Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle.

For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.

State of inbreeding and genetic trends for estimated breeding values in IVF embryos and oocyte donors in the Brazilian Guzerá cattle.

The main objective of this study was to verify genetic trends for milk production (MY305) and age at first calving (AFC). Were also considered levels of inbreeding practiced in the Brazilian dual-purpose Guzerá population (TPOP) comparing it with the same parameters estimated for two sub-populations derived from the reference (TPOP): female donors submitted to ovum-pick up (DPOP) and in vitro embryos produced (EPOP) between 2003 and 2013. Estimated breeding values (EBV) and inbreeding coefficients (F) were regressed by the year of birth (or year of in vitro fertilization) of each animal or embryo in order to obtain annual trends for these parameters separately for each of the three populations studied. A positive quadratic (ß2 = +0.000075) effect was detected for the F values in TPOP. Both DPOP and EPOP showed positive linear coefficients (ß1), respectively, +0.00084 (P < 0.001) and +0.00024 (P > 0.05). Annual mean F for EPOP was higher than TPOP and DPOP through the time series studied. The frequency of individuals with more than 7% F was higher in DPOP. Genetic trends for AFC were -0.187 days/year (P > 0.05); -0.557 days/year (P < 0.05) and -1.48 days/year (P < 0.05), respectively for TPOP; DPOP and EPOP. Genetic trends for MY305 were +6.75 kg/year (P < 0.001); +8.2 kg/year (P < 0.001) and +10.5 kg/year (P < 0.05), respectively for TPOP; DPOP and EPOP. For both traits analyzed, EPOP showed the highest regression coefficients, which confirms a higher selection pressure and lower generation intervals previously expected from this sub-population. Results reported in the present study suggest that mean F is increasing in the Guzerá population. Efforts for controlling inbred mating on in vitro fertilization should be considered, as the presence of a bottleneck effect seems to be getting shape on DPOP and EPOP.

Pedigree analysis and inbreeding effects over morphological traits in Campolina horse population.

Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameters were computed using proper softwares. The effective population size was estimated based on the rate of inbreeding and census information, and the stratification of the population was verified by the average relationship coefficient between animals born in different regions of Brazil. The effects of inbreeding on morphological traits were made by the use of inbreeding coefficient as a covariate in the model of random regression. The inbreeding coefficient increased from 1990 on, impacting effective population size and, consequently, shrinking genetic variability. The paternal inbreeding was greater than maternal, which may be attributed to the preference for inbred animals in reproduction. The average genetic relationship coefficient of animals born in different states was lower than individuals born within the same state. The increase in the inbreeding coefficient was negatively associated with all studied traits, showing the importance to avoid genetic losses in the long term. Although results do not indicate a severe narrowing of the population until the present date, the average relationship coefficient shows signs of increase, which could cause a drastic reduction in genetic variability if inbred mating is not successfully controlled in the Campolina horse population.

Inbreeding effects on in vitro embryo production traits in Guzerá cattle.

Inbreeding has been associated with the impairment of reproductive performance in many cattle breeds. Although the usage of reproductive biotechnologies has been increasing in bovine populations, not much attention has been given to the impact of inbreeding over cow's performance on artificial reproduction. The objective of this study was to estimate the impact of inbreeding on in vitro embryo production in a Guzerá breed population. The inbreeding coefficient (F), calculated as half of the co-ancestry of the individual's parents, was used as an estimate of inbreeding. The inbreeding coefficients of the donor, sire (used on in vitro fertilization) and of the embryos were included, separately, in the proposed models either as classificatory or continuous variables (linear and quadratic effects). The percentage of non-inbred individuals (or embryos) and mean F of donors, embryos and sires were 29.38%; 35.76%; 42.86% and 1.98±2.68; 1.32±3.13; 2.08±2.79, respectively. Two different models were considered, one for oocyte production traits and other for embryo production traits. The increase of F of the donor significantly (P<0.05) impaired the number of viable oocytes (N OV), number of grade I oocytes (N GI) and number of cleaved embryos (N CLV). Moreover, the donor's F influenced the percentage of grade I oocytes (P GI), percentage of viable embryos (P EMB) and percentage of cleaved embryos that turned into embryos (P CXE). No significant (P>0.05) effects were observed for the sire (father of the embryos) inbreeding coefficient over the traits analysed. Embryo's F influenced (P<0.05) the number of viable embryos (N EMB), percentage of viable embryos (P EMB) and percentage of cleaved embryos that turn into embryos (P CXE). Results suggested that an increase in the inbreeding coefficient might impair the embryos ability to survive through challenges imposed by the in vitro environment. Submitting highly inbred Guzerá female donors to in vitro embryo production may, in the long-term, have negative implications on the number of embryos obtained per cow and increase the relative costs of the improvement programmes based on this technology. High levels of inbreeding should be avoided when selecting Guzerá female donors and planning in vitro fertilization mating.

Red Sindhi cattle in Brazil: population structure and distribution.

The Red Sindhi cattle breed was imported to Brazil in small numbers. Nowadays, the herds of this breed are distributed in the Northeast, Southeast and Midwest regions of the country. In this study, DNA samples of animals originating from 15 herds in the Northeast and Southeast regions have been analyzed to obtain the ancestry proportions, and to gain a better understanding of the current population structure of this breed in Brazil. Samples were genotyped using three different single nucleotide polymorphism (SNP) marker panels. Those markers have been used with the approach of unsupervised hierarchical clustering of individuals, and consequently, the ancestry of the population was divided into six different subpopulations. Three of those ancestry subpopulations were identified to be present in various different herds, while the other three were restricted to only one or two herds each. One of those herds has been kept isolated for more than 30 years, and it was identified to contain two almost exclusive subpopulations. To avoid important losses in the genetic diversity within the Red Sindhi breed in Brazil, we recommend the identification of superior sires from every subpopulation in the establishment of a breeding program for this breed.

Polymorphisms and alternative splicing of the luteinizing hormone receptor of dairy cattle.

The aim of this study was to screen for variability in the luteinizing hormone/choriogonadotropin receptor (LHCGR) and to determine the occurrence of LHCGR mRNA isoforms in two dairy breeds of cattle. Granulosa cells from dominant ovarian follicles were recovered from 16 Gir and 16 Holstein cows, and total RNA was extracted. Complementary DNA was synthesized and PCR was used to generate amplicons for sequencing. Chromatograms were evaluated, and multiple sequences were aligned and analyzed for the presence of polymorphisms, allele frequency, polymorphic information content (PIC), and Hardy-Weinberg equilibrium (HWE). Twenty-one single nucleotide polymorphisms (SNPs) were identified in LH receptor mRNA. Seventeen SNPs were identified in Gir cattle (seven exclusively), and 14 were found in Holstein cattle (four exclusively). Seven of the 21 polymorphisms found did not alter which amino acid was translated. Eight SNPs caused a change to an amino acid in a different chemical group. Classification of SNPs according to PIC values identified 12 as being highly informative in Gir cattle and five in Holstein. Eight SNPs deviated from HWE in Gir compared with 11 in Holstein, and eight in both breeds. Two isoforms were also identified, one in exon 1, which lacks 30 nucleotides beginning at position 118, and the other in exon 10. Taken together, these data show that LHCGR in dairy cattle breeds has a high frequency of polymorphism and exists in multiple isoforms resulting from alternative splicing.

Genetic analysis of oocyte and embryo production traits in Guzerá breed donors and their associations with age at first calving.

The objective of this study was to estimate variance components for oocyte and embryo production traits in Guzerá breed female donors, and investigate their associations with age at first calving (AFC). The traits analyzed were the number of viable oocytes (NOV), the number of grade I oocytes (NGI), the number of cleaved embryos (NCLV), and viable embryos produced (NEMB), and the percentages of viable oocytes (POV), grade I oocytes (PGI), cleaved embryos (PCLV), and viable embryos (PEMB). Data were obtained from 5173 ovary puncture and in vitro fertilization (IVF) sessions using 1080 Guzerá female donors of different ages, occurred from March 2005 to July 2013. Variables were log-transformed (logeX+1) prior to analysis. (Co)variance components were estimated by restricted maximum likelihood (REML), using one- and two-trait animal models. Permanent environment and IVF sire (father of the embryos) random effects were included. Estimated heritabilities for NOV, NGI, NCLV, NEMB, POV, PGI, PCLV, and PEMB were 0.19, 0.08, 0.16, 0.14, 0.04, 0.03, 0.01, and 0.07, respectively. Repeatabilities for count traits (NOV, NGI, NCLV, and NEMB) varied from 0.14 and 0.32, higher than estimated for percentage traits (POV, PGI, PCLV, and PEMB), which varied from 0.01 to 0.08. Selection for NOV may be more appropriate in breeding programs than selection for NEMB, because of its strong genetic correlation (0.68) with NEMB and its greater time- and cost-effectiveness. AFC was only weakly associated with the oocyte and embryo production traits, which indicates that there would be no effect on AFC when selecting for these traits.

Genetic parameters of test-day milk yield in Guzerá cattle under tropical conditions.

The objective of this study was to estimate genetic parameters for test-day milk yield (TDMY) in Guzerá cows using random regression models. Additive and permanent environmental random effects were modeled by random regression on fourth- and fifth-order orthogonal Legendre polynomials, respectively. The residual variances were heterogeneous, with seven classes. Heritability estimates for TDMY ranged from 0.24 to 0.52, with higher heritabilities for yields during early lactation. Genetic correlations between TDMYs ranged from -0.03 to 0.95. The phenotypic and permanent environmental correlations were all positive, and the highest estimates were between adjacent TDMYs. The results suggest that TDMYs obtained with random regression models may be used as selection criteria for Guzerá cattle.

Genetic parameters for milk production traits and breeding goals for Gir dairy cattle in Brazil.

To implement an animal breeding program, it is important to define the production circumstances of the animals of interest to determine which traits of economic interest will be selected for the breeding goal. The present study defined breeding goals and proposed selection indices for milk production and quality traits of Gir dairy cattle. First, a bioeconomic model was developed to calculate economic values. The genetic and phenotypic parameters were estimated based on records from 22,468 first-lactation Gir dairy cows and their crosses for which calving occurred between 1970 and 2011. Statistical analyses were carried out for the animal model, with multitrait analyses using the restricted maximum likelihood method. Two situations were created in the present study to define the breeding goals: 1) including only milk yield in the breeding goal (HGL1) and 2) including fat and protein in addition to the milk yield (HGL2). The heritability estimates for milk, protein, and fat production were 0.33 ± 0.02, 0.26 ± 0.02, and 0.24 ± 0.02, respectively. All phenotypic and genetic correlations were highly positive. The economic values for milk, fat, and protein were US$0.18, US$0.27, and US$7.04, respectively. The expected economic responses for HGL2 and for HGL1 were US$126.30 and US$79.82, respectively. These results indicate that milk component traits should be included in a selection index to rank animals evaluated in the National Gir Dairy Breeding Program developed in Brazil.

Viable offspring after successful non-surgical embryo transfer in goats / Nascimento de fetos viáveis após transferência de embriões não-cirúrgica em caprinos

O objetivo do presente estudo foi avaliar a viabilidade da técnica de transferência não cirúrgica em cabras. Quatro cabras não-lactantes pluríparas da raça Toggenburg foram utilizadas como receptoras de embriões, sendo que duas receberam um embriões e duas receberam dois embriões coletados não cirurgicamente cabras doadoras. Os corpos lúteos das receptoras foram detectados um dia antes da transferência de embriões por ultrassonografia transretal. Uma seringa de 5mL contendo 2mL de meio holding foi acoplada em um cateter tomcat, no qual os embriões foram aspirados em uma coluna central a duas outras colunas. Um espéculo Colin número 2 foi inserido na vulva e na vagina, e com o uso de uma fonte de luz, a cerviz foi localizada e imobilizada com uma pinça de Allis. Um cateter uretral número seis acoplado a um mandril e lubrificado com meio PBS foi inserido na cérvix, e assim os aneis cervicais foram gradualmente transpostos. Após perder a resistência, o cateter uretral foi movido lateralmente para o corno uterino desejado. O mandril e a pinça de Allis foram retirados e o conjunto seringa e tomcat foi acoplado ao cateter uretral e o conteúdo injetado no corno uterino ipsilateral ao corpo lúteo com posterior retirada do cateter. Cabras que ovularam em apenas um ovário foram usadas para testar a eficiência da deposição do embrião. O tempo gasto entre a inserção do espéculo e a sua remoção foi inferior a três minutos. O tempo para transpor a cérvix foi inferior a um minuto. A ultrassonografia revelou a deposição de líquido no corno desejado. Receptoras que receberam dois embriões tornaram-se gestantes e pariram três crias. Estes primeiros resultados encorajam a técnica e demonstram que a transferência de embriões em caprinos pode ser feita totalmente por procedimentos não cirúrgicos...

Comparison of random regression models to estimate genetic parameters for milk production in Guzerat (Bos indicus) cows.

Random regression models have been widely used to estimate genetic parameters that influence milk production in Bos taurus breeds, and more recently in B. indicus breeds. With the aim of finding appropriate random regression model to analyze milk yield, different parametric functions were compared, applied to 20,524 test-day milk yield records of 2816 first-lactation Guzerat (B. indicus) cows in Brazilian herds. The records were analyzed by random regression models whose random effects were additive genetic, permanent environmental and residual, and whose fixed effects were contemporary group, the covariable cow age at calving (linear and quadratic effects), and the herd lactation curve. The additive genetic and permanent environmental effects were modeled by the Wilmink function, a modified Wilmink function (with the second term divided by 100), a function that combined third-order Legendre polynomials with the last term of the Wilmink function, and the Ali and Schaeffer function. The residual variances were modeled by means of 1, 4, 6, or 10 heterogeneous classes, with the exception of the last term of the Wilmink function, for which there were 1, 3, 6, or 10 classes. The models gave similar hereditability estimates, ranging from 0.20 to 0.33. Genetic correlations between adjacent records were high values (0.83-0.99), but they declined when the interval between the test-day records increased, and were negative between the first and last records. The model employing the Ali and Schaeffer function with six residual variance classes was the most suitable for fitting the data.

A new tetra-primer ARMS-PCR for genotyping bovine kappa-casein polymorphisms.

Kappa-casein (κ-casein) is one of the most abundant milk proteins. Its main function is to avoid the aggregation of casein micelles, keeping them, and therefore calcium phosphate, in pockets in solution. In bovines, a κ-casein functional polymorphism has been associated with fat, calcium, and protein milk contents and faster curd contraction in cheese production. Quicker curd contraction reduces the loss of milk solids, enhancing cheese yield. This polymorphism induces a double amino acid substitution (Thr136Ile and Ala148Asp). The polymorphism is normally detected by PCR-RFLP, which is a laborious method. An interesting methodological alternative is the tetra-primer amplification refractory mutation system PCR (tetra-primer ARMS-PCR). A tetra-primer ARMS-PCR for the detection of this κ-casein polymorphism has been described. However, specificity was not achieved, probably due to problems with primer design. We developed a new tetra-primer ARMS-PCR for the detection of the κ-casein polymorphism. This new method was validated in a double-blind test, by comparison with the results obtained for 50 Guzerá bulls formerly genotyped by PCR-RFLP. This new method achieved 100% sensitivity and specificity. We conclude that this method is a useful, cost-efficient alternative for the detection of functional κ-casein polymorphisms.

Quantitative trait loci affecting lactose and total solids on chromosome 6 in Brazilian Gir dairy cattle.

Fourteen Brazilian Gir sire families with 657 daughters were analyzed for quantitative trait loci (QTL) on chromosome 6 affecting lactose and total solids. Cows and sires were genotyped with 27 microsatellites with a mean spacing between markers of 4.9 cM. We used a 1% chromosome-wide threshold for QTL qualification. A QTL for lactose yield was found close to marker MNB66 in three families. A QTL for total solid yield was identified close to marker BMS2508 in three families. A QTL for lactose percentage, close to marker DIK1182, was identified in two families. A QTL for total solid percentage, close to marker MNB208, was identified in four families. These QTLs could be used for selection of animals in dairy production systems.

Perfil de ácidos graxos no leite de vacas holandês em pastagens tropicais suplementadas com dois níveis de concentrado / Milk fatty acids profile of Holstein cows grazing tropical forages supplemented with two concentrate levels

Milk fatty acids profile was evaluated using 12 Holstein cows producing 15 kg/day of milk with 4.0% of fat. The animals were assigned to four treatments in a 2 x 2 factorial arrangement (two tropical grasses - Brachiaria brizantha cv. Xaraés and Panicum maximum cv. Tanzania, supplemented with two concentrate levels - 3 and 6 kg/cow/day) in a completely randomized block design. There was no effect of forage and concentrate level (P>0.05) on concentrations of rumenic, vaccenic, (C18: 1 trans-11) and oleic acids in milk fat (mean values of 1.01, 1.79, and 22.55 g/100 g of total fatty acids, respectively). The concentrations of lauric (C12:0), myristic (C14:0), and palmitic (C16:0) acids were also unaffected by treatments (mean values of 2.63, 9.77, and 27.44g/100g of total fatty acids, respectively). Overall, the results illustrate the potential of tropical grasses in producing milk containing a more desirable fatty acids profile in terms of human health.

Quantitative trait loci affecting milk production traits on bovine chromosome 6 in zebuine Gyr breed.

Fourteen Brazilian dairy Gyr sire families with 657 daughters were analyzed for quantitative trait loci (QTL) on chromosome 6 by using a daughter design for 5 economic traits: milk, fat, and protein production, fat and protein percentage. The cows and sires were genotyped for 27 microsatellites with average spacing between markers of 4.9 cM. In the analyses across 14 families, for the largest significant families, and within family, a QTL was located for milk yield and fat yield close to marker BMS2508 at the 5% chromosome-wide significance level across families and 1% chromosome-wide within families. For fat percentage, a QTL near DIK4482 was identified at the 5% chromosome-wide significance level when all families were analyzed together and at the 1% chromosome-wide significance level within the largest significant families. The different analyses yielded results that were generally consistent for milk yield, fat yield, and fat percentage. The order of the markers in the derived map was consistent with that in the consensus map. Some QTL and candidate genes in dairy cattle for milk production traits are probably preserved in Bos taurus and Bos indicus.

Avaliação da persistência na lactação da raça Guzerá, utilizando modelos de regressão aleatória / Evaluation of lactation persistency of Guzerat cows using random regression models

Estimaram-se a herdabilidade e as correlações genéticas e de ambiente permanente entre seis medidas de persistência da lactação de vacas da raça Guzerá, utilizando modelo de regressão aleatória. Foram considerados 8276 registros de produção de leite no dia do controle, na primeira lactação, de 1021 vacas. A regressão aleatória foi calculada pela função logarítmica de Ali e Schaeffer e pelo polinômio de Legendre, obtendo-se os coeficientes para os efeitos fixos, genético aditivo e de ambiente permanente. A função que mais se adequou aos dados foi a de Ali e Schaeffer, mas apresentou problemas de convergência. Os resultados evidenciaram que a persistência é uma característica com herdabilidade de valor moderado e de baixa correlação com o valor genético para produção de leite aos 305 dias, indicando a possibilidade de se obter resposta à seleção para mudança na curva de lactação sem afetar negativamente a produção total de leite na lactação. A medida de persistência que calcula a diferença de produção de leite entre as fases intermediária e inicial da lactação apresentou alta correlação com a produção aos 305 dias.

The heritability and the genetic and permanent environment correlations were estimated among six different measures of persistency in the lactation of Guzerat cow, using the Random Regression Model. A total of 8,403 records from 1,034 first lactation cows were evaluated. The Random Regression Model was calculated by the logarithmic function of Ali and Schaeffer and Legendre polynomials to get coefficients for fixed, additive genetic and permanent environment effects. Ali and Schaeffer was the function that better fit to the data, but it had convergence problems. The results showed that persistence is a trait with moderate heritability, and low correlation with genetic value for 305-d milk production which allows to select animals in order to alter the format of the curve of production without affecting the total productivity. The measure of persistence that calculates the difference of milk production between the medium and initial phases was highly correlated with 305-d milk production.

Variations in genotype-phenotype correlations in phenylketonuria patients.

Phenylalanine hydroxylase deficiency is a trait inherited in an autosomal recessive pattern; the associated phenotype varies considerably. This variation is mainly due to the considerable allelic heterogeneity in the phenylalanine hydroxylase enzyme locus. We examined the genotype-phenotype correlation in 54 phenylketonuria (PKU) patients from Minas Gerais, Brazil. Two systems were used. The first was a phenotype prediction system based on arbitrary values (AV) attributed to each mutation and the second was a correlation analysis. An AV was assigned to each mutation: AV = 1 for classical PKU mutation; AV = 2 for moderate PKU mutation; AV = 4 for mild PKU mutation, and AV = 8 for non-PKU hyperphenylalaninemia mutation. The observed phenotype for AV analysis was the clinical diagnosis established by the overloading phenylalanine test. Among the 51 PKU patients that we analyzed based on this trait, in 51% the predicted phenotype did not match the observed phenotype; the highest degree of concordance was found in patients with null/null genotypes. The genotype was observed to be a good predictor of the clinical course of the patients and significant correlations were found between phenylalanine values at first interview and predicted residual activity, genotype and arbitrary value sum.

Detecção de QTL em dados de famílias estruturadas como as de um núcleo MOET por meio do método da regressão / QTL detection in MOET nucleus family structure-like data using the regression method

O objetivo deste trabalho foi avaliar a eficiência do método de regressão em detectar QTL com base na utilização de dados da estrutura de família (irmãos completos e meios-irmãos), como aqueles gerados em um núcleo MOET. Foram simulados dados fenotípicos e genotípicos em uma estrutura de núcleo MOET fechado de seleção. Três arquivos foram analisados, contendo: a) informações conjuntas de irmãos completos e meios-irmãos; b) apenas informações de irmãos completos e c) apenas informações de meios-irmãos. Verificou-se que o método da regressão, para dados discretos ou contínuos, foi capaz de detectar associações entre marcador e QTL em níveis bastante expressivos de significância (P<0.001 e P<0,0001), quando se utilizou o arquivo que continha informações conjuntas de irmãos completos e meios-irmãos. Os resultados indicaram a possibilidade de utilização dessa metodologia para estudos de detecção/validação de QTL em rebanhos ou núcleos de seleção que utilizam MOET.

The objective of this study was to evaluate the efficiency of the regression method to detect QTL using data from full and half-sib families, like those generated in a MOET nucleus. For this study, genotypic and phenotypic data were simulated in a structure of a closed selection MOET nucleus. Three files were analyzed containing: a) the joint information of full and half sibs; b) only full sibs data; and c) only half sibs data. The method of regression, for continuous or discrete data, was able to detect associations of marker and QTL in very expressive levels of significance (P<0.001 P<0.0001), when the file containing the joint information of full and half sisters was used. The results indicated the possibility of using this methodology for studies of QTL detection / validation in MOET nucleus or herds under selection.

Technical note: A new and cost-effective method for detection of the bovine acyl-CoA:diacylglycerol acyltransferase 1 K232A polymorphism in cattle.

A new, quick, and inexpensive method for detecting the bovine acyl-CoA:diacylglycerol acyltransferase1 (DGAT1) polymorphism (K232A) through tetra-primer amplification refractory mutation system by PCR (ARMS-PCR) was developed in the present investigation. The DGAT1 gene was recently identified as underlying variation in milk production traits. To date, PCR techniques such as PCR-RFLP have been used for detecting the DGAT1 K232A polymorphism, despite being expensive and laborious. The method proposed here, a tetra-primer ARMS-PCR, showed 100% sensitivity and specificity when compared with PCR-RFLP results obtained in a sample of 80 animals tested in a double-blind system. Our results suggest that the use of tetra-primer ARMS-PCR for DGAT1 K232A polymorphism genotyping could greatly reduce costs providing information for both research purposes and for dairy cattle breeders who perform DGAT1 genotyping for gene-assisted selection.

Genetic diversity and population structure in Brazilian Mangalarga Marchador horses.

One hundred and fifteen unrelated Mangalarga Marchador horses were sampled from three geographically distinct regions of Minas Gerais State, Brazil (South, Southeast, and Northeast) and tested for 10 microsatellite loci. Genetic diversity and population structure parameters were estimated with ARLEQUIN 3.0, CERVUS 2.0, POPGENE 1.31, GENEPOP on the web, STRUCTURE 2.0, and SPAGEDI 1.2 software packages. Under Hardy-Weinberg assumptions, seven markers were at equilibrium (LEX014, LEX017, LEX019, SGCV23, TKY321, VHL20, and VIASH39), while two (ASB3 and LEX031) presented significant homozygote excess. Seventy-four alleles were identified in these nine markers, with a mean of 8.22 alleles. Mean heterozygosity was 0.637 and polymorphism information content was 0.662. Markers ASB3, LEX019, SGCV23, TKY321, and VHL20 were highly informative (PIC >0.7) and may be useful for eventual expansion of parentage test panels. The F(ST) value (0.0562) indicated relatively little geographical structure. However, based on a Bayesian-based cluster analysis under a three-cluster model, 94% of the 115 individuals were correctly assigned to the subpopulations from where they were sampled. Mean pairwise f was relatively high (0.11), and in spite of the efforts towards non-consanguineous sampling, 1% of the pairs of individuals shared over 50% of the alleles. These results strongly suggest that the population is genetically structured. Under a conservation genetics approach, two strategies are recommended: avoidance of crosses between highly endogamic individuals and stimulation of crosses between individuals from those regions for which low genetic flow was identified.