Genetic relationship of discrete-time survival with fertility and production in dairy cattle using bivariate models

Bivariate analyses of functional longevity in dairy cattle measured as survival to next lactation (SURV) with milk yield and fertility traits were carried out. A sequential threshold-linear censored model was implemented for the analyses of SURV. Records on 96 642 lactations from 41 170 cows were used to estimate genetic parameters, using animal models, for longevity, 305 d-standardized milk production (MY305), days open (DO) and number of inseminations to conception (INS) in the Spanish Holstein population; 31% and 30% of lactations were censored for DO and INS, respectively. Heritability estimates for SURV and MY305 were 0.11 and 0.27 respectively; while heritability estimates for fertility traits were lower (0.07 for DO and 0.03 for INS). Antagonist genetic correlations were estimated between SURV and fertility (-0.78 and -0.54 for DO and INS, respectively) or production (-0.53 for MY305), suggesting reduced functional longevity with impaired fertility and increased milk production. Longer days open seems to affect survival more than increased INS. Also, high productive cows were more problematic, less functional and more liable to being culled. The results suggest that the sequential threshold model is a method that might be considered at evaluating genetic relationship between discrete-time survival and other traits, due to its flexibility

A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project

 Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits

Response: Commentary: Past, present and future of epigenetics applied to livestock breeding

Following our recent Review article (González-Recio et al., 2015), we received correspondence by Steele (2016). We thank Dr. Steele for his comments, which provide a thorough review of his work on human immunology, which has persuaded him that “hard types of soma-to-germline transfer are ongoing at very high frequency in human immune system germlines.” His and other researchers' studies on reverse transcriptase (RT) based feedback mechanisms showed that RNA could be retrotranscripted to DNA, and it can be inserted into the mammalian germline, and therefore be transferred to the progeny

A bio-economic model to improve profitability in a large national beef cattle population

A bio-economic model was developed for estimating economic values for use in improving profitability in a large national beef cattle population from birth to slaughter. Results were divided into fattening costs, production costs and income. Economic values were derived for 17 traits for two regions, mature weight (-0.43 € and -0.38 €/+1 kg of live weight), age at first calving (-0.13 € and -0.11 €/+1d), calving interval (-1.06 € and -1.02 €/+1d), age at last calving (0.03 € and 0.03 €/+1d), mortality 0-48 h (-5.86 € and -5.63 €/1% calves per cow and year), pre-weaning mortality (-5.96 € and -5.73 €/+1% calves per cow and year), fattening mortality (-8.23 € and -7.88 €/+1% calves per cow and year), adult mortality (-8.92 € and -7.34 €/+1% adult cows per cow and year), pre-weaning average daily gain (2.56 € and 2.84 €/+10g/d), fattening young animals average daily gain (2.65 € and 3.00 €/+10g/d), culled cow in fattening average daily gain (0.25 € and 0.16 €/+10g/d), culled cow dressing carcass percentage (3.09 € and 2.42 €/+1%), culled cow price (4.59 € and 3.59 €/+0.06 €/kg), carcass conformation score (16.39 € and 15.3 €/+1 SEUROP class), dressing carcass rate of calf (18.22 € and 18.23 €/+1%), carcass growth (9.00 € and 10.09 €/+10g of carcass weight/d) and age at slaughter (0.27 € and 0.44 €/+1d). Two sample herds were used to show the economic impact of calving interval and age at first calving shortening in the profit per slaughtered young animal, which was 178 € and 111 € for Herds A and B, respectively. The economic values of functional traits were reduced and production traits were enhanced when fertility traits were improved. The model could be applied in a Spanish national program

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle

The current research was carried out to determine the associations between the rumen microbiota and traits related with feed efficiency in a Holstein cattle population (n = 30) using whole metagenome sequencing. Improving feed efficiency (FE) is important for a more sustainable livestock production. The variability for the efficiency of feed utilization in ruminants is partially controlled by the gastrointestinal microbiota. Modulating the microbiota composition can promote a more sustainable and efficient livestock. This study revealed that most efficient cows had larger relative abundance of Bacteroidetes (P = 0.041) and Prevotella (P = 0.003), while lower, but non-significant (P = 0.119), relative abundance of Firmicutes. Methanobacteria (P = 0.004) and Methanobrevibacter (P = 0.003) were also less abundant in the high-efficiency cows. A de novo metagenome assembly was carried out using de Bruijn graphs in MEGAHIT resulting in 496,375 contigs. An agnostic pre-selection of microbial contigs allowed high classification accuracy for FE and intake levels using hierarchical classification. These microbial contigs were also able to predict FE and intake levels with accuracy of 0.19 and 0.39, respectively, in an independent population (n = 31). Nonetheless, a larger potential accuracy up to 0.69 was foreseen in this study for datasets that allowed a larger statistical power. Enrichment analyses showed that genes within these contigs were mainly involved in fatty acids and cellulose degradation pathways. The findings indicated that there are differences between the microbiota compositions of high and low-efficiency animals both at the taxonomical and gene levels. These differences are even more evident in terms of intake levels. Some of these differences remain even between populations under different diets and environments, and can provide information on the feed utilization performance without information on the individual intake level.info:eu-repo/semantics/publishedVersio

Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences

Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows.Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database.Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota

Challenge-based learning: Cross-university implementation in Animal Breeding

[ES] En este trabajo se examinan los resultados obtenidos de la implementación interuniversitaria del aprendizaje basado en retos (ABR) a través del uso de las tecnologías de la información y comunicación (TIC) en la asignatura de Mejora Genética Animal. El reto consistió en llevar a cabo la mejora genética de un rebaño de vacuno lechero, mediante de un software en línea, en un entorno con limitaciones de manejo y económicas reales. Los alumnos obtuvieron una evolución positiva de los resultados a lo largo del reto, confirmando al ABP como una herramienta útil en el aprendizaje de la aplicación de la mejora genética animal. Por otra parte, las encuestas realizadas a los alumnos mostraron, en todas las universidades, una alta satisfacción con este tipo de aprendizaje, aunque indicaron posibles mejoras en la explicación inicial del reto. La aplicación de ABR ha sido muy positiva tanto desde un punto de vista de participación y motivación de los alumnos, como con el desarrollo del pensamiento crítico a través de la aplicación práctica de conceptos teóricos.[EN] This paper examines the results obtained from the interuniversity implementation of challenge-based learning (RBL) using information and communication technologies (ICTs) in animal breeding. The challenge faced by students consisted of managing the genetic improvement of a dairy cattle herd in an environment with real management and economic constraints using an online software online. The students achieved a positive evolution of the results along the challenge, confirming the PBA as a useful tool in learning the application of animal breeding. On the other hand, the student surveys showed, in all universities, a high satisfaction with this type of learning, although they indicated possible improvements in the initial explanation of the challenge. The application of ABR has been very positive both from the point of view of student participation and motivation, as well as with the development of critical thinking by the practical application of theoretical concepts.Al Instituto de Ciencias de la Educación de la Universidad Politécnica de València por financiar el proyecto de innovación educativa PIME/20-21/203.Ibáñez-Escriche, N.; Casto-Rebollo, C.; Formoso Rafferty, N.; González Recio, O.; Casellas Vidal, J. (2021). Aprendizaje basado en retos: Implementación interuniversitaria en la asignatura de Mejora Genética Animal. Servicio de Publicaciones Universidad Zaragoza. 290-294. https://doi.org/10.26754/CINAIC.2021.0056S29029

Identification of loci associated with pathological outcomes in Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis using whole-genome sequence data

[EN]Bovine paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic granulomatous enteritis that affects cattle worldwide. According to their severity and extension, PTB-associated histological lesions have been classified into the following groups; focal, multifocal, and diffuse. It is unknown whether these lesions represent sequential stages or divergent outcomes. In the current study, the associations between host genetic and pathology were explored by genotyping 813 Spanish Holstein cows with no visible lesions (N = 373) and with focal (N = 371), multifocal (N = 33), and diffuse (N = 33) lesions in gut tissues and regional lymph nodes. DNA from peripheral blood samples of these animals was genotyped with the bovine EuroG MD Bead Chip, and the corresponding genotypes were imputed to whole-genome sequencing (WGS) data using the 1000 Bull genomes reference population. A genome-wide association study (GWAS) was performed using the WGS data and the presence or absence of each type of histological lesion in a case-control approach. A total of 192 and 92 single nucleotide polymorphisms (SNPs) defining 13 and 9 distinct quantitative trait loci (QTLs) were highly-associated (P <= 5 x 10(-7)) with the multifocal (heritability = 0.075) and the diffuse (heritability = 0.189) lesions, respectively. No overlap was seen in the SNPs controlling these distinct pathological outcomes. The identified QTLs overlapped with some QTLs previously associated with PTB susceptibility, bovine tuberculosis susceptibility, clinical mastitis, somatic cell score, bovine respiratory disease susceptibility, tick resistance, IgG level, and length of productive life. Pathway analysis with candidate genes overlapping the identified QTLs revealed a significant enrichment of the keratinization pathway and cholesterol metabolism in the animals with multifocal and diffuse lesions, respectively. To test whether the enrichment of SNP variants in candidate genes involved in the cholesterol metabolism was associated with the diffuse lesions; the levels of total cholesterol were measured in plasma samples of cattle with focal, multifocal, or diffuse lesions or with no visible lesions. Our results showed reduced levels of plasma cholesterol in cattle with diffuse lesions. Taken together, our findings suggested that the variation in MAP-associated pathological outcomes might be, in part, genetically determined and indicative of distinct host responses.Financial support for this study was provided by a Grant from the Spanish Ministry of Science, Innovation, and Universities (RTI2018-094192-R-C21) and by European Regional Development Funds (FEDER) to MAH. MC and GBB have been awarded fellowships from the National Institute for Agricultural Research (INIA) and the Spanish Ministry of Science, Innovation and Universities programs, respectively. This work has been possible thanks to the support of the computing infrastructure of the i2BASQUE Research and Academic Network. We gratefully acknowledge the Bull Genomes Consortium for providing accessibility to the WGS data that was used in this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Aplicación interuniversitaria del aprendizaje basado en retos en la asignatura de Mejora Genética Animal

[EN] This paper presents the results of the first year of the inter-university implementation of challenge-based learning (CBL) in animal breeding. The challenge faced by students from the Universitat Autónoma de Barcelona, the Universidad Politécnica de Madrid and the Universitat Politècnica de València consisted of managing the genetic improvement of a cattle herd in an environment with real management and economic constraints using DCBSP software. The results obtained by the students in the challenge showed an improvement throughout the challenge, which would indicate its usefulness in learning the application of animal breeding. Regarding the students' evaluation of the challenge. The results of the surveys showed high satisfaction with this type of learning in all universities, although they indicated possible improvements in the initial explanation of the challenge. The experience during the first course of pilot application of the CBL has been very positive from the point of view of student participation and motivation, as well as with the development of critical thinking through the practical application of theoretical concepts.[ES] En este trabajo se presentan los resultados del primer año de la implementación interuniversitaria del aprendizaje basado en retos en la asignatura de Mejora Genética Animal. El reto al que se enfrentaron los alumnos de la Universitat Autònoma de Barcelona, la Universidad Politécnica de Madrid y la Universitat Politècnica de València consistió en gestionar la mejora genética de un rebaño de vacuno lechero en un entorno con limitaciones de manejo y económicas reales a través de un software informático DCBS. Los resultados obtenidos por los alumnos en el reto evidenciaron una mejoría a lo largo del mismo, lo que indicaría su utilidad en el aprendizaje de la aplicación de de la mejora genética animal. Respecto a la valoración del reto por parte de los estudiantes, los resultados de las encuestas mostraron una satisfacción elevada con este tipo de aprendizaje en todas las universidades, aunque indicaron posibles mejoras en la explicación incial del reto. La experiencia durante el primer curso de aplicación piloto del ABR ha sido muy positiva tanto desde un punto de vista de participación y motivación de los alumnos, como con el desarrollo del pensamiento crítico a través de la aplicación práctica de conceptos teóricos.Ibáñez Escriche, N.; Casto Rebollo, C.; Formoso-Rafferty Castilla, N.; González Recio, O.; Casellas Vidal, J. (2021). Aplicación interuniversitaria del aprendizaje basado en retos en la asignatura de Mejora Genética Animal. En IN-RED 2021: VII Congreso de Innovación Edicativa y Docencia en Red. Editorial Universitat Politècnica de València. 104-113. https://doi.org/10.4995/INRED2021.2021.13464OCS10411