Morphological traits and type of dairy goats registered in Brazil from 1976 to 2009

Data from 2439 goats of the Saanen, Alpine, Anglo Nubian and Toggenburg breeds recorded from 1976 to 2009 by the Association of Goats and Sheep Breeders of Minas Gerais were used in principal component analysis. After consistency of data, six morphological variables (thorax perimeter, body length, withers height, height, width and length of the rump) and 12 variables related to breed standard score and fitness (breed characteristic, head, palette and topline, feet and legs, dairy type, body capacity, udder, rear and front ligament, udder texture, teat and final score) were analyzed. Based on the magnitude of the eigenvalue (lower than 0.7), eleven variables considered redundant were discarded, resulting in reduced costs of technician labor to evaluate the animals. Maintenance of records on height, length, rump width, breed characteristic, dairy type, front ligament and udder texture is recommended.

A comparative study of production performance and animal health practices in organic and conventional dairy systems

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Accuracy of genotype imputation in Nelore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The physiology and impact on fertility of the period of proestrus in lactating dairy cows

In cattle, proestrus begins with the initiation of luteolysis and ends with initiation of estrus and the GnRH/LH surge. This period is marked by a dramatic decrease in circulating progesterone (P4) that reaches a nadir by about 36-48 h in cows undergoing natural or prostaglandin F2 alpha (PGF)-induced luteolysis. Inadequate luteolysis is a cause of reduced fertility particularly in timed AI programs with small elevations in circulating P4 reducing fertility. Increasing circulating estradiol (E2) during proestrus is dependent on presence, size, and function of the dominant follicle and this varies during natural proestrus, due to whether animals have two or three follicular waves, and during PGF-induced proestrus, according to stage of the follicular wave at time of PGF treatment. Inadequate circulating E2 can limit fertility and increase pregnancy loss in some specific circumstances such as in cows with low BCS and in cows during heat stress. Thus, studies to optimize the length of proestrus and the concentrations of E2 and P4 during proestrus could produce substantial improvements in fertility and reductions in pregnancy loss.

Prediction of genomic-enabled breeding values and genome-wide association study for feedlot average daily weight gain in Nelore cattle

Pós-graduação em Genética e Melhoramento Animal - FCAV

Changes in maternal body composition and metabolism of dairy goats during pregnancy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mineral metabolism in singleton and twin-pregnant dairy goats

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synaptomenal complex analysis of four breeds of Bos taurus taurus x B. taurus indicus hybrids

The synaptonemal complex (SC) was analyzed in four F1 hybrids of Bos taurus taurus and B. taurus indicus including Gyr-Simmental (G-S), Nelore Simmental (N-S), Gyr-Holstein-Friesian (G-H) and Nelore-Piemontese (N-P). We analysed the frequency of various types of SC abnormalities and the frequency of cells with SC abnormalities. The results were compared with similar observations made on purebred animals. All the animals studied possessed 29 autosomal and one sex bivalent. The frequency of cells with abnormalities in the hybrids were 28.0% in the N-P, 29.1% in the G-S, 33.3% in the N-S and 40.0% in the G-H. The frequency of cells with abnormalities in the four hybrids was 31.5%; 57.9% of these abnormalities occurred in zygotene and 42.0% occurred in pachytene. The comparisons among the hybrids and among the hybrids and their parental breeds showed that the only significant difference was between Gyr and Gyr-Holstein-Friesian animals. Some aspects of the relationship between the frequency of cells with anomalies and the fertility of hybrids are discussed.

Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle

The slick hair coat (SLICK) is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity. Previous studies localized the SLICK locus to a 4 cM region on chromosome (BTA) 20 and identified signatures of selection in this region derived from Senepol cattle. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds. Genome-wide association (GWA), haplotype analysis, signatures of selection, runs of homozygosity (ROH), and identity by state (IBS) calculations were used to identify a 0.8 Mb (37.7-38.5 Mb) consensus region for the SLICK locus on BTA20 in which contains SKP2 and SPEF2 as possible candidate genes. Three specific haplotype patterns are identified in slick individuals, all with zero frequency in non-slick individuals. Admixture analysis identified common genetic patterns between the three slick breeds at the SLICK locus. Principal component analysis (PCA) and admixture results show Senepol and Romosinuano sharing a higher degree of genetic similarity to one another with a much lesser degree of similarity to Carora. Variation in GWA, haplotype analysis, and IBS calculations with accompanying population structure information supports potentially two mutations, one common to Senepol and Romosinuano and another in Carora, effecting genes contained within our refined location for the SLICK locus.

Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Prospecting major genes in dairy buffaloes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.