Miriam Piles

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

 PhD in Quantitative Genetics and Animal Breeding

About

133
Publications
12,858
Reads
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1,525
Citations
Citations since 2016
63 Research Items
699 Citations
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
Introduction
Miriam Piles currently works at the Animal Breeding and Genetics Programme, IRTA Institute of Agrifood Research and Technology. Miriam does research in Animal Science.

Publications

Publications (133)
Article
Full-text available
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....
Article
Full-text available
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...
Article
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Poster
Full-text available
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...
Article
Full-text available
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...
Chapter
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Poster
Full-text available
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...
Poster
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Book
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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)...
Book
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...
Book
Full-text available
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...
Conference Paper
Full-text available
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...
Article
Full-text available
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...
Data
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.
Data
Whole body weight of male and female CBA and STR/Ort mice at 10, 20 and 40 weeks of age.
Article
Full-text available
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...
Article
Full-text available
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[...
Article
Full-text available
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
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)...
Conference Paper
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...
Article
Full-text available
The objective of this study was to determine whether rabbits fed in a restricted regimen (75%) showed increased competition for feeding, drinking and use of specific areas of the cages as compared with those provided feed ad libitum . This evaluation was carried out by measuring their space utilisation in the cage, the incidence of agonistic behavi...
Article
The present work is focussed on the behavioural response of rabbits (Oryctolagus cuniculus) housed in typical commercial conditions subjected to two different environmental temperature circadian cycles: one below the combination of temperature and humidity that is considered as stressful for rabbits, and the other with some hours a day subjected to...
Article
Full-text available
The general aim of this research was to study the effect of high ambient temperature on the performance of does during lactation, specifically the following factors: average daily feed (ADFI) and water (ADWI) intakes, daily milk yield (DMY); milk composition: dry matter (DM), CP and gross energy (GE); doe BW (DW); individual kit weaning weight (IWW...
Article
Response on litter size ( LS: ) to selection based on EBV of the own trait and several indexes including EBV of one or more parameters of a reaction norm model ( RNM: ) was evaluated by simulation. The RNM described animal's performance under different environmental temperatures assuming that this has an animal-specific effect on LS beyond an anima...
Conference Paper
Abstract Text: Feed intake from 520 Duroc pigs distributed in pens of 10 animals was registered to obtain both daily Individual Feed Intake (IFI) and daily Pen average Feed Intake (PaFI). Correlation coefficients between Breeding Value (BV) predictions from PaFI and IFI records were computed with two models, including or not the pen effect. We ob...
Article
Summary The generation of reactive oxygen species associated with cryopreservation could be responsible for mammalian sperm damage and the limitable value of stored semen in artificial insemination. The aim of this study was to assess several antioxidant agents supplemented in a commercial freezing extender (Gent B®) in order to improve post-thaw r...
Article
The objective of this research was assess the male contribution to the number of implanted embryos and embryo survival estimated as the rate of variance due male genetic and permanent environmental effects regarding total variance. In prolific species, the number of embryos and embryo survival at early stages of gestation could be considered as fer...
Article
This research aimed at assessing the efficacy of non-parametric procedures to improve the classification of the ejaculates in the artificial insemination (AI) centers according to their fertility rank predicted from characteristics of the AI doses. A total of 753 ejaculates from 193 bucks were evaluated at three different times from 5 to 9 months o...
Article
Full-text available
This paper reviews the current genetic knowledge on issues related with the efficient use of bucks in artificial insemination (AI). Differences between lines have been found to be relevant in semen production and quality traits not necessarily related to their specialisation as maternal or paternal lines. Accurate heritability estimates indicate th...