Genetic relationships among European cattle breeds

Genetic relationships among 37 European cattle breeds were investigated using blood group and serum protein polymorphisms. The 18 859 animals included in the study represented a random sample from pedigree populations in the UK. Within-breed variation was estimated by average heterozygosity and number of alleles observed, and breed relationships were evaluated by genetic distance. Standard errors of the heterozygosity, number of alleles and genetic distance were obtained by bootstrapping. The significance of breed differences was tested using an exact test of differentiation. French, Italian and Channel Island breeds were found to have generally higher heterozygosities and a greater number of alleles than breeds from mainland Britain and North Europe. Genetic distances ranged between 0·011 (±0·005) and 0·309 (±0·071). Two major breed groups were identified; a group of French, Italian and Channel Island breeds together with the Simmental and Gelbvieh, and a second group consisting of the mainland British and North European breeds. The exact test of breed differentiation showed all breeds to be significantly different from one another ( P < 0·0001). Overall relationships among breeds reflected their geographical origin and common ancestry rather than the agricultural use for which the breeds have been selected.     

Population structure of lake‐type and river‐type sockeye salmon in transboundary rivers of northern British Columbia

The population structure of 'lake‐type' and 'river‐type' sockeye salmon Oncorhynchus nerka , primarily in transboundary rivers in northern British Columbia, was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed from c . 3000 lake‐type and 3200 river‐type sockeye salmon from 47 populations in six river drainages in British Columbia. The mean F _ST for the 14 microsatellite loci and 47 populations was 0·068, and 0·034 over all river‐type populations. River‐type sockeye salmon were more genetically diverse than lake‐type sockeye salmon, with expected heterozygosity of river‐type sockeye salmon 0·72 and with an average 12·7 alleles observed per locus, whereas expected heterozygosity of lake‐type sockeye salmon was 0·65 with and average 10·5 alleles observed per locus. River drainage of origin was a significant unit of population structure. There was clear evidence of genetic differentiation among river‐type populations of sockeye salmon from different drainages over a broad geographic range in British Columbia.     

Geographic variation in growth and food conversion efficiency of juvenile Atlantic halibut related to latitude

Higher growth capacity and food conversion efficiency was observed in populations of juvenile halibut from high Hippoglossus hippoglossus compared lower latitudes. In addition, temperature adaptation shown by the lower temperature optimum for growth in the Norwegian population (mean±S.E. 12·9±0·10 C) compared with the Icelandic and Canadian populations (14·2±0·2 and 13·9±0±30 C respectively), seems to occur. Overall the data support the hypothesis of countergradient variation in growth. These results have implications firstly for selection focusing on growth performance in halibut culture; and secondly, for safe prediction of growth, since if countergradient variation in growth performance occurs one cannot assume automatically that a species will respond to the same set of physiological parameters in the same way throughout its range.     

Loss of genetic variation in hatchery-reared Indian major carp, Catla catla

The hypothesis that effective population sizes are low in hatchery-reared catla ( Catla catla ) from Bangladesh, possibly leading to inbreeding and loss of variation, was tested. The study was based on analysis of seven microsatellite loci in three samples of hatchery-reared catla and four samples representing wild populations. Pair-wise estimates of genetic differentiation between samples were low between wild samples (θ ranging from 0·012 to 0·034), but high between hatchery samples (θ ranging from 0·153 to 0·185), suggesting strong genetic drift in hatcheries. Genetic variation, both in terms of expected heterozygosity and allelic richness, was significantly lower in hatchery samples than in samples of wild catla. Application of a method for reconstructing families among offspring without parental genetic data showed that the hatchery samples consisted of very few half- and full-sib families, whereas the wild samples consisted of a high number of families, suggesting that most individuals were unrelated. Finally, estimation of the effective number of parents ( N _b) in the largest sample of hatchery fish confirmed that effective population size was low ( N _b= 14·9 for multiallelic loci and N _b= 10·6 if alleles were pooled into two composite alleles). The results show that low effective population sizes leading to loss of variation and possibly inbreeding depression should be a matter of serious concern in aquaculture production of catla.     

Global diversity and genetic contributions of chicken populations from African,Asian and European regions

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (F_ST) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour‐Net genetic clustering and structure analysis revealed two main groups of Asian and north‐west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north‐west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds.     

A molecular assessment of homing in the tidepool sculpin

Molecular analyses of the mitochondrial genome using restriction fragment length polymorphism (RFLP) were utilized to determine the existence of discrete populations of the tidepool sculpin Oligocottus maculosus from the Barkley Sound region of south-western Vancouver Island, British Columbia. Fifty-five haplotypes were found with three haplotypes making up 38, 16 and 8% of the total sample, respectively. Within individual tidepools, haplotype diversity ranged from 0·30 to 0·92, but haplotypes were typically closely related to one another (nucleotide diversity ranged from 0·0004 to 0·005). The majority of haplotype variation (96–97%) was located within tidepools, but a significant amount of variation ( c . 3–4%) was detected among tidepools within single islands. By contrast, there was no significant differentiation among islands or between samples from the Barkley Sound area and a single sample from north-eastern Vancouver Island. The results suggest a low level of population structure within the sample area and that the distribution of haplotypes and haplotype divergences represents a demographic expansion from a single ancestral lineage beginning between 300 000 and 1 000 000 years ago. The low level of population subdivision resolved suggests that despite their ecological specialization in tidepool habitats, tidepool sculpins are influenced by demographic and genetic processes that operate on spatial scales much larger than single tidepools or islands.     

Genetic variation in mortality of chinook salmon during a bloom of the marine alga Heterosigma akashiwo

Mortality in a netpen-reared population of 3-year-old chinook salmon Oncorhynchus tshawytscha during an extensive 1997 bloom of the alga Heterosigma akashiwo in Puget Sound, Washington, was low (7·2%), and corresponded to a reduction in variance effective population size of 9·4%. Under a liability threshold model, the heritability of mortality (± S.E.), based on paternal half-sibs, was estimated at 0·15 ± 0·04. No significant genetic variation was detected for date of death. Despite the low overall mortality, the consequences for variation in family size underscore the importance of maximizing genetic variation in cultured fish populations later released to the wild as a precaution against mortality and losses of genetic variation over the life cycle. The pattern of family variation in response to this algal bloom provides evidence for potentially selective mortality of anadromous salmonids in the marine environment during natural perturbations.     

Allozymic variation and relationships of the endangered cyprinodontid genus Valencia and its implications for conservation

Allozyme analysis was used to determine patterns of genetic variation and relationships within the genus Valencia , a group with two allopatric species, V. letourneuxi inhabiting the Balkan Peninsula, and V. hispanica which is endemic to the Iberian Peninsula. Products of 25 gene loci were analysed with AK *, FH *, LDH -1* and LDH -2* monomorphic when Fundulus heteroclitus macrolepidotus was not taken into account. Nine loci were diagnostic for both species of the genus Valencia . Levels of genetic variation of V. hispanica ( P =0·416, H ^e=0·118) and V. letourneuxi ( P =0·160, H _e=0·040) were higher than values reported previously. High population subdivision ( F _st=0·321) among V. hispanica populations indicates a clear interruption of genetic exchange among populations. High genetic variation and differentiation exhibited by populations of V. hispanica suggest that a recovery program should be carried out with natural stocks from the same localities.     

Genetic analysis of fish genomes and populations: allozyme variation within and among Atlantic salmon from Downeast rivers of Maine

Analysis of genetic variation within and among samples of naturally produced Atlantic salmon ( n  = 372) from 7 Maine (U.S.A.) and one Canadian river were conducted based on 54 allozyme loci. Eight of the 54 loci proved polymorphic, and estimated heterozygosities ( H _S) based on all loci ranged from 0·012 to 0·026 (mean = 0·021, s . e . = 0·002). Only one of 56 tests revealed genotypic proportions that deviated significantly from Hardy–Weinberg expectations. Genetic distances ( D ) between samples ranged from 0·002 to 0·022. No obvious association existed between genetic and geographic distances. Cluster analysis of genetic distances revealed the Dennys River sample as the most differentiated when all samples were included in the analysis, though bootstrap support of the cluster analysis was generally weak. G ‐tests revealed significant differences in allele frequencies among samples at five of the polymorphic loci, and the G ‐value summed over all loci also indicated significant differences among samples. F _ST values indicated that 3·4% of the total genetic diversity was due to variability among samples, while 96·6% was due to variability within samples. These results indicate that the Atlantic salmon analyzed in this study had levels of genetic variability and differentiation among samples comparable to native populations from other areas collected across a similar geographic range.     

Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair-wise population differentiation ( F _ST-value) between the cohorts within a population and among three populations. Estimates of the effective population size ( N _e) based on maximum-likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size ( N _e/ N ) ranged from 0·004 to 0·023. These estimates of N _e/ N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of N _e/ N , similar to marine species with a pelagic life cycle.     

Distinguishing between two sympatric Acanthopagrus species from Dapeng Bay, Taiwan, using morphometric and genetic characters

Morphometric and genetic data were used to compare two sympatric and morphologically similar species, Acanthopagrus berda and Acanthopagrus taiwanensis , in Dapeng Bay, South-western Taiwan. A principle component analysis of morphological data indicated a distinction between the two species, with pectoral fin length and eye diameter accounting for 32·27% of the variation. Interspecific sequence divergence, based on mtDNA cytochrome b (0·118 ± 0·01), was larger than intraspecific divergences between haplotypes (0·007 for A. taiwanensis and 0·003 for A. berda ). Individuals of the two species clustered into different groups in three phylogenetic trees with 100% bootstrap support. The mean observed heterozygosity for eight microsatellite loci was 0·471 ± 0·202 for A. taiwanensis and 0·637 ± 0·145 for A. berda . Nei's unbiased measure of interspecific genetic distance ( D _S) was 1·334. F _ST (0·134) and R _ST (0·404) values indicated significant differentiation between species. An unrooted neighbour-joining tree was constructed by allele-sharing distances and the factorial correspondence analysis split all specimens into two distinct clusters. The results of morphometric, mtDNA and microsatellite analyses indicated the presence of two species, A. taiwanensis and A. berda .     

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.     

Countergradient variation in growth and food conversion efficiency of juvenile turbot

Growth performance of a high latitude (Norway) population of juvenile turbot Scophthalmus maximus , was superior to that of two other lower latitude populations (Scotland, France) especially at 18° and 22° C. Overall these results lend some support to the hypothesis of countergradient variation in growth. The Norwegian population had the highest estimated temperature optimum for growth ( T _opt.G, ±S.E.) (23·0±0·9°C) and food conversion efficiency ( T _opt.Ec) (17·5±0·3), followed by the French ( T _opt.G 21·1±1·0; T _opt.Ec, 16·7±0·1) population, whereas the Scottish population had the lowest optimum ( T _opt.G, 19·6±0·6; T _{opt Ec}, 16·5±0·1°C). These results have two major implications: firstly, for turbot culture, particularly in selection work focusing on growth performance; secondly, if countergradient variation in growth performance takes place within a species one cannot assume automatically that one set of physiological parameters, in this case growth-related parameters, is satisfactory to predict growth for a species throughout its range as different populations might show a difference in response towards different physiological parameters.     

Gene diversity analysis in natural populations and cultured stocks of turbot (Scophthalmus maximus L.)

The genetic variability of eight fish-farm and three natural populations of turbot was studied by electrophoretic analysis of 35 enzymatic loci. The results showed low genetic variability in natural populations of turbot ( H _T = 0·029 ± 0·013) in comparison with other flatfish species. Great genetic similarity was revealed among the natural populations studied, which indicates high rates of gene flow in this species. The hatchery stocks showed less genetic variation than the wild populations analysed, which suggests genetic drift phenomena involved in the foundation and management of broodstocks. In addition, the heterozygosity differences detected among the hatchery stocks analysed are correlated with inverted levels of fluctuating asymmetry, which supports the existence of inbreeding depression phenomena in turbot culture.     

Inference of population structure of purebred dairy and beef cattle using high-density genotype data

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (H_O=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (H_O=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F_st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.     

Regional differentiation of North American Atlantic salmon at allozyme loci

Allozyme variation was characterised by starch gel electrophoresis at 23 enzyme coding loci and one regulatory locus in Atlantic salmon from 53 rivers in Eastern Canada, encompassing the majority of the species' North American range. Variation among rivers was highly heterogeneous and eight of the 15 polymorphisms showed regionally restricted distributions. Nearest neighbour joining (NJ) analysis and multi‐dimensional scaling suggest six distinct regional groups; Labrador/Ungava, Gulf of Saint Lawrence, Newfoundland (excluding Gulf rivers), the Atlantic shore/Southern Uplands of Nova Scotia, the inner Bay of Fundy, and the outer Bay of Fundy. Approximately 25% of observed genetic variation was distributed among these regions with a weak though significant overall correlation of genetic and geographic distance (Mantel Test, r  = 0·255, P  = 0·005). Collectively, the rivers showed consistent divergence from European populations with strong bootstrap support for the two clusters across loci in the NJ analysis. Mean heterozygosity was 0·061 for both continental groups, but the European population showed more than twice the variation among populations. F _ST values were 0·076 and 0·176 for North America and Europe, respectively, with an overall F _ST of 0·330.     

Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study

Genetic variability in purebred dogs is known to be highly structured, with differences among breeds accounting for ∼30% of the genetic variation. However, analysis of the genetic structure in non-cosmopolitan breeds and local populations is still limited. Nine Portuguese native dog breeds, and other peripheral dog populations (five) with regional affinities, were characterized using 16 microsatellites and 225 amplified fragment length polymorphism (AFLP) markers, and the pattern of genetic differentiation was investigated. Although the level of breed differentiation detected is below that of other dog breeds, there is in most cases a correlation between breed affiliation and molecular structure. AFLP markers and Bayesian clustering methods allowed an average of 73.1% of individuals to be correctly assigned to source populations, providing robust genotypic assessment of breed affiliation. A geographical genetic structure was also detected, which suggests a limited influence of African dogs on the Iberian breeds. The sampling effect on the estimation of population structure was evaluated and there was a 2.2% decrease in genetic differentiation among breeds when working animals were included. Genetic diversity of stray dogs was also assessed and there is no evidence that they pose a threat to the preservation of the gene pool of native dog breeds.     

Population dynamics of fisheries stock enhancement

A comparative analysis was performed on sixteen morphometric characters, in three different juvenile sterlet Acipenser ruthenus L. populations. Specimens were collected from a wild population in the Serbian part of the Danube River ( n  = 46), from aquaculture stocks in the Czech Republic originating from Russia ( n  = 40), and aquaculture stocks in the Slovak Republic originating from Slovakian part of the Danube River ( n  = 28). Average values for total length were 29·9 ± 3·9 cm, 29·1 ± 3·7 cm and 27·3 ± 7·7 cm for Serbia, Czech Republic and Slovak Republic, respectively. Populations were compared using t ‐test and sequential Bonferroni correction for multiple comparisons was applied in order to determine significant differences between them. Results of analysis showed that all three populations differed in prebarbel length, interocular distance and maximum head width. Although all these characters are head‐related, head length itself was very uniform among all populations. The natural population from the Serbian part of the Danube River differed from the populations reared in aquaculture in seven morphometric characters. The two populations reared in aquaculture consistently showed lower morphological variability than the wild population, even though they had different genetic backgrounds (Russia and Slovakia). Future genetic studies will show if this tendency is caused by a reduction in genetic variability.     

Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations

Ethiopian cattle are under threat from uncontrolled mating practices and are at high risk of becoming genetically homogeneous. Therefore, to evaluate genetic diversity, population structure and degree of admixture, 30 microsatellite markers were genotyped using 351 DNA samples from 10 Ethiopian cattle populations and the Holstein breed. The mean number of alleles per cattle population ranged from 6.93 ± 2.12 in Sheko to 7.50 ± 2.35 in Adwa. The mean observed and expected heterozygosities were 0.674 ± 0.015 and 0.726 ± 0.019 respectively. Ethiopian cattle populations have maintained a high level of within-population genetic differentiation (98.7%), the remainder being accounted for by differentiation among populations (1.3%). A highly significant deficiency in heterozygotes was detected within populations ( F _IS = 0.071; P  <   0.001) and total inbreeding ( F _IT = 0.083; P  <   0.001). The study populations were highly admixed but distinct from pure Bos taurus and Bos indicus breeds. The various levels of admixture and high genetic diversity make Ethiopian cattle populations suitable for future genetic improvement and utilization under a wide range of agro-ecologies in Ethiopia.     

Evaluation of Genetic Differentiation in Bos indicus Cattle Breeds from Marathwada Region of India Using Microsatellite Polymorphism

Elucidation of genetic variability and genetic relationship among breeds has direct relevance with the issues of sustainable use of domestic animal genetic resources. In the present study, genetic polymorphism was evaluated using 22 microsatellite loci in unrelated samples of Red Kandhari and Deoni cattle breeds inhabiting the same geographical area of Marathwada region in Maharashtra state (western India). This work was mainly aimed at assessing the current genetic diversity to understand whether the two zebu populations in question are genetically differentiated. A total of 164 alleles were detected with an average of 5.82 and 5.86 alleles per locus (MNA) in Red Kandhari and Deoni breeds, respectively. The estimated mean observed (Ho) and expected (He) heterozygosity were 0.47 and 0.64 in Red Kandhari vs. 0.57 and 0.69 in Deoni cattle, respectively, demonstrating considerable level of genetic variation in both the populations. Mean estimates of F statistics were: F (FIT) = 0.315±0.035, f(FIS) = 0.231±0.031, θ(FST) = 0.110±0.022, with both the breeds exhibiting significant deficit of heterozygotes (FIS = 0.179 in Deoni; 0.278 in Red Kandhari). The multilocus FST values implied that 11.0% of the total genetic variation corresponds to breed and were statistically greater than zero for the two populations, suggesting population division. The evaluation of exact test also indicated that allele frequencies across all the loci differed significantly (P < 0.001) between two zebu breeds, further supporting population differentiation. Different genetic distance measures showed considerable levels of distances between the two cattle breeds (0.318 = Nei's standard DS; 0.250 = Nei's DA; 0.416 = Cavalli-Sforza and Edwards's DC; 0.164 = Reynold's, and 2.64 = Delta mu square (dμ)2. Bayesian statistical approach to assign each individual to the population also supported considerable differentiation between the two cattle breeds, possibly reflecting the limited gene flow between the two Marthwada cattle populations. The existence of cohesive breeding structure of both the breeds was further substantiated by allele-sharing distance measures (DAS) among individual animals. The results of this study thus revealed that the two Bos indicus breeds sharing the common breeding tracts are genetically differentiated enough as separate breeds.