F. Baldi

GENETIC PARAMETER ESTIMATES FOR BUFFALO MILK YIELD, MILK QUALITY AND MOZZARELLA PRODUCTION AND BAYESIAN INFERENCE ANALYSIS OF THEIR RELATIONSHIPS

Buffalo milk has excellent physical and chemical qualities as a consequence of the high percentage of constituents. This milk property is desirable for the dairy industry because it facilitates manufacture of mozzarella cheese. We estimated genetic parameters for milk yield, milk fat and protein and their effects on mozzarella cheese production using Bayesian inference. Using information from 4907 lactation records of buffaloes, genetic and non-genetic parameters were estimated for accumulated 305-day milk yield (MY), milk fat (%F) and protein (%P) percentages and mozzarella production per lactation (MP). The (co)variance components were obtained by Bayesian inference using a multiple trait model, which included as fixed effects contemporary group, milking number and buffalo age at calving as covariables (linear and quadratic), along with the additive genetic, permanent environmental and residual random effects. Mean a posteriori heritability distributions for MY, %F, %P, and MP were 0.25, 0.30, 0.38, and 0.23, respectively. The genetic correlation estimates between MY with %P and %F were negative and moderate. Positive genetic correlation estimates varying from 0.19 (%P/MP) to 0.95 (MY/MP) were obtained among the traits. Milk yield, milk components, and mozzarella production in Murrah buffaloes have enough genetic variation for selection purposes. We conclude that selection to increase milk yield would be effective in improving mozzarella production.

Genome-Wide Association Study of Meat Quality Traits in Nellore Cattle

The objective of this study was to identify genomic regions that are associated with meat quality traits in the Nellore breed. Nellore steers were finished in feedlots and slaughtered at a commercial slaughterhouse. This analysis included 1,822 phenotypic records of tenderness and 1,873 marbling records. After quality control, 1,630 animals genotyped for tenderness, 1,633 animals genotyped for marbling, and 369,722 SNPs remained. The results are reported as the proportion of variance explained by windows of 150 adjacent SNPs. Only windows with largest effects were considered. The genomic regions were located on chromosomes 5, 15, 16 and 25 for marbling and on chromosomes 5, 7, 10, 14 and 21 for tenderness. These windows explained 3,89% and 3,80% of the additive genetic variance for marbling and tenderness, respectively. The genes associated with the traits are related to growth, muscle development and lipid metabolism. The study of these genes in Nellore cattle is the first step in the identification of causal mutations that will contribute to the genetic evaluation of the breed.

Runs of homozygosity: current knowledge and applications in livestock

This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a populations genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (FROH ) is more accurate for estimating autozygosity and for detecting bothxa0past and more recent inbreeding effects than are estimates from pedigree data (FPED ). The better results of FROH suggest that FROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genomes architecture can disclose a populations genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.

Association between single-nucleotide polymorphisms and milk production traits in buffalo

The aim of this study was to identify single-nucleotide polymorphisms (SNPs) in buffaloes associated with milk yield and content, in addition to somatic cell scores based on the cross-species transferability of SNPs from cattle to buffalo. A total of 15,745 SNPs were analyzed, of which 1562 showed 1% significance and 4742 with 5% significance, which were associated for all traits studied. After application of Bonferronis correction for multiple tests of the traits analyzed, we found 2 significant SNPs placed on cattle chromosomes BTA15 and BTA20, which are homologous to buffalo chromosomes BBU16 and BBU19, respectively. In this genome association study, we found several significant SNPs affecting buffalo milk production and quality. Furthermore, the use of the high-density bovine BeadChip was suitable for genomic analysis in buffaloes. Although extensive chromosome arm homology was described between cattle and buffalo, the exact chromosomal position of SNP markers associated with these economically important traits in buffalo can be determined only through buffalo genome sequencing.

Expression of genes related to mitochondrial function in Nellore cattle divergently ranked on residual feed intake

Several measures have been proposed to investigate and improve feed efficiency in cattle. One of the most commonly used measure of feed efficiency is residual feed intake (RFI), which is estimated as the difference between actual feed intake and expected feed intake based on the animal’s average live weight. This measure permits to identify and select the most efficient animals without selecting for higher mature weight. Mitochondrial function has been indicated as a major factor that influences RFI. The analysis of genes involved in mitochondrial function is therefore an alternative to identify molecular markers associated with higher feed efficiency. This study analyzed the expression of PGC1α, TFAM, UCP2 and UCP3 genes by quantitative real-time PCR in liver and muscle tissues of two groups of Nellore cattle divergently ranked on RFI values in order to evaluate the relationship of these genes with RFI. In liver tissue, higher expression of TFAM and UCP2 genes was observed in the negative RFI group. Expression of PGC1α gene did not differ significantly between the two groups, whereas UCP3 gene was not expressed in liver tissue. In muscle tissue, higher expression of TFAM gene was observed in the positive RFI group. Expression of PGC1α, UCP2 and UCP3 genes did not differ significantly between the two groups. These results suggest the use of TFAM and UCP2 as possible candidate gene markers in breeding programs designed to increase the feed efficiency of Nellore cattle.

Genetic correlation estimates between beef fatty acid profile with meat and carcass traits in Nellore cattle finished in feedlot

The objective of this study was to estimate the genetic–quantitative relationships between the beef fatty acid profile with the carcass and meat traits of Nellore cattle. A total of 1826 bulls finished in feedlot conditions and slaughtered at 24xa0months of age on average were used. The following carcass and meat traits were analysed: subcutaneous fat thickness (BF), shear force (SF) and total intramuscular fat (IMF). The fatty acid (FA) profile of the Longissimus thoracis samples was determined. Twenty-five FAs (18 individuals and seven groups of FAs) were selected due to their importance for human health. The animals were genotyped with the BovineHD BeadChip and, after quality control for single nucleotide polymorphisms (SNPs), only 470,007 SNPs from 1556 samples remained. The model included the random genetic additive direct effect, the fixed effect of the contemporary group and the animal’s slaughter age as a covariable. The (co)variances and genetic parameters were estimated using the REML method, considering an animal model (single-step GBLUP). A total of 25 multi-trait analyses, with four traits, were performed considering SF, BF and IMF plus each individual FA. The heritability estimates for individual saturated fatty acids (SFA) varied from 0.06 to 0.65, for monounsaturated fatty acids (MUFA) it varied from 0.02 to 0.14 and for polyunsaturated fatty acids (PUFA) it ranged from 0.05 to 0.68. The heritability estimates for Omega 3, Omega 6, SFA, MUFA and PUFA sum were low to moderate, varying from 0.09 to 0.20. The carcass and meat traits, SF (0.06) and IMF (0.07), had low heritability estimates, while BF (0.17) was moderate. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with BF were 0.04, 0.64 and −0.41, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with SF were 0.29, −0.06 and −0.04, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with IMF were 0.24, 0.90 and −0.67, respectively. The selection to improve meat tenderness in Nellore cattle should not change the fatty acid composition in beef, so it is possible to improve this attribute without affecting the nutritional beef quality in zebu breeds. However, selection for increased deposition of subcutaneous fat thickness and especially the percentage of intramuscular fat should lead to changes in the fat composition, highlighting a genetic antagonism between meat nutritional value and acceptability by the consumer.

Reaction norms for the study of genotype-environment interaction for growth and indicator traits of sexual precocity in Nellore cattle

The objective of this study was to quantify the magnitude of genotype-environment interaction (GxE) effects on age at first calving (AFC), scrotal circumference (SC), and yearling weight (YW) in Nellore cattle using reaction norms. For the study, 89,152 weight records of female and male Nellore animals obtained at yearling age were used. Genetic parameters were estimated with a single-trait random-regression model using Legendre polynomials as base functions. The heritability estimates were of low to medium magnitude for AFC (0.05 to 0.47) and of medium to high magnitude for SC (0.32 to 0.51) and YW (0.13 to 0.72), and increased as the environmental gradient became more favorable. The genetic correlation estimates ranged from 0.25 to 1.0 for AFC, from 0.71 to 1.0 for SC, and from 0.42 to 1.0 for YW. High Spearman correlation coefficients were obtained for the three traits, ranging from 0.97 to 0.99. The reaction norms along the environmental gradient of 10 sires each with the highest or lowest breeding value for YW predicted by single-trait analysis demonstrated more plastic phenotypes for YW and more robust phenotypes for SC. The effect of GxE was most important for YW and AFC with respect to SC. When animals are selected for higher SC or YW or lower AFC, considering or not the GxE effect, it is expected that the same animals will be selected. The reaction norms obtained based on sire breeding values along the environmental gradient showed that animals with extreme breeding values respond differently as environmental conditions improve.

Study of lipid metabolism-related genes as candidate genes of sexual precocity in Nellore cattle.

The objective of this study was to identify associations between known polymorphisms in genes related to adipose tissue and sexual precocity in Nellore cattle. A total of 1689 precocious and non-precocious heifers belonging to farms participating in Conexão Delta G breeding program were studied. SNPs from the Illumina High-Density Bovine SNP BeadChip were used. This chip contains 777,000 SNPs located within the region of the candidate genes at a distance of up to 5 kb, considering that linkage disequilibrium (LD) exists at this distance. Linear models were used for statistical analysis. The fastPHASE and GenomeStudio programs were used for haplotype reconstruction and LD analysis based on r2 statistics. Fifty-seven candidate genes and 443 SNPs were analyzed: among the latter, 370 SNPs formed 83 haplotypes, while the remaining SNPs were studied separately. Statistical analysis showed that only three haplotypes, one haplotype consisting of two SNPs located in the FABP4 gene and two haplotypes consisting of four and two SNPs located in the PPP3CA gene, had a significant effect on sexual precocity at P < 0.05. It can be concluded that the FABP4 and PPP3CA genes influence sexual precocity and may therefore be used in selection programs designed to improve sexual precocity in Nellore cattle.

Water buffalo genome characterization by the Illumina BovineHD BeadChip.

To define the best strategies for genomic association studies and genomic selection, it is necessary to determine the extent of linkage disequilibrium (LD) and the genetic structure of the study population. The current study evaluated the transference of genomic information contained in the Illumina BovineHD BeadChip from cattle to buffaloes, and assessed the extent of the LD in buffaloes. Of the 688,593 bovine single nucleotide polymorphism (SNP) that were successfully genotyped from the 384 buffalo samples, only 16,580 markers were polymorphic, and had minor allele frequencies greater than 0.05. A total of 16,580 polymorphic SNPs were identified, which were uniformly distributed throughout the autosomes, because the density and mean distance between markers were similar for all autosomes. The average minor allele frequency for the 16,580 SNPs was 0.23. The overall mean LD for pairs of adjacent markers was 0.29 and 0.71, when measured as for r2 and |D|, respectively. The 16,580 polymorphic SNPs were matched to Bos taurus chromosome in the current bovine genome assembly (Btau 4.2), and could be utilized in association studies. In conclusion, the Illumina BovineHD BeadChip contains approximately 16,580 polymorphic markers for the water buffalo, which are broadly distributed across the genome. These data could be used in genomic association and genomic selection studies; however, it might be necessary to develop a panel with specific SNP markers for water buffaloes.

Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr ( Bos indicus ) dairy cattle

BackgroundRuns of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED).ResultsROH were identified in all animals, with an average number of 55.12u2009±u200910.37 segments and a mean length of 3.17xa0Mb. Short segments (ROH1–2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28xa0Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length.ConclusionsGenes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records.