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Cattle Population (cattle + population)
Selected AbstractsA male bovine linkage map for the ADR granddaughter designJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2000H. Thomsen Summary The aim of this paper is to present the construction of a male genetic linkage map as a result of the bovine genome mapping project, which is a common effort of the German cattle breeding federation (ADR), four animal breeding institutes, three blood group laboratories and two animal data and breeding value evaluation centres. In total 20 grandsires with 1074 sires were provided from the German cattle population as reference families, 16 of these paternal half-sib groups are German Holstein families (DH), three are German Simmental (ST) families, and one is a Brown Swiss family (BS). Of 265 markers included in the linkage map, 248 were microsatellite markers, five were bovine blood group systems, eight SSCP markers and four proteins and enzymes. More than 239 000 genotypes resulted from typing the offspring for the respective markers and these were used for the construction of the map. On average 478 informative meioses were provided from each marker of the map. The summarized map length over all chromosomes was 3135.1 cM with an average interval size of 13.34 cM. About 17, 35.7 and 79.1% of the map intervals showed a maximum genetic distance between the adjacent markers of 5, 10 and 20 cM, respectively. The number of loci ranged from two (pseudoautosomal region of the sex chromosome, BTAY) to 15 (BTA23) with an average of 8.8 markers per chromosome. Comparing the length of the chromosomes shows variation from 49.6 cM for BTA26 to 190.5 cM for BTA1 with a mean of 107.7 cM for all autosomes of the genetic linkage map. It was possible to identify chromosomal discrepancies in locus order and map intervals by comparison with other published maps. The map provided sufficient marker density to serve as a useful tool for a scan of segregating quantitative trait loci. Zusammenfassung Im vorliegenden Artikel wird die Erstellung der genetischen Markerkarten für das Rindergenom im Rahmen des Genomanalyseprojektes der Arbeitsgemeinschaft Deutscher Rinderzüchter (ADR) vorgestellt. Auf der Basis des ,Granddaughter Designs' wurde ein Familienmaterial bestehend aus 20 väterlichen Halbgeschwistergruppen mit 1074 Söhnen für die Typisierung mit genetischen Markern bereitgestellt. Insgesamt 16 dieser paternalen Halbgeschwisterfamilien lassen sich der Rasse Deutsche Holsteins zuordnen, drei Familien entstammen der Rasse Deutsches Fleckvieh, und eine Familie gehört der Rasse Deutsches Braunvieh an. Dabei variiert die Anzahl der Söhne von 19,128 pro Vater. Für die Typisierung wurden 248 Mikrosatellitenmarker aus bereits publizierten Karten ausgewählt. Zusätzlich konnten 8 SSCP-und RFLP Marker, 5 Blutgruppensysteme und 4 Proteinmarker zur Entwicklung der genetischen Karte herangezogen werden. Die Anzahl der Marker variierte von 2 (pseudoautosomaler Bereich des Geschlechtschromosoms) bis 15 (Chromosom 23), wobei durchschnittlich 8.8 genetische Marker pro Chromosom typisiert wurden. Im Durchschnitt lieferten die genetischen Marker 478 informative Meiosen pro Marker. Alle Typisierungsergebnisse wurden in die Kieler Markerdatenbank übertragen und auf etwaige Fehler geprüft. Als Ergebnis konnten die genetischen Karten für alle 29 Autosomen und den pseudoautosomalen Bereich des Geschlechtschromosoms erstellt werden. Dabei wurde ein Bereich von 3135.1 cM des Rindergenoms abgedeckt, wobei die Länge des durchschnittlichen Markerintervalls 13.34 cM beträgt. Die Längen der Chromosomen zeigten eine Variation von 49.6 cM für Chromosom 26 bis zu 190.5 cM für Chromosom 1. Aufgrund der Anzahl informativer Meiosen und der Markerdichte bildet diese genetische Markerkarte in gutes Instrument für eine genomweite Suche nach segregierenden Genorten, die für die Variation von quantitativen Merkmalen verantwortlich sind. [source] Escherichia coli serogroup O26 , a new look at an old adversaryJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2008C. Jenkins Summary Escherichia coli serogroup O26 played an important part in the early work on Verocytotoxin and is an established diarrhoeal pathogen. Recently, Verocytotoxigenic E. coli (VTEC) O26 has been increasingly associated with diarrhoeal disease and frequently linked to outbreaks and cases of haemolytic uraemic syndrome (HUS). This review investigates the pathogenicity, geographical distribution, changing epidemiology, routes of transmission and improved detection of VTEC O26. Laboratory data on VTEC O26 isolates and clinical data on HUS suggest a true difference in the incidence of VTEC O26 in different geographic locations. However, few diagnostic laboratories use molecular methods to detect VTEC and so it is difficult to assess the role of VTEC O26 in causing diarrhoeal disease. VTEC O26 is frequently found in the cattle population but rarely in food. However, the small number of outbreaks analysed to date are thought to be food-borne rather than associated with direct or indirect contact with livestock or their faeces. The increase in awareness of VTEC O26 in the clinical and veterinary setting has coincided with the development of novel techniques that have improved our ability to detect and characterize this pathogen. [source] Expansion of human settlement in Kenya's Maasai Mara: what future for pastoralism and wildlife?JOURNAL OF BIOGEOGRAPHY, Issue 6 2004Richard H. Lamprey Abstract Aim, Wildlife and pastoral peoples have lived side-by-side in the Mara ecosystem of south-western Kenya for at least 2000 years. Recent changes in human population and landuse are jeopardizing this co-existence. The aim of the study is to determine the viability of pastoralism and wildlife conservation in Maasai ranches around the Maasai Mara National Reserve (MMNR). Location, A study area of 2250 km2 was selected in the northern part of the Serengeti-Mara ecosystem, encompassing group ranches adjoining the MMNR. Emphasis is placed on Koyake Group Ranch, a rangeland area owned by Maasai pastoralists, and one of Kenya's major wildlife tourism areas. Methods, Maasai settlement patterns, vegetation, livestock numbers and wildlife numbers were analysed over a 50-year period. Settlement distributions and vegetation changes were determined from aerial photography and aerial surveys of 1950, 1961, 1967, 1974, 1983 and 1999. Livestock and wildlife numbers were determined from re-analysis of systematic reconnaissance flights conducted by the Kenya Government from 1977 to 2000, and from ground counts in 2002. Corroborating data on livestock numbers were obtained from aerial photography of Maasai settlements in 2001. Trends in livestock were related to rainfall, and to vegetation production as indicated by the seasonal Normalized Difference Vegetation Index. With these data sets, per capita livestock holdings were determined for the period 1980,2000, a period of fluctuating rainfall and primary production. Results, For the first half of the twentieth century, the Mara was infested with tsetse-flies, and the Maasai were confined to the Lemek Valley area to the north of the MMNR. During the early 1960s, active tsetse-control measures by both government and the Maasai led to the destruction of woodlands across the Mara and the retreat of tsetse flies. The Maasai were then able to expand their settlement area south towards MMNR. Meanwhile, wildebeest (Connochaetes taurinus) from the increasing Serengeti population began to spill into the Mara rangelands each dry season, leading to direct competition between livestock and wildlife. Group ranches were established in the area in 1970 to formalize land tenure for the Maasai. By the late 1980s, with rapid population growth, new settlement areas had been established at Talek and other parts adjacent to the MMNR. Over the period 1983,99, the number of Maasai bomas in Koyake has increased at 6.4% per annum (pa), and the human population at 4.4% pa. Over the same period, cattle numbers on Koyake varied from 20,000 to 45,000 (average 25,000), in relation to total rainfall received over the previous 2 years. The rangelands of the Mara cannot support a greater cattle population under current pastoral practices. Conclusions, With the rapid increase in human settlement in the Mara, and with imminent land privatization, it is probable that wildlife populations on Koyake will decline significantly in the next 3,5 years. Per capita livestock holdings on the ranch have now fallen to three livestock units/reference adult, well below minimum pastoral subsistence requirements. During the 1980s and 90s the Maasai diversified their livelihoods to generate revenues from tourism, small-scale agriculture and land-leases for mechanized cultivation. However, there is a massive imbalance in tourism incomes in favour of a small elite. In 1999 the membership of Koyake voted to subdivide the ranch into individual holdings. In 2003 the subdivision survey allocated plots of 60 ha average size to 1020 ranch members. This land privatization may result in increased cultivation and fencing, the exclusion of wildlife, and the decline of tourism as a revenue generator. This unique pastoral/wildlife system will shortly be lost unless land holdings can be managed to maintain the free movement of livestock and wildlife. [source] Characterization of a QTL region affecting clinical mastitis and protein yield on BTA6ANIMAL GENETICS, Issue 5 2009H. Nilsen Summary Quantitative trait loci affecting clinical mastitis were detected and fine mapped to a narrow region on bovine chromosome 6 in the Norwegian Red cattle population. The region includes the casein gene cluster and several candidate genes thought to influence clinical mastitis. The most significant results were found for SNPs within the Mucin 7 gene. This gene encodes an antimicrobial peptide and constitutes part of the first line of defence for the mucosal immune system. Detection of long haplotypes extending several Mb may indicate that artificial selection has influenced the haplotype structures in the region. A search for selection sweeps supports this observation and coincides with association results found both by single SNP and haplotype analyses. Our analyses identified haplotypes carrying quantitative trait loci alleles associated with high protein yield and simultaneously fewer incidences of clinical mastitis. The fact that such haplotypes are found in relative high frequencies in Norwegian Red may reflect the combined breeding goal that is characterized by selection for both milk production and disease resistance. The identification of these haplotypes raises the possibility of overcoming the unfavourable genetic correlation between these traits through haplotype-assisted selection. [source] Analysis of segregation distortion and association of the bovine FGF2 with fertilization rate and early embryonic survivalANIMAL GENETICS, Issue 5 2009X. Wang Summary Fibroblast growth factor 2 (FGF2) plays an important role in fertility and early embryo development. The objectives of this study were to test the association of FGF2 polymorphisms with fertilization success in cattle using an in vitro fertilization experimental system and to investigate the mechanisms leading to the presence of rare alleles of FGF2 in the Holstein population. A total of 7502 fertilizations were performed and a total of 5049 embryos were produced to collect fertilization and embryo survival records. A total of 444 ovaries, from which oocytes were aspirated and fertilized, were genotyped for two single nucleotide polymorphisms (SNPs) previously identified in FGF2 (g.23G>T and g.11646A>G). Frequency of the TT genotype of the g.23G>T SNP was low in the ovary population (5.4%) and in a different Holstein cattle population (6.6%) examined in this study. Single SNP analysis showed that both SNPs were associated with early embryonic survival rate. Two-way interaction analysis revealed significant association of epistatic interaction between the SNPs with fertilization rate. To test whether or not low frequency of allele T for the g.23G>T SNP in the population is a result of a fertilization failure of T oocytes, semen from six GG bulls was used to fertilize a total of 458 oocytes obtained from 19 GT ovaries. A significant segregation distortion was observed for 169 embryos genotyped for the g.23G>T SNP. We conclude that oocytes carrying the T allele show a reduced fertilization rate and that segregation distortion leads to rarity of the TT genotype in the population. [source] Linkage disequilibrium in the North American Holstein populationANIMAL GENETICS, Issue 3 2009E.-S. Kim Summary Linkage disequilibrium was estimated using 7119 single nucleotide polymorphism markers across the genome and 200 animals from the North American Holstein cattle population. The analysis of maternally inherited haplotypes revealed strong linkage disequilibrium (r2 > 0.8) in genomic regions of ,50 kb or less. While linkage disequilibrium decays as a function of genomic distance, genomic regions within genes showed greater linkage disequilibrium and greater variation in linkage disequilibrium compared with intergenic regions. Identification of haplotype blocks could characterize the most common haplotypes. Although maximum haplotype block size was over 1 Mb, mean block size was 26,113 kb by various definitions, which was larger than that observed in humans (,10 kb). Effective population size of the dairy cattle population was estimated from linkage disequilibrium between single nucleotide polymorphism marker pairs in various haplotype ranges. Rapid reduction of effective population size of dairy cattle was inferred from linkage disequilibrium in recent generations. This result implies a loss of genetic diversity because of the high rate of inbreeding and high selection intensity in dairy cattle. The pattern observed in this study indicated linkage disequilibrium in the current dairy cattle population could be exploited to refine mapping resolution. Changes in effective population size during past generations imply a necessity of plans to maintain polymorphism in the Holstein population. [source] Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selectionANIMAL GENETICS, Issue 1 2007K. R. Zenger Summary Past breeding strategies for dairy cattle have been very effective in producing rapid genetic gain to achieve industry targets and raise profitability. Such gains have been largely facilitated by intense selection of sires combined with the use of artificial insemination. However, this practice can potentially limit the level of genetic diversity through inbreeding and selection plateaus. The rate of inbreeding in Australia is increasing, primarily as a result of semen importation from a small number of prominent bulls from the USA. The effect of this genetic influx in the Australian dairy cattle population is poorly understood both in terms of diversity and local adaptation/divergence. This study uses 845 genome-wide SNP genetic markers and 431 bulls to characterize the level of genetic diversity and genetic divergence within the Australian and international Holstein Friesian dairy population. No significant differences in genetic diversity (as measured by heterozygosity [Ho] and allelic richness [A]) were observed over the 25-year time period (1975,1999) for bulls used in Australia. The importation of foreign semen into Australia has increased the effective population size until it was in effect a sub-sample of the global population. Our data indicate that most individuals are equally closely related to one another, regardless of country of origin and year of birth. In effect, the global population can be considered as one single population unit. These results indicate that inbreeding, genetic drift and selection has had little effect at reducing genetic diversity and differentiating the Australian Holstein Friesian population at a genome-wide level. [source] Genetic variation in the bovine myostatin gene in UK beef cattle: Allele frequencies and haplotype analysis in the South DevonANIMAL GENETICS, Issue 5 2000J A Smith Work on Belgian Blue cattle revealed that an 11 base pair (bp) deletion within the bovine myostatin gene (GDF8) is associated with the double-muscled phenotype seen in this breed. Investigations focusing on other European breeds known to show double-muscling identified several mutations within the coding region of the gene associated with the double-muscled phenotype in different breeds. The number of mutations found suggest that myostatin is highly variable within beef cattle. Variations that alter the structure of the gene product such that the protein is inactivated are associated with the most pronounced form of double-muscling as seen in the Belgian Blue. However, other mutations may have a less extreme affect on muscle development. While overt double-muscling gives rise to a high incidence of dystocia (calving difficulty), it is possible that some variants may give enhanced muscling, but with limited calving problems. We describe sequence analysis of the myostatin gene in ten beef breeds commonly used in the UK and show that the 11-bp deletion responsible for double-muscling in the Belgian Blue is also present in the South Devon cattle population. Allele frequencies and haplotypes in the South Devon and a polymerase chain reaction (PCR) based test for the deletion are described. PCR amplification across the deleted region provides a quick and effective test with clear identification of heterozygous individuals. We discuss our results with regard to the effect of genotype on phenotype and differences observed between the Belgian Blue and the South Devon. [source] Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole-genome genotyping assayANIMAL SCIENCE JOURNAL, Issue 4 2010Kazuhiro HARA ABSTRACT Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers. The allelic frequencies for each SNP were estimated using additional individuals by PCR-RFLP (restriction fragment length polymorphism). A total of 87 SNP markers added in conjunction with previously developed 27 SNPs were evaluated to assess the utility of the test. The estimated identity power was 2.01 × 10,34. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.99999997 and 0.99998010, respectively. This developed SNP panel was quite powerful and could successfully exclude false sires with a probability of >0.9999 even if the dam's genotype information was not obtained. The SNP system would contribute to management of the beef industry in Japan. [source] Development of SNP markers for individual identification and parentage test in a Japanese Black cattle populationANIMAL SCIENCE JOURNAL, Issue 2 2010Kazuhiro HARA ABSTRACT This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers. The allelic frequencies for each marker were estimated by using PCR-RFLP in the Japanese Black population. Based on the frequency data, the estimated identity power of these markers was 2.73 × 10,12. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.96929 and 0.99693, respectively. This panel of SNP markers is theoretically sufficient for individual identification, and would also be a powerful tool for a parentage test in Japanese Black cattle. The markers could contribute to the management of the beef industry in Japan. [source] Association of a single nucleotide polymorphism in ribosomal protein L27a gene with marbling in Japanese Black beef cattleANIMAL SCIENCE JOURNAL, Issue 6 2009Takahisa YAMADA ABSTRACT Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The c2-11#2 expressed sequence tag (EST) has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus, the ribosomal protein L27a (RPL27A) gene containing the c2-11#2 EST sequence was considered as a positional candidate for the gene responsible for marbling. In the present study, a single nucleotide polymorphism (SNP) in the promoter region of the RPL27A, referred to as g.3109537C>T, was detected between the 2 steer groups. The SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. The effect of genotypes of the SNP on the predicted breeding value for subcutaneous fat thickness was not statistically significant. These findings suggest that the RPL27A SNP may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle. [source] Novel SNP in 5, flanking region of EDG1 associated with marbling in Japanese Black beef cattleANIMAL SCIENCE JOURNAL, Issue 4 2009Takahisa YAMADA ABSTRACT Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 (EDG1) gene has been considered as a positional functional candidate for the gene responsible for marbling. We have recently reported that 2 single nucleotide polymorphisms (SNPs), c.-312A>G in the 5, untranslated region (UTR) and c.*446G>A in the 3, UTR in EDG1 were associated with marbling in Japanese Black beef cattle, but this was not functional and a causal mutation for marbling. In the present study, we detected 2 novel SNPs, referred to as g.1475435G>A and g.1471620G>T, in the 5, flanking region of the EDG1 between low-marbled and high-marbled steer groups, which were previously shown to have EDG1 expression differences in musculus longissimus muscle. The g.1475435G>A SNP seemed not to segregate in Japanese Black beef cattle. The g.1471620G>T SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. Based on these findings, we hypothesized that the g.1471620G>T SNP might have an impact on EDG1 expression and also marbling. [source] Genetic parameters for gestation length and the relationship with birth weight and carcass traits in Japanese Black cattleANIMAL SCIENCE JOURNAL, Issue 3 2008Takayuki IBI ABSTRACT The objectives of this study were to estimate genetic parameters for gestation length (GL), including estimation of maternal effects, and to investigate the genetic relationships of GL with birth weight and carcass traits in a Japanese Black cattle population. The original data comprised 34 775 records of animals born from October 1999 to August 2003. Two different models were used to analyze the data for GL. The first model (M1) included direct genetic effect of the calf and maternal genetic effect as random effects. The second model (M2) treated GL as a trait of the dam and included direct genetic effects only. M1 was used in bi-variate analysis. The direct and maternal heritabilities for GL estimated from M1 were 0.53 and 0.14, respectively. This result shows that GL is moderately inherited and can be controlled genetically. The direct × maternal genetic correlation for GL was ,0.73. Direct genetic correlations of GL with carcass traits were close to zero. However, genetic correlation of maternal GL with carcass weight was moderate (0.25). [source] Top down preselection using marker assisted estimates of breeding values in dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2004Jörn Bennewitz Summary Top down preselection of young bulls before entering progeny testing has been proposed as a practicable form of marker-assisted selection (MAS), especially in dairy cattle populations with large male paternal half-sib families. Linkage phase between the superior (Q) and the inferior (q) QTL alleles of heterozygous sires (Qq at the QTL) with informative markers is established within each paternal half-sib family and may be used for selection among grand-progeny. If, additionally to sires, bulldams are also genotyped and data from consecutive generations are used, then a marker-assisted best linear unbiased prediction (MA-BLUP) model can be employed to connect the information of all generations and families of a top down design, and to select across all families. A customized ,augmented' sire model (with sires and dams of sires as random effects) is introduced for this purpose. Adapted formulae for the mixed model equations are given and their equivalence to a corresponding animal model and to a certain variant of previously proposed reduced animal models is shown. The application of the augmented sire model in MA-BLUP estimation from daughter-yield deviations and effective daughter contributions is presented. Zusammenfassung Die Top down Vorselektion von jungen Bullen vor der Nachkommenschaftsprüfung ist bekannt als eine praktikable Form der markergestützten Selektion in Milchrinderpopulationen. Die Kopplungsphasen zwischen dem günstigen (Q) und dem ungünstigen (q) Allel eines QTL heterozygoten Vaters (Qq am QTL) mit den Allelen gekoppelter genetischer Marker werden innerhalb Familien festgestellt und können zur Vorselektion von Enkeln genutzt werden. Wenn zusätzlich zu den Vätern die Mütter genotypisiert sind und Daten von mehreren Generationen vorliegen, können MA-BLUP Modelle genutzt werden, um Informationen von mehreren Familien und mehreren Generationen eines Top down Designs zusammenzuführen und um eine Vorselektion über Familien hinweg vorzunehmen. Hierfür wird ein geeignetes ,erweitertes' Vatermodell eingeführt, welches die Väter und zusätzlich die Mütter der Väter als zufällige Effekte enthält. Angepasste Formeln für die gemischten Modell Gleichungen werden beschrieben. Die Gleichheit dieses erweiterten Vatermodells mit einem entsprechenden Tiermodell und mit einer Variante des reduzierten Tiermodells wird gezeigt. Die Anwendung des erweiterten Vatermodells zur MA-BLUP Schätzung mit daughter yield deviations und effective daughter contributions ist beschrieben. [source] Effects of culling on spatial associations of Mycobacterium bovis infections in badgers and cattleJOURNAL OF APPLIED ECOLOGY, Issue 5 2007HELEN E JENKINS Summary 1Bovine tuberculosis (TB), caused by Mycobacterium bovis, has serious consequences for Britain's cattle industry. European badgers (Meles meles) can transmit infection to cattle, and for many years the British government culled badgers in a series of attempts to reduce cattle infections. 2We investigated the impact of badger culling on the spatial distribution of M. bovis infection in badger and cattle populations in replicated areas in England. 3M. bovis infection was significantly clustered within badger populations, but clustering was reduced when culls were repeated across wide areas. A significant spatial association between M. bovis infections in badgers and cattle herds likewise declined across successive culls. These patterns are consistent with evidence that badgers are less territorial and range more widely in culled areas, allowing transmission to occur over greater distances. 4Prior to culling, M. bovis infections were clustered within cattle populations. Where badger culling was localised, and in unculled areas just outside widespread culling areas, cattle infections became less spatially clustered as badger culling was repeated. This is consistent with expanded badger ranging observed in these areas. 5In contrast, clustering of infection in cattle persisted over time on lands where badgers were repeatedly culled over wide areas. While this lack of a temporal trend must be interpreted with caution, it might reflect persistent infection within, and continued transmission between, cattle herds in areas where transmission from badgers to cattle had been reduced by badger culling. Continued spatial association of infections in cattle and badgers in such areas might partly reflect transmission from cattle. 6Synthesis and applications: Our findings confirm that badger culling can prompt spatial spread of M. bovis infection, a phenomenon likely to undermine the utility of this approach as a disease control measure. Possible evidence of transmission from cattle, both to other cattle and to badgers, suggests that improved cattle controls might yield multiple benefits for TB management. [source] Population trends of large non-migratory wild herbivores and livestock in the Masai Mara ecosystem, Kenya, between 1977 and 1997AFRICAN JOURNAL OF ECOLOGY, Issue 3 2000Wilber K. Ottichilo The total of all non-migratory wildlife species in the Masai Mara ecosystem has declined by 58% in the last 20 years. This decline ranges from 49% in small brown antelopes to 72% in medium brown antelopes. In individual wildlife species, the decline ranges from 52% in Grant's gazelle to 88% in the warthog. Declines of over 70% have been recorded in buffalo, giraffe, eland and waterbuck. Only elephant, impala and ostrich have not shown any significant decline or increase. Overall, there has not been any significant difference in decline of all wildlife population sizes inside and outside the reserve, except for Thomson's gazelle and warthog. Livestock have not significantly declined over the entire analysis period. However, livestock and cattle populations significantly declined during the 1983,88 period. Donkey declined by 67%, while shoats (goats and sheep) remained stable. In the case of wildlife, land use and vegetation changes, drought effects and poaching are considered to be among the potential factors that may have been responsible for the decline; the decline in livestock during the 1983,84 period was probably due to drought effects. Résumé Le total de toutes les espèces animales non migratrices a baissé de 58% dans l'écosystème du Masai Mara au cours des vingt dernières années. Ce déclin va de 49% chez les petites antilopes brunes à 72% chez les antilopes de taille moyenne. Pour les espèces prises individuellement, la baisse va de 52% pour la Gazelle de Grant à 88% pour le phacochère. On a rapporté des baisses de plus de 70% chez les buffles, les girafes, les élands et les waterbucks. Seuls les éléphants et les autruches ne présentent ni hausse ni baisse significatives. Dans l'ensemble, il n'y a aucune différence significative dans le déclin des tailles de toutes les populations de faune sauvage dans et en dehors de la réserve, sauf pour la Gazelle de Thomson et le phacochère. Le cheptel n'a pas baissé significativement pendant la durée de l'étude. Cependant, les populations du cheptel et du bétail ont baissé significativement entre 1983 et 1988. Les ânes ont diminué de 67%, tandis que chèvres et moutons restaient stables. Dans le cas de la faune sauvage, les changements d'utilisation des terres et de la végétation, les effets de la sécheresse et du braconnage sont à compter parmi les facteurs qui peuvent avoir été responsables du déclin; le déclin du cheptel en 1983,1984 était probablement dûà la sécheresse. [source] The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservationMOLECULAR ECOLOGY, Issue 18 2007MENG-HUA LI Abstract We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within-population differences accounted for ~90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of ,genetic endemism', where cattle populations should be given conservation priority. The results will also be of importance for cost-effective management of their future utilization. [source] Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub-Saharan African cattle breedsMOLECULAR ECOLOGY, Issue 4 2000O. Hanotte Abstract We report for the first time, and for the whole of sub-Saharan Africa, the geographical distribution and the frequency of an indicine and a taurine Y specific allele amongst African cattle breeds. A total of 984 males from 69 indigenous African populations from 22 countries were analysed at the microsatellite locus INRA 124. The taurine allele is probably the oldest one on the continent. However, the taurine and the indicine alleles were present in 291 males (30%), and 693 males (70%), respectively. More particularly, 96% of zebu males (n = 470), 50% of taurine males (n = 263), 29% of sanga males (crossbreed Bos taurus × Bos indicus, n = 263) and 95% of zebu × sanga crossbred males (n = 56) had the indicine allele. The Borgou, a breed classified as zebu × taurine cross showed only the zebu allele (n = 12). The indicine allele dominates today in the Abyssinian region, a large part of the Lake Victoria region and the sahelian belt of West Africa. All the sanga males (n = 64) but only one from the Abyssinian region had the indicine allele. The taurine allele is the commonest only among the sanga breeds of the southern African region and the trypanotolerant taurine breeds of West Africa. In West Africa and in the southern Africa regions, zones of introgression were detected with breeds showing both Y chromosome alleles. Our data also reveal a pattern of male zebu introgression in Mozambique and Zimbabwe, probably originating from the Mozambique coast. The sanga cattle from the Lake Victoria region and the Kuri cattle of Lake Chad, cattle populations surrounded by zebu breeds were, surprisingly, completely devoid of the indicine allele. Human migration, phenotypic preferences by the pastoralists, adaptation to specific habitats and to specific diseases are the main factors explaining the present-day distribution of the alleles in sub-Saharan Africa. [source] Y-specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattleANIMAL GENETICS, Issue 3 2010L. Pérez-Pardal Summary Five cattle Y-specific microsatellites, totalling six loci, were selected from a set of 44 markers and genotyped on 608 Bos taurus males belonging to 45 cattle populations from Europe and Africa. A total of 38 haplotypes were identified. Haplogroups (Y1 and Y2) previously defined using single nucleotide polymorphisms did not share haplotypes. Nine of the 27 Y2-haplotypes were only present in African cattle. Network and correspondence analyses showed that this African-specific subfamily clustered separately from the main Y2-subfamily and the Y1 haplotypes. Within-breed genetic variability was generally low, with most breeds (78%) showing haplotypes belonging to a single haplogroup. amova analysis showed that partitioning of genetic variation among breeds can be mainly explained by their geographical and haplogroup assignment. Between-breed genetic variability summarized via Principal Component Analysis allowed the identification of three principal components explaining 94.2% of the available information. Projection of principal components on geographical maps illustrated that cattle populations located in mainland Europe, the three European Peninsulas and Mediterranean Africa presented similar genetic variation, whereas those breeds from Atlantic Europe and British Islands (mainly carrying Y1 haplotypes) and those from Sub-Saharan Africa (belonging to Y2-haplogroup) showed genetic variation of a different origin. Our study confirmed the existence of two large Y-chromosome lineages (Y1 and Y2) in taurine cattle. However, Y-specific microsatellites increased analytical resolution and allowed at least two different Y2-haplotypic subfamilies to be distinguished, one of them restricted to the African continent. [source] Genetic structure of Eurasian cattle (Bos taurus) based on microsatellites: clarification for their breed classification,ANIMAL GENETICS, Issue 2 2010M.-H. Li Summary We pool three previously published data sets and present population genetic analyses of microsatellite variation in 48 Bos taurus cattle breeds from a wide range of geographical origins in Eurasia, mostly its northern territory. Bayesian model-based clustering reveals six distinct clusters: besides a single-population cluster of the Yakutian Cattle from Far Eastern Siberia and a cluster of breeds characteristic of an early origin, the other four major clusters largely correspond to previously defined morphological subgroups of Red Lowland, Lowland Black-Pied, Longhorned Dairy and North European Polled cattle breeds. The results highlighted past expansion events of the productive breeds such as Danish Red, Angeln, Holstein-Friesian and Ayrshire in northern and Eastern Europe. Based on genetic assignment of the breeds and the availability of breed information, we provide a preliminary classification of the five breeds that were to date undefined. Furthermore, in the analysis of molecular variance, despite some correspondence between geographical proximity and genetic similarity, the breed classification appears to be a better predictor of genetic structure in the cattle populations (the among-group variance component: breed classification, 2.47%, P < 0.001; geographical division, 0.77%, P < 0.001). [source] Polymorphisms in the STAT6 gene and their association with carcass traits in feedlot cattleANIMAL GENETICS, Issue 6 2009G. Rincon Summary Identification of the genes and polymorphisms underlying quantitative traits, and understanding how these genes and polymorphisms affect economic traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle populations. Signal transducer and activator of transcription 6 (STAT6) gene is tightly connected to IL-4 and IL-13 signalling and plays a key role in TH2 polarization of the immune system. In addition, STAT6 acts as a mediator of leptin signalling and has been associated with body weight regulation. The objective of this study was to determine if SNPs within the bovine STAT6 gene are associated with economically important traits in feedlot cattle. The approach consisted of resequencing STAT6 using a panel of DNA from unrelated animals of different beef breeds. Specifically, 16 kb of STAT6 was resequenced in 47 animals and the process revealed 39 SNPs. From the 39 SNPs, a panel of 15 tag SNPs was genotyped in 1500 beef cattle samples with phenotypes to perform a marker-trait association analysis. Among the 15 tag SNPs, five and six were polymorphic in Bos taurus and Bos indicus respectively. An association analysis was performed between the 15 tag SNPs and 14 performance and production traits. SNP ss115492459:C > A, ss115492461:A > G and ss115492458:G > C were significantly associated with back fat, calculated yield grade, cutability, hot carcass weight, dry matter intake, days on feed, back fat rate and average daily gain. These three SNPs were present in all Bos taurus beef breeds examined. Our results provide evidence that polymorphisms in STAT6 are associated with carcass and growth efficiency traits, and may be used for marker-assisted selection and management in feedlot cattle. [source] Association analyses of a SNP in the promoter of IGF1 with fat deposition and carcass merit traits in hybrid, Angus and Charolais beef cattleANIMAL GENETICS, Issue 5 2009K. K. Islam Summary A SNP in the promoter region of insulin like growth factor-1 (IGF1) (c.,512C>T) was analysed for associations with 10 fat deposition and carcass merit traits in hybrid (n = 455), Angus (n = 204) and Charolais (n = 186) beef cattle populations. Significant associations of the SNP were found for ultrasound backfat thickness (P = 0.030), carcass average backfat (P = 0.015) and carcass lean meat yield (LMY) (P = 0.023) in the Angus beef population, with the ,CC' genotype showing higher fat depth and lower LMY than the ,TT' genotype. Analyses of transcription factor binding sites based on transcription element search system prediction revealed that the ,C' allele introduces a binding site for nuclear factor I, which has an adipose tissue-specific regulatory role and thus may contribute to the SNP effect on fat deposition in the population of pure Angus cattle, a breed with greater fat depth than the hybrid and Charolais breeds. [source] Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populationsANIMAL GENETICS, Issue 4 2009H. Dadi Summary This study describes complete control region sequences of mitochondrial DNA (mtDNA) from 117 Ethiopian cattle from 10 representative populations, in conjunction with the available cattle sequences in GenBank. In total, 79 polymorphic sites were detected, and these defined 81 different haplotypes. The haplotype and nucleotide diversity of Ethiopian cattle did not vary among the populations studied. All mtDNA sequences from Ethiopian cattle converged into one main maternal lineage (T1) that corresponds to African Bos taurus cattle. According to the results of this study, no zebu mtDNA haplotypes have been found in Ethiopia, where the most extensive hybridization took place on the African continent. [source] Assessing SNP markers for assigning individuals to cattle populationsANIMAL GENETICS, Issue 1 2009R. Negrini Summary The effectiveness of single nucleotide polymorphisms (SNPs) for the assignment of cattle to their source breeds was investigated by analysing a panel of 90 SNPs assayed on 24 European breeds. Breed assignment was performed by comparing the Bayesian and frequentist methods implemented in the structure 2.2 and geneclass 2 software programs. The use of SNPs for the reallocation of known individuals to their breeds of origin and the assignment of unknown individuals was tested. In the reallocation tests, the methods implemented in structure 2.2 performed better than those in geneclass 2, with 96% vs. 85% correct assignments respectively. In contrast, the methods implemented in geneclass 2 showed a greater correct assignment rate in allocating animals treated as unknowns to a reference dataset (62% vs. 51% and 80% vs. 65% in field tests 1 and 2 respectively). These results demonstrate that SNPs are suitable for the assignment of individuals to reference breeds. The results also indicate that structure 2.2 and geneclass 2 can be complementary tools to assess breed integrity and assignment. Our findings also stress the importance of a high-quality reference dataset in allocation studies. [source] Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markersANIMAL SCIENCE JOURNAL, Issue 3 2010Bang Zhong LIN ABSTRACT The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE. [source] Effect of SCD and SREBP genotypes on fatty acid composition in adipose tissue of Japanese Black cattle herdsANIMAL SCIENCE JOURNAL, Issue 3 2009Hideki OHSAKI ABSTRACT Fatty acid composition of beef adipose tissue is one of important traits because high proportions of monounsaturated fatty acid are related to favorable beef flavor and tenderness. In this study, we investigated effects of genetic factors such as stearoyl-CoA desaturase (SCD) and sterol regulatory element binding protein (SREBP) on beef carcass traits including fatty acid composition using two cattle populations. Sire effect was significantly related to almost all traits except BMS, suggesting that the trait examined in this study is highly controlled by genetic factors. The effect of SCD genotype on fatty acid composition was detected remarkably in both cattle groups, especially on stearic and oleic acids. This result was consistent with our previous studies and suggests that SCD is associated with fatty acid composition. Unlike SCD genotyping, the effect of SREBP genotype was not identified in this study. Our results suggested that SCD genotype would contribute to improving beef quality in field populations. Further studies about the relationship among these factors will bring an insight into the molecular mechanism of fatty acid metabolism in cattle. [source] |