial haplotypes of European wild boars with 2n=36 are closely related to those of European domestic pigs with 2n=38
  • 2006
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 37:5, s. 459-464
  • Journal article (peer-reviewed)abstract
    • Wild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10-fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.
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6.
  • Fitzsimmons, C. J., et al. (author)
  • Detection of sequence polymorphisms in red junglefowl and White Leghorn ESTs
  • 2004
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 35:5, s. 391-396
  • Journal article (peer-reviewed)abstract
    • Over 16 000 high quality expressed sequence tags (ESTs) from red junglefowl (RJ) and White Leghorn (WL) brain and testis cDNA libraries were generated. Here, we have used this resource for detection of single nucleotide polymorphisms (SNPs), and also completed full-length sequencing of 46 pairs of clones, representing the same gene from both the RJ and WL libraries. From the main set of ESTs, which were assembled using Phrap, 746 putative SNPs were identified, of which 76% were transitions and 24% were transversions. A subset of SNPs was evaluated by sequence analysis of five RJ and five WL birds. Nine of 12 SNPs were verified in this limited sample, suggesting that a majority of the putative polymorphisms documented in this study represent real SNPs. During full-length sequencing of the 46 RJ/WL clones 100 SNPs were identified, which translated to a frequency of 1.90 SNPs/1000 bp. The number of transitions and transversions were 77% and 23%, respectively, and the proportion of non-synonymous vs. synonymous SNPs was 20% and 80%, respectively. Four large insertions/deletions were identified between the RJ and WL full-length sequences, and they appear to represent different splice variants.
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7.
  • Jacobsen, M, et al. (author)
  • Refined candidate region specified by haplotype sharing for Escherichia coli F4ab/F4ac susceptibility alleles in pigs
  • 2010
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 41:1, s. 21-25
  • Journal article (peer-reviewed)abstract
    • Infection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.
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8.
  • Johansson, A, et al. (author)
  • Polymorphism at the porcine Dominant white/KIT locus influence coat colour and peripheral blood cell measures
  • 2005
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 36:4, s. 288-296
  • Journal article (peer-reviewed)abstract
    • We have examined the phenotype of different KIT genotypes with regard to coat colour and several blood parameters (erythrocyte numbers and measures, total and differential leucocyte numbers, haematocrit and haemoglobin levels and serum components). The effect of two different iron supplement regimes (one or two iron injections) on the blood parameters was also examined. For a total of 184 cross-bred piglets (different combinations of Hampshire, Landrace and Yorkshire) blood parameters were measured four times during their first month of life, and the KIT genotypes of these and 70 additional cross-bred piglets were determined. Eight different KIT genotypes were identified, which confirms the large allelic diversity at the KIT locus in commercial pig populations. The results showed that pigs with different KIT genotypes differ both in coat colour and in haematological parameters. In general, homozygous Dominant white (I/I) piglets had larger erythrocytes with lower haemoglobin concentration, indicating a mild macrocytic anaemia. The effect of two compared with one iron injection was also most pronounced for the I/I piglets.
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9.
  • Joller, D, et al. (author)
  • Refined localization of the Escherichia coli F4ab/F4ac receptor locus on pig chromosome 13
  • 2009
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 40:5, s. 749-752
  • Journal article (peer-reviewed)abstract
    • Diarrhoea in newborn and weaned pigs caused by enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbriae leads to considerable losses in pig production. In this study, we refined the mapping of the receptor locus for ETEC F4ab/F4ac adhesion (F4bcR) by joint analysis of Nordic and Swiss data. A total of 236 pigs from a Nordic experimental herd, 331 pigs from a Swiss experimental herd and 143 pigs from the Swiss performing station were used for linkage analysis. Genotyping data of six known microsatellite markers, two newly developed markers (MUC4gt and HSA125gt) and an intronic SNP in MUC4 (MUC4-8227) were used to create the linkage map. The region for F4bcR was refined to the interval SW207-S0075 on pig chromosome 13. The most probable position of F4bcR was in the SW207-MUC4 region. The order of six markers was supported by physical mapping on the BAC fingerprint contig from the Wellcome Trust Sanger Institute. Thus, the region for F4bcR could be reduced from 26 to 14 Mb.
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10.
  • Karlskov-Mortensen, Peter, et al. (author)
  • Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace I : carcass traits
  • 2006
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 37:2, s. 156-162
  • Journal article (peer-reviewed)abstract
    •   We report the identification of quantitative trait loci (QTL) affecting carcass composition, carcass length, fat deposition and lean meat content using a genome scan across 462 animals from a combined intercross and backcross between Hampshire and Landrace pigs. Data were analysed using multiple linear regression fitting additive and dominance effects. This model was compared with a model including a parent-of-origin effect to spot evidence of imprinting. Several precisely defined muscle phenotypes were measured in order to dissect body composition in more detail. Three significant QTL were detected in the study at the 1% genome-wide level, and twelve significant QTL were detected at the 5% genome-wide level. These QTL comprise loci affecting fat deposition and lean meat content on SSC1, 4, 9, 10, 13 and 16, a locus on SSC2 affecting the ratio between weight of meat and bone in back and weight of meat and bone in ham and two loci affecting carcass length on SSC12 and 17. The well-defined phenotypes in this study enabled us to detect QTL for sizes of individual muscles and to obtain information of relevance for the description of the complexity underlying other carcass traits.
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11.
  • Kerje, S., et al. (author)
  • Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken
  • 2003
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 34:4, s. 241-248
  • Journal article (peer-reviewed)abstract
    • The co-segregation of plumage colour and sequence polymorphism in the melanocortin 1-receptor gene (MC1R) was investigated using an intercross between the red junglefowl and White Leghorn chickens. The results provided compelling evidence that the Extended black (E) locus controlling plumage colour is equivalent to MC1R. E/MC1R was assigned to chromosome 11 with overwhelming statistical support. Sequence analysis indicated that the E92K substitution, causing a constitutively active receptor in the sombre mouse, is the most likely causative mutation for the Extended black allele carried by the White Leghorn founders in this intercross. The MC1R sequence associated with the recessive buttercup (ebc) allele indicated that this allele evolved from a dominant Extended black allele as it shared the E92K and M71T substitutions with some E alleles. It also carried a third missense mutation H215P which thus may interfere with the constitutive activation of the receptor caused by E92K (and possibly M71T).
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12.
  • Kerje, S., et al. (author)
  • The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs
  • 2003
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 34:4, s. 264-274
  • Journal article (peer-reviewed)abstract
    • A large intercross between the domestic White Leghorn chicken and the wild ancestor, the red junglefowl, has been used in a Quantitative Trait Loci (QTL) study of growth and egg production. The linkage map based on 105 marker loci was in good agreement with the chicken consensus map. The growth of the 851 F2 individuals was lower than both parental lines prior to 46 days of age and intermediate to the two parental lines thereafter. The QTL analysis of growth traits revealed 13 loci that showed genome-wide significance. The four major growth QTLs explained 50 and 80% of the difference in adult body weight between the founder populations for females and males, respectively. A major QTL for growth, located on chromosome 1 appears to have pleiotropic effects on feed consumption, egg production and behaviour. There was a strong positive correlation between adult body weight and average egg weight. However, three QTLs affecting average egg weight but not body weight were identified. An interesting observation was that the estimated effects for the four major growth QTLs all indicated a codominant inheritance.
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13.
  • Klütsch, Cornelya, et al. (author)
  • Regional occurrence, high frequency but low diversity of mitochondrial DNA haplogroup d1 suggests a recent dog-wolf hybridization in Scandinavia
  • 2011
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 42:1, s. 100-103
  • Journal article (peer-reviewed)abstract
    • P>The domestic dog mitochondrial DNA (mtDNA)-gene pool consists of a homogenous mix of haplogroups shared among all populations worldwide, indicating that the dog originated at a single time and place. However, one small haplogroup, subclade d1, found among North Scandinavian/Finnish spitz breeds at frequencies above 30%, has a clearly separate origin. We studied the genetic and geographical diversity for this phylogenetic group to investigate where and when it originated and whether through independent domestication of wolf or dog-wolf crossbreeding. We analysed 582 bp of the mtDNA control region for 514 dogs of breeds earlier shown to harbour d1 and possibly related northern spitz breeds. Subclade d1 occurred almost exclusively among Swedish/Finnish Sami reindeer-herding spitzes and some Swedish/Norwegian hunting spitzes, at a frequency of mostly 60-100%. Genetic diversity was low, with only four haplotypes: a central, most frequent, one surrounded by two haplotypes differing by an indel and one differing by a substitution. The substitution was found in a single lineage, as a heteroplasmic mix with the central haplotype. The data indicate that subclade d1 originated in northern Scandinavia, at most 480-3000 years ago and through dog-wolf crossbreeding rather than a separate domestication event. The high frequency of d1 suggests that the dog-wolf hybrid phenotype had a selective advantage.
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20.
  • Wiik, A. C., et al. (author)
  • A population study of a mutation allele associated with cone-rod dystrophy in the standard wire-haired dachshund
  • 2009
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 40:4, s. 572-574
  • Journal article (peer-reviewed)abstract
    • Cone-rod dystrophy in the standard wire-haired dachshund (SWHD) is inherited as a simple autosomal recessive trait and the recently discovered mutation is widespread within the SWHD population in Norway and other Scandinavian countries. The gene frequency was estimated to be 4.8%. On the basis of the assumption that the size of the ancestral haplotype around a mutation is inversely correlated with the number of generations since the mutation arose, we have found that the mutation is of a relatively recent origin. The conserved haplotype was found to be 8 Mb in size and therefore we estimate that the mutation arose roughly eight generations (approximately 37 years) ago. This indicates that the mutation arose after breed separation.
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21.
  • Wright, Dominic, et al. (author)
  • Quantitative trait loci analysis of egg and meat production traits in a red junglefowl x White Leghorn cross
  • 2006
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 37:6, s. 529-534
  • Journal article (peer-reviewed)abstract
    • Egg and production traits are of considerable economic importance in chickens. Using a White Leghorn x red junglefowl F-2 intercross, standard production measures of liver weight and colour, egg size, eggshell thickness, egg taste and meat quality were taken. A total of 160 markers covering 29 autosomes and the Z chromosome were genotyped on 175-243 individuals, depending on the trait under consideration. A total of nine significant quantitative trait loci (QTL) and three suggestive QTL were found on chicken chromosomes 1, 2, 4, 5, 7, 8, 10, 12, E47W24 and E22C19W28.
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22.
  • Arendt, Maja, et al. (author)
  • Amylase activity is associated with AMY2B copy numbers in dog : implications for dog domestication, diet and diabetes
  • 2014
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 45:5, s. 716-722
  • Journal article (peer-reviewed)abstract
    • High amylase activity in dogs is associated with a drastic increase in copy numbers of the gene coding for pancreatic amylase, AMY2B, that likely allowed dogs to thrive on a relatively starch-rich diet during early dog domestication. Although most dogs thus probably digest starch more efficiently than do wolves, AMY2B copy numbers vary widely within the dog population, and it is not clear how this variation affects the individual ability to handle starch nor how it affects dog health. In humans, copy numbers of the gene coding for salivary amylase, AMY1, correlate with both salivary amylase levels and enzyme activity, and high amylase activity is related to improved glycemic homeostasis and lower frequencies of metabolic syndrome. Here, we investigate the relationship between AMY2B copy numbers and serum amylase activity in dogs and show that amylase activity correlates with AMY2B copy numbers. We then describe how AMY2B copy numbers vary in individuals from 20 dog breeds and find strong breed-dependent patterns, indicating that the ability to digest starch varies both at the breed and individual level. Finally, to test whether AMY2B copy number is strongly associated with the risk of developing diabetes mellitus, we compare copy numbers in cases and controls as well as in breeds with varying diabetes susceptibility. Although we see no such association here, future studies using larger cohorts are needed before excluding a possible link between AMY2B and diabetes mellitus.
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23.
  • Bergvall, Kerstin (author)
  • A second KRT71 allele in curly coated dogs
  • 2019
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 50, s. 97-100
  • Journal article (peer-reviewed)abstract
    • Major characteristics of coat variation in dogs can be explained by variants in only a few genes. Until now, only one missense variant in the KRT71 gene, p.Arg151Trp, has been reported to cause curly hair in dogs. However, this variant does not explain the curly coat in all breeds as the mutant (151)Trp allele, for example, is absent in Curly Coated Retrievers. We sequenced the genome of a Curly Coated Retriever at 22x coverage and searched for variants in the KRT71 gene. Only one protein-changing variant was present in a homozygous state in the Curly Coated Retriever and absent or present in a heterozygous state in 221 control dogs from different dog breeds. This variant, NM_001197029.1:c.1266_1273delinsACA, was an indel variant in exon 7 that caused a frameshift and an altered and probably extended C-terminus of the KRT71 protein NP_001183958.1:p.(Ser422ArgfsTer?). Using Sanger sequencing, we found that the variant was fixed in a cohort of 125 Curly Coated Retrievers and segregating in five of 14 additionally tested breeds with a curly or wavy coat. KRT71 variants cause curly hair in humans, mice, rats, cats and dogs. Specific KRT71 variants were further shown to cause alopecia. Based on this knowledge from other species and the predicted molecular consequence of the newly identified canine KRT71 variant, it is a compelling candidate causing a second curly hair allele in dogs. It might cause a slightly different coat phenotype than the previously published p.Arg151Trp variant and could potentially be associated with follicular dysplasia in dogs.
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24.
  • Brancalion, L., et al. (author)
  • Roan, ticked and clear coat patterns in the canine are associated with three haplotypes near usherin on CFA38
  • 2021
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 52:2, s. 198-207
  • Journal article (peer-reviewed)abstract
    • White coat patterning is a feature of many dog breeds and is known to be coded primarily by the gene micropthalmia-associated transcription factor (MITF). This patterning in the coat can be modified by other factors to produce the attractive phenotypes termed ‘ticked’ and ‘roan’ that describe the presence of flecks of color that vary in distribution and intensity within otherwise ‘clear’ white markings. The appearance of the pigment in the white patterning caused by ticking and roaning intensifies in the weeks after birth. We applied genome-wide association to compare English Cocker Spaniels of roan phenotype (N = 34) with parti-color (non-roan) English Cocker Spaniels (N = 9) and identified an associated locus on CFA 38, CFA38:11 057 040 (Praw = 8.9 × 10−10, Pgenome = 2.7 × 10−5). A local case–control association in English Springer Spaniels comparing 11 ticked and six clear dogs identified indicative association with a different haplotype, CFA38:11 122 467G>T (Praw = 1.7 × 10−5) and CFA38:11 124 294A>C (Praw = 1.7 × 10−5). We characterize three haplotypes in Spaniels according to their putative functional variant profiles at CFA38:11 111 286C>T (missense), CFA38:11 131 841–11 143 239DUP.insTTAA (using strongly linked marker CFA38:11 143 243C>T) and CFA38:11 156 425T>C (splice site). In Spaniels, the haplotypes work as an allelic series including alleles (t, recessive clear; T, dominant ticked/parti-color; and TR, incomplete dominant roan) to control the appearance of pigmented spots or flecks in otherwise white areas of the canine coat. In Spaniels the associated haplotypes are t (CCT), T (TCC) and TR (TTT) for SNP markers on CFA38 at 11 111 286C>T, 11 143 243C>T and 11 156 425T>C respectively. It is likely that other alleles exist in this series and together the haplotypes result in a complex range of patterning that is only visible when dogs have white patterning resulting from the epistatic gene Micropthalmia-associated transcription factor (the S-locus).
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25.
  • Carneiro, Miguel, et al. (author)
  • Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits
  • 2015
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 46:4, s. 418-425
  • Journal article (peer-reviewed)abstract
    • Reproductive seasonality is a trait that often differs between domestic animals and their wild ancestors, with domestic animals showing prolonged or even continuous breeding seasons. However, the genetic basis underlying this trait is still poorly understood for most species, and because environmental factors and resource availability are known to play an important role in determining breeding seasons, it is also not clear in most cases to what extent this phenotypic shift is determined by the more lenient captive conditions or by genetic factors. Here, using animals resulting from an initial cross between wild and domestic rabbits followed by two consecutive backcrosses (BC1 and BC2) to wild rabbits, we evaluated the yearly distribution of births for the different generations. Similar to domestic rabbits, F1 animals could be bred all year round but BC1 and BC2 animals showed a progressive and significant reduction in the span of the breeding season, providing experimental evidence that reduced seasonal breeding in domestic rabbits has a clear genetic component and is not a simple by-product of rearing conditions. We then took advantage of a recently published genome-wide scan of selection in the domesticated lineage and searched for candidate genes potentially associated with this phenotypic shift. Candidate genes located within regions targeted by selection include well-known examples of genes controlling clock functions (CRY1 and NR3C1) and reproduction (PRLR).
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26.
  • De Koning, Dirk-Jan (author)
  • Efficiency of genomic prediction for boar taint reduction in Danish Landrace pigs
  • 2015
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 46, s. 607-616
  • Journal article (peer-reviewed)abstract
    • Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (0.3g/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross-validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome-wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h(2), were 0.54-0.56 and 0.75-0.94 for androstenone and skatole respectively. The whole-genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole.
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27.
  • De Koning, Dirk-Jan (author)
  • Validated quantitative trait loci for eggshell quality in experimental and commercial laying hens
  • 2018
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 49, s. 329-333
  • Journal article (peer-reviewed)abstract
    • Compromised eggshell quality causes considerable economic losses for the egg industry. Breeding for improved eggshell quality has been very challenging. Eggshell quality is a trait that would greatly benefit from marker-assisted selection, which would allow the selection of sires for their direct contribution to the trait and would also allow implementation of measurements integrating a number of shell parameters that are difficult to measure. In this study, we selected the most promising autosomal quantitative trait loci (QTL) affecting eggshell quality on chromosomes 2, 3, 6 and 14 from earlier experiments and we extended the F-2 population to include 1599 F-2 females. The study was repeated on two commercial populations: Lohmann Tierzucht Rhode Island Red line (n=692 females) and a Hy-Line White Plymouth Rock line (n=290 progeny tested males). We analyzed the selected autosomal QTL regions on the three populations with SNP markers at 4-13 SNPs/Mb density. QTL for eggshell quality were replicated on all studied regions in the F-2 population. New QTL were detected for eggshell color on chromosomes 3 and 6. Marker associations with eggshell quality traits were validated in the tested commercial lines on chromosomes 2, 3 and 6, thus paving the way for marker-assisted selection for improved eggshell quality.
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28.
  • Ekesten, Björn (author)
  • Progressive retinal atrophy in Shetland sheepdog is associated with a mutation in the CNGA1 gene
  • 2015
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 46, s. 515-521
  • Journal article (peer-reviewed)abstract
    • Progressive retinal atrophy (PRA) is the collective name of a class of hereditary retinal dystrophies in the dog and is often described as the equivalent of retinitis pigmentosa in humans. PRA is characterized by visual impairment due to degeneration of the photoreceptors in the retina, usually leading to blindness. PRA has been reported in dogs from more than 100 breeds and can be genetically heterogeneous both between and within breeds. The disease can be subdivided by age at onset and rate of progression. Using genome-wide association with 15 Shetland Sheepdog (Sheltie) cases and 14 controls, we identified a novel PRA locus on CFA13 (P-raw = 8.55 x 10(-7), P-genome = 1.7 x 10(-4)). CNGA1, which is known to be involved in human cases of retinitis pigmentosa, was located within the associated region and was considered a likely candidate gene. Sequencing of this gene identified a 4-bp deletion in exon 9 (c. 1752_1755delAACT), leading to a frameshift and a premature stop codon. The study indicated genetic heterogeneity as the mutation was present in all PRA-affected individuals in one large family of Shelties, whereas some other cases in the studied Sheltie population were not associated with this CNGA1 mutation. To our knowledge, this is the first report of a mutation in CNGA1 causing PRA in dogs.
  •  
29.
  • Felkel, S., et al. (author)
  • Asian horses deepen the MSY phylogeny
  • 2018
  • In: Animal Genetics. - : WILEY. - 0268-9146 .- 1365-2052. ; 49:1, s. 90-93
  • Journal article (peer-reviewed)abstract
    • Humans have shaped the population history of the horse ever since domestication about 5500years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 +/- 872years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.
  •  
30.
  • Hidalgo, André, et al. (author)
  • Asian low-androstenone haplotype on pig chromosome 6 does not unfavorably affect production and reproduction traits
  • 2014
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 45, s. 874-877
  • Journal article (peer-reviewed)abstract
    • European pigs that carry Asian haplotypes of a 1.94-Mbp region on pig chromosome 6 have lower levels of androstenone, one of the two main compounds causing boar taint. The objective of our study was to examine potential pleiotropic effects of the Asian low-androstenone haplotypes. A single nucleotide polymorphism marker, rs81308021, distinguishes the Asian from European haplotypes and was used to investigate possible associations of androstenone with production and reproduction traits. Eight traits were available from three European commercial breeds. For the two sow lines studied, a favorable effect on number of teats was detected for the low-androstenone haplotype. In one of these sow lines, a favorable effect on number of spermatozoa per ejaculation was detected for the low-androstenone haplotype. No unfavorable pleiotropic effects were found, which suggests that selection for low-androstenone haplotypes within the 1.94Mbp would not unfavorably affect the other eight relevant traits.
  •  
31.
  • Hidalgo, André (author)
  • Genome-wide association study reveals regions associated with gestation length in two pig populations
  • 2016
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 47, s. 223-226
  • Journal article (peer-reviewed)abstract
    • Reproduction traits, such as gestation length (GLE), play an important role in dam line breeding in pigs. The objective of our study was to identify single nucleotide polymorphisms (SNPs) that are associated with GLE in two pig populations. Genotypes and deregressed breeding values were available for 2081 Dutch Landrace-based (DL) and 2301 Large White- based (LW) pigs. We identified two QTL regions for GLE, one in each population. For DL, three associated SNPs were detected in one QTL region spanning 0.52 Mbp on Sus scrofa chromosome (SSC) 2. For LW, four associated SNPs were detected in one region of 0.14 Mbp on SSC5. The region on SSC2 contains the heparin-binding EGF-like growth factor (HBEGF) gene, which promotes embryo implantation and has been described to be involved in embryo survival throughout gestation. The associated SNP can be used for marker-assisted selection in the studied populations, and further studies of the HBEGF gene are warranted to investigate its role in GLE.
  •  
32.
  • Jensen Waern, Marianne (author)
  • Comparative analysis of swine leukocyte antigen gene diversity in European farmed pigs
  • 2021
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 52, s. 523-531
  • Journal article (peer-reviewed)abstract
    • In Europe, swine represent economically important farm animals and furthermore have become a preferred preclinical large animal model for biomedical studies, transplantation and regenerative medicine research. The need for typing of the swine leukocyte antigen (SLA) is increasing with the expanded use of pigs as models for human diseases and organ-transplantation experiments and their use in infection studies and for design of veterinary vaccines. In this study, we characterised the SLA class I (SLA-1, SLA-2, SLA-3) and class II (DRB1, DQB1, DQA) genes of 549 farmed pigs representing nine commercial pig lines by low-resolution (Lr) SLA haplotyping. In total, 50 class I and 37 class II haplotypes were identified in the studied cohort. The most common SLA class I haplotypes Lr-04.0 (SLA-1*04XX-SLA-3*04XX(04:04)-SLA-2*04XX) and Lr-32.0 (SLA-1*07XX-SLA-3*04XX(04:04)-SLA-2*02XX) occurred at frequencies of 11.02 and 8.20% respectively. For SLA class II, the most prevalent haplotypes Lr-0.15b (DRB1*04XX(04:05/04:06)-DQB1*02XX(02:02)-DQA*02XX) and Lr-0.12 (DRB1*06XX-DQB1*07XX-DQA*01XX) occurred at frequencies of 14.37 and 12.46% respectively. Meanwhile, our laboratory has contributed to several vaccine correlation studies (e.g. Porcine Reproductive and Respiratory Syndrome Virus, Classical Swine Fever Virus, Foot-and-Mouth Disease Virus and Swine Influenza A Virus) elucidating the immunodominance in the T-cell response with antigen specificity dependent on certain SLA-I and SLA-II haplotypes. Moreover, these SLA-immune response correlations could facilitate tailored vaccine development, as SLA-I Lr-04.0 and Lr-32.0 as well as SLA-II Lr-0.15b and Lr-0.12 are highly abundant haplotypes in European farmed pigs.
  •  
33.
  • Jäderkvist Fegraeus, Kim, et al. (author)
  • Gaitedness is associated with the DMRT3 'Gait keeper' mutation in Morgan and American Curly horses
  • 2014
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 45, s. 908-909
  • Other publication (peer-reviewed)abstract
    • The nonsense mutation in the DMRT3 gene is known to affect locomotion pattern and gait ability in horses[1] and performance of Standardbred and Nordic trotters.[1, 2] The mutation (a change from cytosine, C, to adenine, A) has been found in all tested gaited breeds and in breeds used for harness racing, whereas it is absent in most of the three-gaited breeds, such as the Swedish Warmblood and Thoroughbreds.[3] Previous studies have shown that the mutation is strongly associated with horses' ability to perform alternate gaits.[1, 3, 4] In the study by Promerová etal.,[3] breeds with a frequency of the mutation at 50% or higher were classified as either gaited or breeds used for harness racing. There are many different types of alternate gaits, for example foxtrot, running walk, tölt and pace.[3] In this study, we investigated if there is a connection between the genotype in DMRT3 and gaitedness in Morgan and American Curly horses. Previous study showed that the frequency of the mutated A allele in these breeds was 14.0% and 16.7% respectively.[3]
  •  
34.
  • Jäderkvist Fegraeus, Kim, et al. (author)
  • To pace or not to pace : a pilot study of four- and five-gaited Icelandic horses homozygous for the DMRT3 'Gait Keeper' mutation
  • 2017
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 48:6, s. 694-697
  • Journal article (peer-reviewed)abstract
    • The Icelandic horse is a breed known mainly for its ability to perform the ambling four-beat gait 'tolt' and the lateral two-beat gait pace. The natural ability of the breed to perform these alternative gaits is highly desired by breeders. Therefore, the discovery that a nonsense mutation (C>A) in the DMRT3 gene was the main genetic factor for horses' ability to perform gaits in addition to walk, trot and canter was of great interest. Although several studies have demonstrated that homozygosity for the DMRT3 mutation is important for the ability to pace, only about 70% of the homozygous mutant (AA) Icelandic horses are reported to pace. The aim of the study was to genetically compare four-and five-gaited (i.e. horses with and without the ability to pace) AA Icelandic horses by performing a genome-wide association (GWA) analysis. All horses (n = 55) were genotyped on the 670K Axiom Equine Genotyping Array, and a GWA analysis was performed using the GENABEL package in R. No SNP demonstrated genome-wide significance, implying that the ability to pace goes beyond the presence of a single gene variant. Despite its limitations, the current study provides additional information regarding the genetic complexity of pacing ability in horses. However, to fully understand the genetic differences between four-and five-gaited AA horses, additional studies with larger sample materials and consistent phenotyping are needed.
  •  
35.
  • Longo, Alessio, et al. (author)
  • Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data
  • 2024
  • In: Animal Genetics. - 0268-9146 .- 1365-2052. ; 55, s. 87-98
  • Journal article (peer-reviewed)abstract
    • Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest restriction-site-associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the F-ST fixation index was similar to 0.01 between the industry populations and similar to 0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (N-e) and inbreeding (based on runs of homozygosity; F-ROH) were similar amongst the three populations (N-e approximate to 50-80; median F-ROH approximate to 0.11). Finally, the haplotype-based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management.
  •  
36.
  • Mukiibi, Robert, et al. (author)
  • The use of endogenous retroviruses as markers to describe the genetic relationships among local Swedish sheep breeds
  • 2015
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 46, s. 220-223
  • Journal article (peer-reviewed)abstract
    • The aim of this study was to describe the genetic relationships among five Swedish sheep breeds using insertional polymorphisms of six endogenous Jaagsiekte retroviruses of sheep. Although the Swedish breeds were found to have genomes of primitive' origin, there also are indications of the presence of more recently derived sheep breeds within the ancestries of three of the breeds.
  •  
37.
  • Negro, S., et al. (author)
  • Association analysis of KIT, MITF, and PAX3 variants with white markings in Spanish horses
  • 2017
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 48:3, s. 349-352
  • Journal article (peer-reviewed)abstract
    • Several variants in the KIT, PAX3 and MITF genes have previously been associated with white markings in horses. In this study, we examined eight variants of these genes in 70 Menorca Purebred horses (PRMe, only black solid-coloured horses) and 70 Spanish Purebred horses (PRE, different coat colour patterns) that were scored for the extent of white markings. A maximum-likelihood chi-square test, logistic regression model and ridge regression analyses showed that a missense mutation (p.Arg682His) in KIT was associated with white facial markings (P<0.05) and with total white markings (P<0.05) in PRMe horses. The relative contribution of this variant to white markings in PRMe horses was estimated at 47.6% (head) and 43.4% (total score). In PRE horses, this variant was also associated with hindlimb scores (P<0.05) with a relative contribution of 41.2%. The g.20147039C>T intronic variant located 29.9kb downstream from the transcription start site of the MITF gene was associated with less white markings on forelimbs (P<0.05) in PRMe horses, with a relative contribution of 63.9%, whereas in PRE horses this variant was associated with white facial markings (P<0.05), with a relative contribution of 63.9%. No significant associations were found for PAX3 variants in these breeds. These results show that KIT and MITF variants are involved in the white marking patterns of both PRMe and PRE horses, providing breeders with an opportunity to use genetic testing to aid in breeding for their desired level of white markings.
  •  
38.
  • Nunes, J. R. S., et al. (author)
  • Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum)
  • 2020
  • In: Animal Genetics. - : WILEY. - 0268-9146 .- 1365-2052. ; 51:6, s. 899-909
  • Journal article (peer-reviewed)abstract
    • The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (P-adj < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.
  •  
39.
  • Ohlsson, Åsa, et al. (author)
  • The TNNT2:c.95-108G>A variant is common in Maine Coons and shows no association with hypertrophic cardiomyopathy
  • 2022
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 53, s. 526-529
  • Journal article (peer-reviewed)abstract
    • Hypertrophic cardiomyopathy (HCM) is a common and potentially fatal heart disease in many cat breeds. An intronic variant in TNNT2, c.95-108G>A, was recently reported as the cause of HCM in the Maine Coon. The aim of this study was to determine this variant's allele frequency in different populations and its possible association with HCM. Based on 160 Maine Coon samples collected in Belgium, Italy, Sweden and the USA, the variant's allele frequency was estimated to be 0.32. Analysis of the 99 Lives feline whole genome sequencing database showed that the TNNT2 variant also occurs in other breeds, as well as mixed-breed cats. Comparison of 31 affected and 58 healthy cats did not reveal significantly increased odds for HCM in homozygotes. Based on the combined evidence and in agreement with the standards and guidelines for the interpretation of sequence variants, this variant is currently classified as a variant of unknown significance and should not be used for breeding decisions regarding HCM.
  •  
40.
  • Park, H B, et al. (author)
  • Melanocortin-4 receptor (MC4R) genotypes have no major effect on fatness in a Large White x Wild Boar intercross.
  • 2002
  • In: Animal Genetics. - 0268-9146 .- 1365-2052. ; 33:2
  • Journal article (peer-reviewed)abstract
    • The melanocortin-4 receptor (MC4R), a G-protein coupled receptor, is implicated in mediating the effect of leptin on food intake and energy balance. A previous candidate gene study reported an association between an MC4R missense mutation (Asp298Asn) and fatness, growth and feed intake in pigs. To assess this association further, we analysed the segregation of this missense mutation in relation to variation in fatness traits using a Wild Boar x Large White intercross. The Wild Boar and Large White founders were homozygous for different MC4R alleles. The MC4R was assigned to the expected region on pig chromosome 1. The statistical evaluation did not reveal any indication of a significant effect on fatness related traits in this pedigree.
  •  
41.
  • Promerová, Marta, et al. (author)
  • Worldwide frequency distribution of the 'Gait keeper' mutation in the DMRT3 gene
  • 2014
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 45:2, s. 274-282
  • Journal article (peer-reviewed)abstract
    • For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four-beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.
  •  
42.
  • Rochus, Christina, et al. (author)
  • Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations
  • 2019
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 50, s. 712-717
  • Journal article (peer-reviewed)abstract
    • By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short-tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D-5) and/or g.5172T>A] were associated with black coat colour in Klovsjo and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Varmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Varmland sheep and evidence of a duplication of MC1R in Gotland sheep.
  •  
43.
  • Staiger, E. A., et al. (author)
  • The evolutionary history of the DMRT3 'Gait keeper' haplotype
  • 2017
  • In: Animal Genetics. - : WILEY. - 0268-9146 .- 1365-2052. ; 48:5, s. 551-559
  • Journal article (peer-reviewed)abstract
    • A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow-up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3: Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits.
  •  
44.
  • Upadhyay, Maulik (author)
  • Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
  • 2018
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 49, s. 59-70
  • Journal article (peer-reviewed)abstract
    • Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H-O) and expected (H-E) heterozygosity across breeds was 0.355 +/- 0.147 and 0.384 +/- 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f(4) statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.
  •  
45.
  • Velie, Brandon, et al. (author)
  • Frequencies of polymorphisms in myostatin vary in Icelandic horses according to the use of the horses
  • 2015
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 46, s. 467-468
  • Journal article (peer-reviewed)abstract
    • The recent association of the myostatin gene (MSTN) with best race distance has provided valuable insight into the influence of MSTN on racing performance. However, the importance of MSTN in horses is unlikely to be limited to racing performance. First described in mice, the effects of mutations in MSTN have long been associated with heavily muscled cattle. In cattle, some of the morphological variability between breeds can be attributed to MSTN and its effects on muscle fiber development. As such, it is highly probable that MSTN polymorphisms influence not only racing performance, but also the general use of a horse or breed. This variability would likely be reflected in the genotype frequencies of horses used for specific purposes, as certain genotypes would undoubtedly yield more desirable phenotypes. The aim of this study was to explore this idea by estimating the genotype frequencies of three SNPs in MSTN in the Icelandic horse breed, a breed traditionally used for both meat production and riding.
  •  
46.
  • Yusnizar, Yulnawati, et al. (author)
  • Microphthalmia-associated transcription factor mutations are associated with white-spotted coat color in swamp buffalo
  • 2015
  • In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 46:6, s. 676-682
  • Journal article (peer-reviewed)abstract
    • A candidate gene analysis of the microphthalmia-associated transcription factor (MITF) gene was used in an attempt to identify the genetic basis for a white-spotted coat color phenotype in the Asian swamp buffalo (Bubalus bubalis carabanensis). Ninety-three buffaloes32 solid, 38 spotted and 23 white individualswere Sanger-sequenced for all MITF exons as well as highly conserved intronic and flanking regions. MITFcDNA representing skin and iris tissue from six spotted, nine solid and one white buffaloes was also Sanger-sequenced to confirm detected mutations. Two independent loss-of-function mutations, a premature stop codon (c.328C>T, p.Arg110*) and a donor splice-site mutation (c.840+2T>A, p.Glu281_Leu282Ins8), both of which cause white-spotted coat color in swamp buffaloes, were identified. The nonsense mutation leads to a premature stop codon in exon 3, and likely removal of the resulting mRNA via nonsense-mediated decay pathway, whereas the donor splice-site mutation leads to aberrant splicing of exon 8 that encodes part of a highly conserved region of MITF. The resulting insertion of eight amino acid residues is expected to perturb the leucine zipper part in the basic helix-loop-helix leucine zipper (bHLH-Zip) domain and will most likely influence dimerization and DNA binding capacity. Electrophoretic mobility shift assay was performed using mutant and wild-type MITF proteins and showed that the mutant MITF protein resulting from the splice-site mutation decreased invitro DNA binding capacity compared to wild-type MITF. White-spotted buffalo bulls are sacrificed in funeral ceremonies in Tana Toraja, Indonesia, because they are considered holy, and our results show that genetic variation causes a tie to the cultural use of these buffaloes.
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