Assessment of FecGE genotypes on reproductive traits in Brazilian Morada Nova and Santa Inês sheep

The aim of this study was to evaluate the effect of the polymorphic FecGE allele on reproductive traits in Santa Inês and Morada Nova ewes. The traits evaluated were as follows: total progeny weights at birth (PWB) and weaning (PWW) and progeny survival rates at birth (PSRB) and weaning (PSRW). A total of 389 animals, belonging to two Santa Inês herds and one Morada Nova herd, were genotyped. There was a difference between the averages for all the traits studied regarding type of parturition, herd/breed, genotype/herd, and genotype/type of parturition. For each additional progeny, if the female was FecGE/E, the PWB decreased by 1.02 kg and the PWW by 3.16 kg, also with a 0.04% reduction in PSRB and no change in PSRW. If the female was FecGE/+, the reduction in PWB was 0.24 kg, with an increase in PSRW by 0.11%, but no change in PWW and PSRB. In general, these results demonstrate that FecG+/+ females have a better ability to increase their number of progenies without reducing PWB and PWW (also similar to FecGE/+). Thus, it is suggested that further studies on the association between the traits of interest and candidate genes in sheep should be carried out so that the regions which have the greatest effect on the expression of these traits are actually identified. It was not possible to verify the effect of the FecGE allele on the PWB, PWW, PSRB, and PSRW in these Morada Nova and Santa Inês herds.

Landscape Genetics for Brazilian Equines

Optimization of DNA collection for National gene bank and conservation programs requires information on spatial and genetic distribution of animals countrywide. The relationship between genetic and geographic distances were examined in 8 Brazilian horse breeds (Baixadeiro, Crioulo, Campeiro, Lavradeiro, Marajoara, Mangalarga Marchador, Pantaneiro and Puruca) using Single Nucleotide Polymorphism markers and collection point locations. Mantel correlations, Genetic Landscape Shape Interpolation, Allelic Aggregation Index Analyses and Spatial autocorrelation tests indicated a nonrandom distribution of horses throughout the country. Minimum collection distances for the national Gene Bank should be 530km, with clear divisions seen in genetic structure of horse populations in both North/South and East/West directions. Comparing Pantaneiro and North/Northeastern breeds, physical distance is not necessarily the defining factor for genetic differentiation. This should be considered when sampling these local breeds. These data can help optimise GenBank collection routines and conservation strategies for these breeds.

Lentivirus Susceptibility in Brazilian and US Sheep with TMEM154 Mutations

Small ruminant lentiviruses (SRLVs) affect sheep and goats worldwide. The major gene related to SRLV infections is the Transmembrane Protein Gene 154 (TMEM154). We estimated the haplotype frequencies of TMEM154 in the USA (USDA-ARS) and Brazil (Embrapa) Gene Banks by using two different SNP genotyping methodologies, Fluidigm^TM and KASP^TM. We also genotyped the ZNF389_ss748775100 deletion variant in Brazilian flocks. A total of 1040 blood samples and 112 semen samples from 15 Brazilian breeds were genotyped with Fluidigm for the SNP ZNF389_ss748775100 and 12 TMEM154 SNPs. A total of 484 blood samples from the Santa Inês breed and 188 semen samples from 14 North American sheep breeds were genotyped with KASP for 6 TMEM154 SNPs. All the Brazilian samples had the "I/I" genotype for the ZNF389_ss748775100 mutation. There were 25 TMEM154 haplotypes distributed across the Brazilian breeds, and 4 haplotypes in the US breeds. Haplotypes associated with susceptibility were present in almost all breeds, which suggests that genetic testing can help to improve herd health and productivity by selecting non-susceptible animals as founders of the next generations. Fluidigm and KASP are reliable assays when compared with Beadchip arrays. Further studies are necessary to understand the unknown role of TMEM154 mutations, host-pathogen interaction and new genes associated with the clinical condition.

Selection signatures for heat tolerance in Brazilian horse breeds

Since domestication, horse breeds have adapted to their environments and differentiated from one another. This paper uses two methods to detect selection signatures in 23 horse breeds, eight of which are Brazilian (610 animals), both cold-blooded and warm-blooded, from temperate and tropical regions. These animals were genotyped using the GGP Equine BeadChip and we analysed the data by Principal Component Analysis (PCA). The samples were separated into groups based on their geographical area of origin and PCA results studied. The genomic regions under selection were detected by hapFLK and PCAdapt methodologies, identifying six regions under selection with at least one Brazilian horse breed. These regions contain genes associated with heat tolerance, skin colour, body size, energy production/metabolism, genes involved in protein degradation/turnover/DNA repair, genes reducing the impact of oxidative stress/cellular repair, and transcriptional regulation. This work confirmed LCORL and NCAPG gene regions in previous studies associated with body size on Equine Chromosome Autosome 3 (ECA3). On the same ECA3, a region implicating genes linked to coat colour was identified, also previously related to heat stress. Regions with genes coding heat shock proteins were found on ECA1 and 2, and many candidate genes for oxidation-reduction which are a natural response to heat stress. However, a larger sample size and whole-genome SNPs are needed to understand better and identify new candidate regions as well as their functional relation with heat tolerance.

Origin and population structure of Brazilian hair sheep breeds

Brazilian hair sheep constitute a genetic diversity hotspot. These animals are found in the harsh environments of the Brazilian Northwest (semi-arid) region. Genotypes (50K SNP chip) from seven Brazilian sheep breeds (five hair and two coarse wool types) and 87 worldwide breeds were used to test for population structure, admixture and genetic diversity. Moreover, phylogenetic trees evaluating migration events between genetic groups were built. Brazilian Somali, a fat-tailed breed, had a close relationship with East African breeds and clustered distinctly from other Brazilian breeds. Brazilian Blackbelly and Barbados Blackbelly had a close relationship. The Morada Nova breed did not show close relationships with European or African breeds, revealing a single migration event from an Algerian hair breed. Brazilian Fat-tail and Morada Nova share a common ancestor, but the former showed introgressions from Brazilian Somali and Afrikaner breeds, explaining the fat-tail phenotype. The Santa Inês breed received a substantial contribution from Brazilian Bergamasca and showed an admixed origin with recent introgressions from other breeds, mainly from Suffolk. Furthermore, Brazilian Somali and Brazilian Fat-tail are the most endangered sheep genetic resources in Brazil and should be the focus for ex situ conservation programs. In conclusion, Brazilian hair sheep show an African origin and are characterized by diverse genetic composition, reinforcing the need for conservation of these genetic resources, and at the same time, this highly diverse group has variability that can be used in breeding programs.

Occurrence, morphology, and morphometry of follicles containing multiple oocytes in FecGE mutant Santa Inês ewes

This study was conducted to characterize the morphology and morphometry of follicles containing multiple oocytes (MOFs) and determine the association with the FecG^E mutation in Santa Inês ewes. Based on the genotypes, 65 ewes were characterized as being homozygous wild-type (n = 25; FecG^+/+), heterozygous mutant (n = 27, FecG^+/E), and homozygous mutant (n = 13, FecG^E/E). The variables evaluated were follicle developmental stage, number of oocytes per follicle, morphology, and morphometry of MOFs. The FecG^E mutation did not affect the frequency of MOFs (P > 0.05) (3.0 % in FecG^+/+; 3.3 % in FecG^+/E; and 3.5 % in FecG^E/E). The greater viability (P < 0.05) of MOFs was identified in transitory stage of the FecG^E/E (95.0 %) and FecG^+/E (90.9 %) when compared to the FecG^+/+ genotype (73.3 %). Furthermore, the morphology of transitory follicles with two oocytes was the variable and when evaluated was the most reliable determinant for predicting which ewes had an FecG^E mutation. In conclusion, the FecG^E mutation did not affect the frequency of MOFs. The ewes with FecG^E mutation had a greater frequency of morphologically normal MOFs in the transitory stage. Furthermore, the ewes with the FecG^E mutation had a greater likelihood of having MOFs containing two morphologically normal oocytes.

Low mtDNA diversity in a highly differentiated population of spinner dolphins (Stenella longirostris) from the Fernando de Noronha Archipelago, Brazil

Spinner dolphins (Stenella longirostris, Gray 1828) are widely distributed in tropical waters around the world. Although they occur in large, pelagic groups in the Eastern Tropical Pacific, elsewhere in the Pacific they are found in small and genetically isolated populations associated with islands. This species is considered to be “Least Concern” (LC) by the World Conservation Union (IUCN). To assess genetic diversity and population structure of an island-associated population in the South Atlantic Ocean we surveyed 162 spinner dolphins throughout the Fernando de Noronha Archipelago of the northeast coast of Brazil using ten microsatellite loci and sequencing a 413-bp section of the mitochondrial DNA (mtDNA) control region. Eleven mtDNA haplotypes were identified and haplotype diversity (h) and nucleotide diversity (π) were 0.3747 and 0.0060, respectively. Median-Joining Network revealed the presence of two very divergent haplotypes and F-statistics indicated some heterogeneity between two sampling years. All microsatellite loci were polymorphic (H_o: 0.767; H_e: 0,764) but, revealed no detectable substructure. We also compared the mtDNA haplotypes from Noronha to 159 haplotypes representing 893 individuals from 14 locations worldwide. We found that the two common haplotypes from the Fernando de Noronha Archipelago were absent in all other populations. These comparisons showed that Noronha spinner dolphins are likely more differentiated than other island populations, suggesting that they form societies with strong site fidelity mediated by females.

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine

Invasive alien species are a significant threat to both economic and ecological systems. Identifying the processes that give rise to invasive populations is essential for implementing effective control strategies. We conducted an ancestry analysis of invasive feral swine (Sus scrofa, Linnaeus, 1758), a highly destructive ungulate that is widely distributed throughout the contiguous United States, to describe introduction pathways, sources of newly emergent populations and processes contributing to an ongoing invasion. Comparisons of high-density single nucleotide polymorphism genotypes for 6,566 invasive feral swine to a comprehensive reference set of S. scrofa revealed that the vast majority of feral swine were of mixed ancestry, with dominant genetic associations to Western heritage breeds of domestic pig and European populations of wild boar. Further, the rapid expansion of invasive feral swine over the past 30 years was attributable to secondary introductions from established populations of admixed ancestry as opposed to direct introductions of domestic breeds or wild boar. Spatially widespread genetic associations of invasive feral swine to European wild boar deviated strongly from historical S. scrofa introduction pressure, which was largely restricted to domestic pigs with infrequent, localized wild boar releases. The deviation between historical introduction pressure and contemporary genetic ancestry suggests wild boar-hybridization may contribute to differential fitness in the environment and heightened invasive potential for individuals of admixed domestic pig-wild boar ancestry.

Dynamics of genomic architecture during composite breed development in cattle

Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

Evaluation of morphology, morphometry and follicular dynamics in FecGE genotyped ewes

This study aimed to evaluate the effect of FecG^E mutation on the development of ovarian follicles. To this end, 42 Santa Inês ewes were genotyped for FecG^E mutation and classified as wild-type (FecG^+/+), heterozygous (FecG^+/E) or mutant homozygous (FecG^E/E). Ovarian fragments were processed, and the follicles were analyzed with regard to the morphology and morphometry using classical histology. For the evaluation of follicular dynamics, ewes underwent oestrous synchronization and were monitored throughout an interovulatory period. A higher (P < 0.05) percentage of morphologically normal follicles in the primordial stage was identified in FecG^E/E (90.0%) and FecG^+/E (88.1%) ewes than in the FecG^+/+ (73.0%) ewes. There was also a significantly greater (P < 0.05) number of morphologically normal follicles in the FecG^E/E (87.3%) and FecG^+/E (83.3%) ewes than in FecG^+/+ (76.8%) ewes in the transitional stage. A smaller (P < 0.05) diameter was observed in the secondary follicles in FecG^E/E (93.8 μm) ewes than in FecG^+/E (171.8 μm) ewes. Regarding follicular dynamics, FecG^E/E ewes showed a greater (P < 0.05) number of ovulations (2.5 ± 0.2) than FecG^+/+ ewes (1.5 ± 0.3) ewes. Ovulatory follicles were smaller (P < 0.05) in the FecG^E/E (5.1 mm) and FecG^+/E (5.2 mm) ewes than in FecG^+/+ (5.8 mm) ewes. Santa Inês nulliparous ewes carrying the FecG^E mutation showed a greater proportion of morphologically normal follicles in the primordial and transitional stages than those not carrying the mutation. FecG^E/E ewes demonstrated a higher number of ovulated follicles and that FecG^E/E and FecG^+/E ewes presented ovulatory follicles with a smaller diameter.

Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011-0.134). The frequency of these markers indicated a clear north-south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.

D-loop haplotype diversity in Brazilian horse breeds

The first horses were brought to Brazil by the colonizers after 1534. Over the centuries, these animals evolved and adapted to local environmental conditions usually unsuitable for exotic breeds, thereby originating locally adapted Brazilian breeds. The present work represents the first description of maternal genetic diversity in these horse breeds based on D-loop sequences. A D-Loop HSV-I fragment of 252 bp, from 141 horses belonging to ten Brazilian breeds / genetic groups (locally adapted and specialized breeds) were analysed. Thirty-five different haplotypes belonging to 18 haplogroups were identified with 33 polymorphic sites. Haplotype diversity (varying from 0.20 to 0.96) and nucleotide diversity (varying from 0.0039 to 0.0239) was lower for locally adapted than for specialized breeds, with the same pattern observed for F_ST values. Haplogroups identified in Brazilian breeds are in agreement with previous findings in South American samples. The low variability observed mainly in locally adapted breeds, indicates that, to ensure conservation of these breeds, careful reproductive management is needed. Additional genetic characterization studies are required to support accurate decision-making.

Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

Background

Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance.

Results

Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively.

Conclusions

Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2752-9) contains supplementary material, which is available to authorized users.

Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle

High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

Tolerância ao calor em bovinos das raças Nelore branco, Nelore vermelho e Pantaneira

A identificação de parâmetros/ métricas associados à adaptação ambiental é uma das principais tendências e desafios da pecuária mundial. Desta forma, o objetivo deste trabalho foi avaliar as características de tolerância ao calor de bovinos da raça Nelore e Pantaneiro no ecossistema do Pantanal matogrossense no pico de calor da região. Estes animais foram mantidos por duas horas à sombra (8:00h às 10:00h) e em seguida uma hora ao sol (10:00h às 11:00h). Após a exposição foram analisados parâmetros de frequência cardíaca (FC), frequência respiratória (FR), temperatura retal (TR), temperatura superficial da costela (TSC), temperatura superficial do pescoço (TSP) e temperatura superficial da garupa (TSG). Também foram avaliados a taxa de sudação (TXS), comprimento e densidade de pelos e calculados o índice de tolerância ao calor (ITC). No período estudado, a temperatura ambiental variou de 29,0 a 40,0ºC e a média para umidade relativa foi de 75%. O ambiente teve influência marcante sobre as variáveis fisiológicas, com exceção da FR. A TR e a TXS diferiram significativamente entre os grupos genéticos, sendo da raça Nelore mais elevada em relação à Pantaneira, mas todas dentro dos limites fisiológicos. A análise multivariada mostrou a importância de variáveis como taxa de sudação e comprimento de pelos para adaptação de bovinos na região. Apesar do Nelore vermelho estar separado dos outros dois grupos, foi possível concluir que ambas as raças analisadas apresentaram capacidade de adaptação e tolerância ao calor às condições climáticas do Pantanal e podem ser produzidas de modo sustentável na região.

Identification of selection signatures in livestock species

The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.

Validation of a microsatellite panel for parentage testing of locally adapted and commercial goats in Brazil

Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.

Impact of genetic drift on access and benefit sharing under the Nagoya Protocol: the case of the Meishan pig

Genetic drift (GD) randomly impacts small breeds and imported populations. Therefore, it can impact policies that affect conservation of animal genetic resources. This paper evaluates GD for a population of Meishan pigs imported into the United States and explores the ramifications of GD on access and benefit sharing of genetic resources under the Nagoya Protocol (NP) of the United Nations' Convention on Biological Diversity. The NP was motivated by concerns about fair and equitable benefit sharing of genetic resources across life forms. In this experiment, 35 microsatellite markers were used to quantify the level of GD that occurred between Meishan pigs (Meishan-China; n = 22) imported into the United States in the late 1980s and contemporary Meishan (Meishan-US; n = 42), which have been randomly bred since importation. The Meishan-US consisted of 2 subpopulations (Meishan-MARC and Meishan-ISU). Five other breeds were also included in the analysis to serve as reference populations: Fengjing and Minzhu, which were imported with Meishan-China, and Duroc, Berkshire, and Yorkshire from the United States. Mean shift in allele frequency was 0.11 (SE = 0.019) due to GD for Meishan-US vs. Meishan-China with some loci having changed allele frequencies by greater than 0.20. Principle coordinate analysis confirmed divergence among the Meishan populations. Model-based clustering tended to place the U.S. and Chinese breeds into 2 distinct clusters, likely due to differences in allele frequencies between U.S. and Chinese breeds. Contemporary Meishan-US has become differentiated from the original imported animals due to GD. Attributing future performance of Meishan-US to Meishan-China, as set forth by NP, is problematic due to GD. As an imported breed becomes established there will be an increasing number of breeders who may have different selection goals and private treaty contracts will govern the exchange of stock between them. Therefore, considering biological phenomena and social dynamics simultaneously draws into question whether a rigorous access and benefit sharing protocol as envisioned in the NP will be operational.

ASSOCIATION OF MICROSATELLITE MARKERS WITH PRODUCTION TRAITS IN SANTA INÊS AND CROSSBRED SHEEP

O objetivo deste estudo foi de associar alelos de 13 loci de microssatélites no cromossomo 20 de ovinos (Major Histocompatibility Complex - MHC) com características de desempenho e carcaça bem como resistência à parasitas  gastrointestinais em 138 ovinos Santa Inês e seus cruzamentos com Bergamasca, Texel e Ile de France. Os seguintes loci foram selecionados: BM1818, OarCP73, OarHH56, DYA, OLADRB, CP101, OMHC1, DQA2, DQA1, TFAP2A, DQBA27, Bf94_1, e INRA132.  Dados foram analisados em Cervus e SAS ® para determinar níveis de heterozygosidade e associações de marcadores com peso, carcaça e ovos por grama de fezes (OPG).  Os marcadores mostraram alta variabilidade genética entre indivíduos.  Para características de carcaça oito associações significativas (p<0.05) foram observadas, bem como associação positiva entre OPG e dois marcadores da MHC ovina.

Bulked segregant analysis of the pirarucu (Arapaima gigas) genome for identification of sex-specific molecular markers

Arapaima gigas (Osteoglossidae) is one of the largest fish species in the Amazon Basin, attaining lengths of over 2.5 m and weights of over 100 kg. Its flesh is prized, and it has great potential for production in aquaculture systems. However, live pirarucu cannot be reliably sexed visually, even after sexual development, since this species does not have clear external sexual dimorphism. Simple and inexpensive methods for sexing immature pirarucu based on DNA markers would facilitate production of this species in commercial operations. We analyzed A. gigas male and female DNA pools with 566 RAPD primers, generating 2609 fragments, with an estimated 1341 segregating polymorphic markers, and an estimated average spacing of 714 kb, which corresponds to less than 0.1% of the species' genome. Two putative sex-specific fragments were initially identified in bulked samples; but they were not confirmed in a study of individual male and female samples. We suggest that A. gigas has developed a non-chromosomal system of sex determination or, alternatively, that the species has undergone a recent loss of the chromosome carrying the sex-determining locus.

Incidence of bovine leukocyte adhesion deficiency, complex vertebral malformation, and deficiency of uridine-5-monophosphate synthase carriers in Brazilian Girolando cattle

Among the various hereditary diseases that have been widely studied in dairy cattle, bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine-5-monophosphate synthase (DUMPS), and complex vertebral malformation (CVM) are noteworthy because of their high impact on overall herd productivity as a consequence of increased calf mortality. The aim of this study was to verify the frequency of carriers of BLAD, CVM, and DUMPS mutant alleles in cows and bulls from the National Girolando Progeny Test carried out in Brazil by using polymerase chain reaction (PCR)-restriction fragment length polymorphism and allele-specific PCR assays. A total of 777 animals were genotyped for BLAD, 783 for CVM, and 122 for DUMPS. The frequencies of carriers for BLAD and CVM were 0.77 and 1.53%, respectively, whereas no carriers of DUMPS were observed.

Porcine colonization of the Americas: a 60k SNP story

The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.

Worldwide genetic relationships of pigs as inferred from X chromosome SNPs

The phylogeography of the porcine X chromosome has not been studied despite the unique characteristics of this chromosome. Here, we genotyped 59 single nucleotide polymorphisms (SNPs) in 312 pigs from around the world, representing 39 domestic breeds and wild boars in 30 countries. Overall, widespread commercial breeds showed the highest heterozygosity values, followed by African and American populations. Structuring, as inferred from FST and analysis of molecular variance, was consistently larger in the non-pseudoautosomal (NPAR) than in the pseudoautosomal regions (PAR). Our results show that genetic relationships between populations can vary widely between the NPAR and the PAR, underscoring the fact that their genetic trajectories can be quite different. NPAR showed an increased commercial-like genetic component relative to the PAR, probably because human selection processes to obtain individuals with high productive parameters were mediated by introgressing boars rather than sows.

Genetic variability in local Brazilian horse lines using microsatellite markers

Genetic variability at 11 microsatellite markers was analyzed in five naturalized/local Brazilian horse breeds or genetic groups. Blood samples were collected from 328 animals of the breeds Campeira (Santa Catarina State), Lavradeira (Roraima State), Pantaneira (Pantanal Mato-Grossense), Mangalarga Marchador (Minas Gerais State), as well as the genetic group Baixadeiro (Maranhão State), and the exotic breeds English Thoroughbred and Arab. We found significant genetic variability within evaluated microsatellite loci, with observed heterozygosis varying between 0.426 and 0.768 and polymorphism information content values of 0.751 to 0.914. All breeds showed high inbreeding coefficients and were not in Hardy-Weinberg equilibrium. The smallest genetic distance was seen between the Pantaneira and Arab breeds. The principal component analyzes and Bayesian approach demonstrated that the exotic breeds have had a significant influence on the genetic formation of the local breeds, with introgression of English Throroughbred in Pantaneira and Lavradeira, as well as genetic proximity between the Arab, Pantaneira and Mangalarga Marchador populations. This study shows the need to conserve traits acquired by naturalized horse breeds over centuries of natural selection in Brazil due to the genetic uniqueness of each group, suggesting a reduced gene flow between them. These results reinforce the need to include these herds in animal genetic resource conservation programs to maximize the genetic variability and conserve useful allele combinations.

Combining US and Brazilian microsatellite data for a meta-analysis of sheep (Ovis aries) breed diversity: facilitating the FAO Global Plan of Action for Conserving Animal Genetic Resources

Microsatellites are commonly used to understand genetic diversity among livestock populations. Nevertheless, most studies have involved the processing of samples in one laboratory or with common standards across laboratories. Our objective was to identify an approach to facilitate the merger of microsatellite data for cross-country comparison of genetic resources when samples were not evaluated in a single laboratory. Eleven microsatellites were included in the analysis of 13 US and 9 Brazilian sheep breeds (N = 706). A Bayesian approach was selected and evaluated with and without a shared set of samples analyzed by each country. All markers had a posterior probability of greater than 0.5, which was higher than predicted as reasonable by the software used. Sensitivity analysis indicated no difference between results with or without shared samples. Cluster analysis showed breeds to be partitioned by functional groups of hair, meat, or wool types (K = 7 and 12 of STRUCTURE). Cross-country comparison of hair breeds indicated substantial genetic distances and within breed variability. The selected approach can facilitate the merger and analysis of microsatellite data for cross-country comparison and extend the utility of previously collected molecular markers. In addition, the result of this type of analysis can be used in new and existing conservation programs.

Adaptation of a low-cost medium-throughput genotyping system for ovine prion protein gene polymorphims associated with scrapie

Resistance and susceptibility to scrapie in sheep have been associated with SNPs located at codons 136, 154 and 171 of the prion protein (PRNP) gene. Many countries have sheep breeding programs selecting for resistance to scrapie based on the genotyping of these SNPs. We adapted a fast and robust method for genotyping sheep flocks for these polymorphisms, with reduced costs. Ninety-six samples were genotyped using an adapted SNaPshot PRNP assay, and the results were checked by resequencing. The results showed 100% concordance, using a method that reduces genotyping costs by 70%, by reducing reagent concentrations in the three main steps of the assay (amplicon purification, base extension and final cleanup). This cost reduction should contribute to the development of selection criteria based on PRNP genotyping in countries where assay costs are an important limiting factor.

Use of multivariate analyses for determining heat tolerance in Brazilian cattle

Adaptability can be evaluated by the ability of an animal to adjust to environmental conditions and is especially important in extreme weather conditions such as that found in tropical Brazil. A multivariate analysis using physical and physiological traits in exotic (Nellore and Holstein) and naturalized (Junqueira, Curraleira, Mocho Nacional, Crioula Lageana, and Pantaneira) cattle breeds was carried out in the Federal District of Brazil to test and determine which traits are important in the adaptation of animal to heat stress as well as the ability of these traits and statistical techniques to separate the breeds studied. Both physical and physiological traits were measured on three occasions and included body measurements, skin and hair thickness, hair number and length, pigmentation, sweat gland area as well as heart and breathing rates, rectal temperature, sweating rate, and blood parameters. The data underwent multivariate statistical analyses, including cluster, discriminate, and canonical procedures. The tree diagram showed clear distances between the groups studied, and canonical analysis was able to separate individuals in groups. Coat traits explained little variation in physiological parameters. The traits which had higher discriminatory power included packed cell volume, shoulder height, mean corpuscular volume, body length, and heart girth. Morphological and physiological traits were able to discriminate between the breeds tested, with blood and size traits being the most important. More than 80% of animals of all breeds were correctly classified in their genetic group.

Genetic structure and diversity among sheep breeds in the United States: identification of the major gene pools

Understanding existing levels of genetic diversity of sheep breeds facilitates in situ and ex situ conservation activities. A comprehensive evaluation of US sheep breeds has not been previously performed; therefore, we evaluated the genetic diversity among and within 28 US sheep breeds. Both major and minor breeds were included in the analysis and consisted of 666 animals from 222 producers located in 38 states. The level of within-breed genetic diversity was variable and not dependent upon status of a breed as a major or minor breed. Bayesian cluster analysis indicated the breeds were grouped more by physiological differences (meat vs. wool production) rather than geographic origin. Results suggest several actionable items to improve in situ and ex situ conservation. The results clearly identify breeds in need of increased in situ and ex situ management (e.g., Hog Island and Karakul) and allow several suggestions for in situ management of flocks. Conversely, several of the breeds appear genetically similar and therefore require less emphasis on collecting germplasm samples for the gene bank. Commercially important breeds (e.g., Rambouillet and Suffolk) were found to have substantial variation, which should enable breeders to proceed, unencumbered by genetic diversity concerns, with selection strategies that maximize profit.

Use of heat tolerance traits in discriminating between groups of sheep in central Brazil

The animal and its environment make up an integrated system, where each acts on the other. Tropical regions are characterized by high levels of solar radiation and environmental temperature which may adversely affect animal production. This study carries out a multivariate analysis of physical and physiological traits in sheep in the Federal District of Brazil to test the ability to separate groups of animals and determine which traits are most important in the adaptation of animal to heat stress. The variables studied included coat thickness, number and length of hairs, pigmentation of the skin and coat, number of sweat glands as well as heart and respiratory rates, rectal and skin temperatures, sweating rate, and blood parameters. Five groups of ten animals were used depending on breed (Bergamasca, crossbred, or Santa Inês) or coat color (Santa Inês--brown, white, and black). The data underwent multivariate statistical analyses including cluster, discriminate, and canonical, using Statistical Analysis System--SAS®. The tree diagram showed clear distances between groups studied and canonical analysis was able to separate individuals in groups, especially Bergamasca and white Santa Inês. The canonical correlation redundancy analysis showed that coat reflectance as well as hair length and number of hairs per unit area were the most useful in explaining changes in physiological traits. Skin and coat traits such as hair length, coat reflectance, percentage of epithelial area occupied by sweat glands, skin reflectance and thickness, as well as heart and breathing rates were the most important in separating these groups.

Molecular and karyotypic phylogeography in the Neotropical Hoplias malabaricus (Erythrinidae) fish in eastern Brazil

The sedentary, predatory characin Hoplias malabaricus has one of the widest distributions of freshwater fishes in South America and is characterized by seven karyomorphs (A-G) that occur in sympatric and allopatric populations. Karyotypical patterns of variation in wild populations have been interpreted as evidence of multiple lineages within this nominal species, a possibility that may limit the validity of experimental data for particular karyomorphs. This study used the phylogeographic and genealogical concordance between cytogenetic (N = 49) and molecular (mitochondrial DNA) (N = 73) data on 17 samples, collected in 12 basins from south-eastern and north-eastern Brazil, to assess the systematic value of cytogenetic data. Cytogenetic patterns show a sex chromosome system in the 2n = 40F karyomorph. Molecular and cytogenetic data indicate a long, independent evolutionary history of karyomorphs and a coastal origin of continental populations in south-eastern Brazil. The lack of fit with molecular clock expectations of divergence between groups is likely to be due to strong demographic fluctuations during the evolution of this species complex. The results indicate that karyotypical identification provides a reliable baseline for placing experimental studies on Hoplias spp. in a phylogenetic context.

Genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population

The genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population were estimated by applying the Average Information Restricted Maximum Likelihood method to an animal model. Data from a flock supported by the Programa de Melhoramento Genético de Caprinos e Ovinos de Corte (GENECOC) were used. The traits studied included birth weight (BW), weaning weight (WW), slaughter weight (SW), yearling weight (YW), weight gain from birth to weaning (GBW), weight gain from weaning to slaughter (GWS), weight gain from weaning to yearling (GWY), age at first lambing (AFL), lambing interval (LI), gestation length (GL), lambing date (LD - number of days between the start of breeding season and lambing), litter weight at birth (LWB) and litter weight at weaning (LWW). The direct heritabilities were 0.35, 0.81, 0.65, 0.49, 0.20, 0.15 and 0.39 for BW, WW, SW, YW, GBW, GWS and GWY, respectively, and 0.04, 0.06, 0.10, 0.05, 0.15 and 0.11 for AFL, LI, GL, LD, LWB and LWW, respectively. Positive genetic correlations were observed among body weights. In contrast, there was a negative genetic correlation between GBW and GWS (-0.49) and GBW and GWY (-0.56). Positive genetic correlations were observed between AFL and LI, LI and GL, and LWB and LWW. These results indicate a strong maternal influence in this herd and the presence of sufficient genetic variation to allow mass selection for growth traits. Additive effects were of little importance for reproductive traits, and other strategies are necessary to improve the performance of these animals.

Multivariate analysis for characteristics of heat tolerance in horses in Brazil

The environment in which the horse is reared affects its ability to maintain thermal balance which is in turn related to thermal characteristics and regulatory physiological mechanisms. In this study a multivariate analysis of physiological traits in relation to heat tolerance in horses was carried out in the Federal District, Brazil. The aim was to test the ability of these analyses to separate groups of animals and determine which physiological traits are most important in the adaptation to heat stress. Forty adult horses (4 to 13 years) were used, ten from each of four different genetic groups (English thoroughbred, Brazilian showjumper, crossbred and Breton). The traits examined included heart and breathing rate, rectal temperature as well as blood parameters. The data underwent multivariate statistical analysis including cluster, discriminate and canonical using Statistical Analysis System - SAS (R) procedures CLUSTER, STEPDISC, CANCORR and DISCRIM. The tree diagram showed clear distances between groups studied and canonical analysis was able to separate individuals in groups. The discriminate analysis identified the variables which were most important in separating these groups. The multivariate analysis was able to separate the animals into groups with RR, HR and RT being important in this separation.

Aromatase gene and its effects on growth, reproductive and maternal ability traits in a multibreed sheep population from Brazil

We determined the polymorphism C242T of the aromatase gene (Cyp19) and its allelic frequency, as well as the effect of the variants on productive and reproductive traits in 71 purebred Santa Inês sheep, 13 purebred Brazilian Somali sheep, nine purebred Poll Dorset sheep, and 18 crossbred 1/2 Dorper sheep. The animals were genotyped using the PCR-RFLP technique. The influence of the animal's genotype on its performance or on the performance of its lambs was analyzed by the least square method. Another factor assessed was the importance of the animal's genotype in analysis models for quantitative breeding value estimates, and whether there were differences among the averages of breeding values of animals with different genotypes for this gene. In the sample studied, no AA individuals were observed; the AB and BB frequencies were 0.64 and 0.36, respectively. All Brazilian Somali sheep were of genotype BB. All 1/2 Dorper BB animals presented a lower age at first lambing, and the Santa Inês BB ewes presented a lower lambing interval. In these same genetic groups, AB ewes presented higher litter weight at weaning. This is evidence that BB ewes have a better reproductive performance phenotype, whereas AB ewes present a better maternal ability phenotype. However, in general, animals with genotype AB presented better average breeding values than those with genotype BB.

Heat tolerance in Brazilian sheep: physiological and blood parameters

Thirty Santa Ines adult, non-lactating, non-pregnant ewes, ten with a brown coat, ten black coated and ten white coated, as well as ten Bergamasca and ten of mixed breed were used to evaluate the effect of climate on physiological and blood parameters in sheep. Two sample collections were taken (6 AM: and 2 PM: ) on six days. Sweating rate (SR), heart (HR) and breathing rates (BR), complete hemogram, rectal (RT) and skin temperatures (ST) were measured. Variance analyses were carried out using SAS(R). In general, there were significant differences between animals due to skin type, time and day of collection. White coated animals showed lower HR, BR and RT, with afternoon parameters higher than morning. Correlations between HR, BR, RT, SR and ST were medium and positive. Correlations between physiological and blood traits were in general negative and medium. Packed Cell Volume (PCV), total plasma proteins, red blood cell count and hemoglobin concentration had high positive correlations between each other. The first two autovectors explained 49% of variation between traits. White coated Santa Ines animals were shown to be better adapted to climatic conditions in Central Brazil and wool sheep more affected by heat.

Anti-inflammatory and anti-ulcerogenic properties of Stachytarpheta cayennensis (L.C. Rich) Vahl

In the present work, the anti-inflammatory and gastroprotective properties of ethanolic extracts of Stachytarpheta cayennesis (L.C. Rich) Vahl (Verbenaceae) were assessed. Chromatographic analysis of the crude ethanolic extract, SC01, revealed high concentrations of the iridoid ipolamiide, whereas the SC02, the second ethanolic extract, presented the arylpropanoid verbacoside as a major constituent. The oral administration of SC01 (100 mg/kg) into Swiss mice failed to inhibit paw oedema and pleural exudation induced by carrageenan and zymosan, whereas SC02 (100 mg/kg, p.o.) inhibited oedema and protein extravasation in all instances. Both extracts inhibited total leukocyte accumulation into the pleural cavity 4 and 24h after the intrathoracic (i.t.) injection of carrageenan, due to the inhibition of neutrophil and mononuclear cell influx, whereas only SC02 was able to inhibit leukocyte mobilization induced by zymosan (100 microg/cavity, i.t.). SC02 inhibited LPS (250 ng/cavity)-induced total leukocyte, neutrophil and eosinophil accumulation in the pleural cavity, whereas SC01 selectively inhibited neutrophil influx. In addition, our data indicates that the extract SC02 presents an important anti-ulcerogenic activity, since it inhibited diclofenac-induced (100 mg/kg, p.o.) gastric ulcera. Overall, these data provide evidence for the anti-inflammatory and gastroprotective properties of Stachytarpheta cayennensis, supporting its use in folk medicine for such purposes.