Effect of genomic X-chromosome regions on Nelore bull fertility.

Scrotal circumference (SC) is a commonly used trait related to sexual precocity in bulls. Genome-wide association studies have uncovered a lot of genes related to this trait, however, only those present on autosomes. The inclusion of the second biggest chromosome (BTAX) can improve the knowledge of the genetic architecture of this trait. In this study, we performed a weighted, single-step, genome-wide association study using a 777 k BovineHD BeadChip (IllumHD) to analyze the association between SNPs and SC in Brazilian Nelore cattle. Phenotypes from 79,300 males and 3263 genotypes (2017 from females and 1246 from males)-(39,367 SNPs markers located at ChrX) were used. We identified eight regions on chromosome X that displayed important associations with SC. The results showed that together the genomic windows explained 28.52% of the genetic variance for the examined trait. Genes with potential functions in reproduction and fertility regulation were highlighted as candidates for sexual precocity rates in Nelore cattle (AFF2 and PJA1). Moreover, we found 10 genes that had not previously been identified as being associated with sexual precocity traits in cattle. These findings will further advance our understanding of the genetic architecture, considering mainly the presence of the chromosome X, for indicine cattle reproductive traits, being useful in the context of genomic prediction in beef cattle.

Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome.

BACKGROUND: Imputation accuracy among other things depends on the size of the reference panel, the marker's minor allele frequency (MAF), and the correct placement of single nucleotide polymorphism (SNP) on the reference genome assembly. Using high-density genotypes of 3938 Nellore cattle from Brazil, we investigated the accuracy of imputation from 50 K to 777 K SNP density using Minimac3, when map positions were determined according to the bovine genome assemblies UMD3.1 and ARS-UCD1.2. We assessed the effect of reference and target panel sizes on the pre-phasing based imputation quality using ten-fold cross-validation. Further, we compared the reliability of the model-based imputation quality score (Rsq) from Minimac3 to the empirical imputation accuracy. RESULTS: The overall accuracy of imputation measured as the squared correlation between true and imputed allele dosages (R2dose) was almost identical using either the UMD3.1 or ARS-UCD1.2 genome assembly. When the size of the reference panel increased from 250 to 2000, R2dose increased from 0.845 to 0.917, and the number of polymorphic markers in the imputed data set increased from 586,701 to 618,660. Advantages in both accuracy and marker density were also observed when larger target panels were imputed, likely resulting from more accurate haplotype inference. Imputation accuracy increased from 0.903 to 0.913, and the marker density in the imputed data increased from 593,239 to 595,570 when haplotypes were inferred in 500 and 2900 target animals. The model-based imputation quality scores from Minimac3 (Rsq) were systematically higher than empirically estimated accuracies. However, both metrics were positively correlated and the correlation increased with the size of the reference panel and MAF of imputed variants. CONCLUSIONS: Accurate imputation of BovineHD BeadChip markers is possible in Nellore cattle using the new bovine reference genome assembly ARS-UCD1.2. The use of large reference and target panels improves the accuracy of the imputed genotypes and provides genotypes for more markers segregating at low frequency for downstream genomic analyses. The model-based imputation quality score from Minimac3 (Rsq) can be used to detect poorly imputed variants but its reliability depends on the size of the reference panel and MAF of the imputed variants.

Mapping genomic regions for reproductive traits in beef cattle: Inclusion of the X chromosome.

Although the second largest chromosome of the genome, the X chromosome is usually excluded from genome-wide association studies (GWAS). Considering the presence and importance of genes on this chromosome that are involved in reproduction, the aim of this study was to evaluate the effect of its inclusion in GWAS on reproductive traits (scrotal circumference [SC], early pregnancy [P16] and age at first calving [AFC]) in a Nelore herd. Genotype data from 3,263 animals with the above-mentioned phenotypes were used. The results showed an increase in the variances explained by the autosomal markers for all traits when the X chromosome was not included. For SC, there was an increase of more than 10% for the windows on chromosomes 2 and 6. For P16, the effect was increased by almost 20% for windows on chromosome 5. The same pattern was found for AFC, with an increase of more than 10% for the most important windows. The results indicate that the noninclusion of the X chromosome can overestimate the effects of autosomes on SC, P16 and AFC not only because of the additive effect of the X chromosome itself but also because of its epistatic effect on autosomal genes.

Prediction of genomic breeding values for reproductive traits in Nellore heifers.

The objective of this study was to assess the accuracy of genomic predictions for female reproductive traits in Nellore cattle. A total of 1853 genotyped cows and 305,348 SNPs were used for genomic selection analyses. GBLUP, BAYESCπ, and IBLASSO were applied to estimate SNP effects. The pseudo-phenotypes used as dependent variables were: observed phenotype (PHEN), adjusted phenotype (CPHEN), estimated breeding value (EBV), and deregressed estimated breeding value (DEBV). Predictive abilities were assessed by the average correlation between CPHEN and genomic estimated breeding value (GEBV) and by the average correlation between DEBV and GEBV in the validation population. Regression coefficients of pseudo-phenotypes on GEBV in the validation population were indicators of prediction bias in GEBV. BAYESCπ showed higher predictive ability to estimate SNP effects and GEBV for all traits.

Dinâmica química, microbiológica e física da silagem de farelo úmido de glúten de milho / Physical, chemical and microbiological dynamics of wet corn gluten feed silage

Objetivou-se avaliar aspectos físico-químicos e microbiológicos do farelo úmido de glúten de milho (FUGM) em função do tempo de ensilagem. O FUGM foi avaliado em silos experimentais e, nos dias um, três, sete, 14, 21, 28 e 42, foram realizadas as avaliações físicas, químicas e microbiológicas da silagem. O delineamento experimental foi inteiramente casualizado com quatro repetições e obtidas equações de regressão em função do tempo. O tempo de ensilagem não afetou (P>0,05) o percentual de fibra em detergente neutro, fibra em detergente ácido, proteína bruta, matéria mineral, extrativos não-nitrogenados, nutrientes digestíveis totais e contagem de clostrídios. Os teores de matéria seca, extrato etéreo, perdas por efluentes, perdas por gases e população de bactérias láticas variaram entre 46,54 e 49,05%; 0,96 e 1,71%; 17,97 e 35,14g kg-1; 1,90 e 5,68% e 5,0 e 6,9log UFCg-1 de silagem, respectivamente, todos com equações com r2≤0,6.O pH (Y=4,12926-0,00894dias+0,00024126dias2,r2=0,75) e a temperatura (Y=19,82657+0,11734dias-0,00502dias2,r2=0,73) tiveram seus menores e maiores valores, respectivamente, em 18,5 e 11,7 dias. A contagem de bolores e leveduras sofreu redução em função do tempo de ensilagem (Y=6,8983-0,0363dias,r2=0,84). A ensilagem permite eficiente conservação dos aspectos químicos, microbiológicos e físicos do FUGM até 42 dias de ensilagem.

This study aimed to evaluate physicochemical and microbiological aspects of wet corn gluten feed (WCGF) according to time of ensilage. The WCGF was evaluated in experimental silos and after one, three, seven, 14, 21, 28 and 42 days, physical, chemical and microbiological evaluation of the silage was carried out. The results were analyzed as a completely randomized design with four replications and regression equations as a function of time. The number of days of ensiling did not affect neutral detergent fiber, acid detergent fiber, crude protein, mineral matter, non-nitrogenous extract and total digestive nutrients percentages, as well as clostridia count. Dry matter, ether extract, effluents losses and percentages of gas losses and lactic acid bacteria count with variations of 46.54 and 49.05%; 0.96 and 1.71%; 17.97 and 35.14g kg-1; 1.90 and 5.68% and 5.0 and 6.9log CFUg-1 of silage, respectively, all had low coefficient of determination (r2≤0.6).The pH (Y=4.12926-0.00894days+0.00024126days2,r2=0.75) and temperature (19.82657+0.11734days-0.00502days2,r2=0.73) had their minor and major values, respectively, in 18.5 and 11.7 days. Moulds and yeasts count decrease with time of ensilage (Y=6.8983-0.0363days,r2=0.84). The ensiling allows efficient conservation of the chemical, microbiological and physical aspects of WCGF until 42 days of ensilage.