Miriam Piles

IRTA Institute of Agrifood Research and Technology | IRTA · Animal Breeding and Genetics Programme

Feed restriction is a common nutritional practice in rabbit farming; however, decreased feed intake can also signal potential digestive disorders at an early stage. This study endeavors to investigate the impact of feed restriction on selected productive traits and the urinary metabolome of juvenile rabbits across diverse genetic backgrounds. Our o...

This study explores how wearable accelerometers, small devices that measure acceleration, can help monitor the activity of growing rabbits. We equipped 16 rabbits with these devices and filmed them for two weeks. By watching the videos and using a special software we figure out what the rabbits were doing -- things like lying down, eating, moving a...

Precision livestock farming aims to individually and automatically monitor animal activity to ensure their health, well-being, and productivity. Computer vision has emerged as a promising tool for this purpose. However, accurately tracking individuals using imaging remains challenging, especially in group housing where animals may have similar appe...

The pig gut microbiota is a complex ecosystem composed of microbial guilds, which until recently were unknown. Here, we decomposed the pig fecal microbiota of 648 healthy pigs during the transition (n=400) and growing-finishing (n=248) periods in co-occurring bacterial communities defined as pig enterosignatures (pig ES). Our results indicate that...

Feeding represents the largest economic cost in meat production; therefore, selection to improve traits related to feed efficiency is a goal in most livestock breeding programs. Residual feed intake (RFI), that is, the difference between the actual and the expected feed intake based on animal's requirements, has been used as the selection criteria...

Background The effect of the cecal microbiome on growth of rabbits that were fed under different regimes has been studied previously. However, the term “effect” carries a causal meaning that can be confounded because of potential genetic associations between the microbiome and production traits. Structural equation models (SEM) can help disentangle...

Background The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits....

Background Feed efficiency during lactation involves a set of phenotypic traits that form a complex system, with some traits exerting causal effects on the others. Information regarding such interrelationships can be used to predict the effect of external interventions on the system, and ultimately to optimize management practices and multi-trait s...

Inbreeding depression in closed populations impairs animal fitness, health, and productivity. However, not all inbreeding is expected to be equally damaging. Recent inbreeding is thought to be more harmful than ancient inbreeding because selection decreases the frequency of unfavourable alleles with time. Accordingly, selection efficiency is improv...

El ciego del conejo alberga la comunidad microbiana más rica y diversa de su tracto gastrointestinal que influye sobre las condiciones ambientales de este órgano y sobre la disponibilidad de nutrientes del hospedador. Esta relación simbiótica hospedador-microbiota sugiere una adaptación evolutiva mutua que promovería el crecimiento de aquellos micr...

The aim of this study was to identify the regions involved in the genetic control of the composition of different microbial communities present in the rabbit cecum. The available material consisted of the genotypes (~200K SNPs) and a set of microbial traits representative of the cecal microbiota of 412 rabbits. Two approaches were used to identify...

This study compares the accuracy of prediction of total genetic effects, i.e. additive and non-additive genetic effects, of average daily gain (ADG) from single-nucleotide polymorphisms (SNPs) using radial basis function Support Vector Machine, (SVM) and a genome-enabled best linear unbiased prediction model (GBLUP) as benchmark. The target example...

Selecting for feed efficiency (FE) is challenging in rabbit breeding programs since individual feed intake (FI) of animals is not usually available. The current study raises the possibility that rabbits' cecal microbiota could be considered to predict FE and its component traits, i.e., growth and FI. Our dataset comprised the individual average dai...

This study aimed at predicting feed conversion ratio (FCR) of young rabbits from abundances of amplicon sequence variants (ASVs) to improve this trait by selecting animals with the most favorable microbiota and identifying the most relevant microorganisms involved in feed efficiency. Data come from two rabbit populations coming from paternal INRA 1...

Rabbit cecum hosts and constantly interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. The heritability of the abundances of these microorganisms remains unknown but previous studies in humans, pigs, or cattle have reported moderate heritabilities for specific microbial taxa. This study repo...

Gut microbiota plays an important role in nutrient absorption and could impact rabbit feed efficiency. This study aims at investigating such impact by evaluating the value added by microbial information for predicting individual growth and cage phenotypes related to feed efficiency. The dataset comprised individual average daily gain and cage-avera...

The purpose of the book is to present in one location a comprehensive overview of the progress of genetics in the rabbit, with a modern vision that integrates genomics to obtain a complete picture of the state of the art and of the applications in this species, defined according to the multiple uses and multi-faceted places that this species has in...

Gut microbiota plays an important role in nutrient absorption and could impact rabbit feed efficiency. This study aims at investigating such impact by evaluating the value added by microbial information for predicting individual growth and cage phenotypes related to feed efficiency. The dataset comprised individual average daily gain and cage-avera...

Background: Feed efficiency is a paramount concept for the environmental and economical sustainability of rabbit production. In this sense, identifying all the components involved in its determinism is highly desirable. Microbial communities inhabiting the intestinal tract play an important role in nutrient absorption and could also impact rabbit g...

Feature selection (FS, i.e., selection of a subset of predictor variables) is essential in high-dimensional datasets to prevent overfitting of prediction/classification models and reduce computation time and resources. In genomics, FS allows identifying relevant markers and designing low-density SNP chips to evaluate selection candidates. In this r...

This research assessed the ability of a Support Vector Machine (SVM) regression model to predict pig crossbred (CB) performance from various sources of phenotypic and genotypic information for improving crossbreeding performance at reduced genotyping cost. Data consisted of average daily gain (ADG) and residual feed intake (RFI) records and genotyp...

Aiming to study the effect of different management factors on rabbit cecal microbial composition and diversity, a 16S rDNA-based assessment through MiSeq platform was performed. Cecal samples were collected from 425 rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with food supplemented or free of...

Rabbit cecum harbors a complex microbial ecosystem whose members constantly interact between them and with their host to ensure homeostatic balance maintenance. Our objective was to estimate heritability of rabbit cecal microbiota in order to assess whether interactions with the host also occur at genetic level. 16S rDNA amplicon MiSeq sequencing w...

Microbial communities inhabiting gastrointestinal tract are expected to affect animal growth and feed efficiency given their well-known role in nutrient absorption and immunological processes. Our objective was to assess whether predictive ability of linear models for growth (G) and cage feed intake (FI) and feed conversion ratio (FCR) is improved...

Background: The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the leve...

The correlation between pedigree and genomic‐based inbreeding coefficients is usually discussed in the literature. However, some of these correlations could be spurious. Using partial correlations and information theory, it is possible to distinguish a significant association between two variables which is independent from associations with a third...

Feed efficiency (FE) is one of the most economically and environmentally relevant traits in the animal production sector. The objective of this study was to gain knowledge about the genetic control of FE in rabbits. To this end, GWASs were conducted for individual growth under two feeding regimes (full feeding and restricted) and FE traits collecte...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the leve...

Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...

Les mesures de l’ingéré sont les clés d’une sélection précise de l’efficacité alimentaire. Elles sont cependant coûteuses. De plus, ces performances dépendent de nombreuses composantes, telles que le niveau de production, l’activité et le comportement des animaux, leur aptitude à répondre à des stress, et leur capacité à digérer l’aliment. L’import...

Background To date, the molecular mechanisms that underlie residual feed intake (RFI) in pigs are unknown. Results from different genome-wide association studies and gene expression analyses are not always consistent. The aim of this research was to use machine learning to identify genes associated with feed efficiency (FE) using transcriptomic (RN...

As a result of the genetic selection for prolificacy and the improvements in the environment and farms management, litter size has increased in the last few years so that energy requirements of the lactating sow are greater. In addition, selection for feed efficiency of growing pigs is also conducted in maternal lines, and this has led to a decreas...

Models for genetic evaluation of feed efficiency (FE) for animals housed in groups when they are either fed ad libitum (F) or on restricted (R) feeding were implemented. Definitions of FE on F included group records of feed intake () and individual records of growth rate (GF) and metabolic weight (MF). Growth rate (GR) as FE measurement on R was us...

This study aimed to compare different nonlinear functions to describe the growth curve of European quails and to estimate growth curve parameters, (co)variance components, and genetic and systematic effects that affected the curve using a hierarchical Bayesian model that allows joint estimation. Three different models were fitted in the first stage...

Background: Indirect genetic effects (IGE) are important components of various traits in several species. Although the intensity of social interactions between partners likely vary over time, very few genetic studies have investigated how IGE vary over time for traits under selection in livestock species. To overcome this issue, our aim was: (1) t...

To gain insight into the importance of carefully selecting the sampling area for intestinal microbiota studies, cecal and fecal microbial communities of Caldes meat rabbit were characterized. The animals involved in the study were divided in two groups according to the feed intake level they received during the fattening period; ad libitum (n = 10)...

Feed efficiency (FE) for maintenance and for growth in two rabbit lines with different productive aptitude was studied. A total of 29 rabbits from Prat line (P; selected for litter size at weaning) and 29 rabbits from Caldes line (C; selected for growth rate at fattening), equally distributed between males (M) and females (F) were used. Kits weaned...

Even if there are evidences that the intensity of social interactions between partners vary with time, very few genetic studies have investigated how social genetic effects (SGEs) vary over time. To overcome this issue, the objectives of the present study were to analyse longitudinal records of average daily gain (ADG) in rabbits and to evaluate, b...

Aiming to study the existence of a genetic determinism of rabbits’ gut microbiota, a 16S rDNA-based assessment through a MiSeq platform was conducted. Cecal samples, collected from 451 rabbits bred in two experimental farms and fed with the same diet supplemented or not with antibiotics but under different intake levels, were assessed. A total of 9...

An alternative implementation of the animal model including indirect genetic effect (IGE) is presented considering pair-mate-specific interaction degrees to improve the performance of the model. Data consisted of average daily gain (ADG) records from 663 pigs kept in groups of 10 to 14 mates during the fattening period. Three types of models were u...

Parameter estimates (95% confidence interval) of the fixed effects and variances for the random effects and residual for the first 4 gait principal components using linear mixed effects models.

Whole body weight of male and female CBA and STR/Ort mice at 10, 20 and 40 weeks of age.

Objectives: Human osteoarthritis (OA) is detected only at late stages. Male STR/Ort mice develop knee OA spontaneously with known longitudinal trajectory, offering scope to identify OA predisposing factors. We exploit the lack of overt OA in female STR/Ort and in both sexes of parental, control CBA mice to explore whether early divergence in tibial...

Background Most rabbit production farms apply feed restriction at fattening because of its protective effect against digestive diseases that affect growing rabbits. However, it leads to competitive behaviour between cage mates, which is not observed when animals are fed ad libitum. Our aim was to estimate the contribution of direct (\documentclass[...

Background Improving feed efficiency (\({\text{FE}}\)) is a key factor for any pig breeding company. Although this can be achieved by selection on an index of multi-trait best linear unbiased prediction of breeding values with optimal economic weights, considering deviations of feed intake from actual needs (\({\text{RFI}}\)) should be of value for...

Osteoarthritis (OA), affecting joints and bone, causes physical gait disability with huge socio-economic burden; treatment remains palliative. Roles for antioxidants in protecting against such chronic disorders have been examined previously. Sulforaphane is a naturally occurring antioxidant. Herein, we explore whether SFX-01®, a stable synthetic fo...

Simultaneous Bacteria and Archaea detection by 16S rDNA-based MiSeq sequencing was performed to assess rabbit gut microbiota composition subjected to different factors: feeding regime (ad libitum (aL) vs. restricted (R)), presence/absence of antibiotics in the diet, and the global environmental conditions defined by the farm. Caecum samples from 66...

Aiming to study the effect of restricted and ad libitum feeding regimes on intestinal microbiome composition in rabbits, a 16S rDNA-based assessment through MiSeq platform was performed. Caecum and faeces samples from eleven 66-days-old animals fed ad libitum and thirteen fed under restricted (75%) standard diet were assessed. With a QIIME pipeline...

The resazurin reduction test (RRT) is a useful technique to assess the metabolic rate of sperm cells. RRT depends on the ability of metabolically active cells to reduce the non-fluorescent dye resazurin to the fluorescent resorufin. The aim of this study was to develop a vital fluorometric method to evaluate metabolic activity of rabbit sperm cells...

The interaction between the genotype and feeding regimen (GxE) for carcass traits was estimated from data corresponding to 4981 animals under ad libitum (AD; 2557 individuals) or restricted (RF; 2424) feeding. Body weight at slaughter (BWS), carcass weight (CW) and dressing out percentage (DoP) were analyzed by using Bayesian multivariate Linear An...

Estimates of the relative importance of use of feed for different biological functions are reported for a commercial Duroc pig line selected since 1991 for backfat thickness (BT180) and final body weight (BW180). Data consisted on daily feed intake (FI), and weekly body weight (BWG) and back thickness gains (BTG) from 1076 pigs (15-25 weeks of age)...

The study aimed at assessing the possible existence of an interaction between genotype and feeding regimen (GxE) for presence/absence of enteropathy (EN) respiratory symptoms (RS), poor body condition (PBC) and mortality (MO) due to unspecific causes during the fattening period. Animals were submitted to two feeding regimens: ad libitum AD (4024 in...