Novel phenotypes of feeding and social behaviour and their relationship with individual rabbit growth and feed efficiency

Due to the lack of a recording system for individual consumption of group-housed rabbits, published studies about feeding behaviour are based on information recorded at the group- and not at the individual level and periods covering only a few days or, in some cases, only part of a day. Such information could be used to inform rabbit management systems but cannot be used for genetic selection. We aimed to generate and use information from a novel automated feeder for group-housed rabbits to identify new phenotypes for individual animals that could be incorporated into breeding programs to improve feed efficiency and social behaviour under different feeding regimens. At 39 d of age, rabbits from 15 batches were placed in cages and fed ad libitum to become used to the electronic feeder. From 42 to 58-59 d, one group of 1 086 rabbits was fed ad libitum (AL), while another group of 1 134 rabbits was fed on a restricted feeding schedule (R) by limiting the feeding time to the period between 1800 and 0600 h of the following day. We implemented a reliable multivariate method to remove anomalous feeding behaviour records. We then defined novel traits for feeding behaviour that apply to both types of feeding regimes, and for social behaviour that indicates an animal's rank within the cage hierarchy. We based these traits on feeder records and a biologically sound definition of a meal. Finally, we estimated the phenotypic correlations of those traits with growth and feed efficiency traits. Our findings demonstrate that variables about resource distribution among cage mates and an animal's priority for feed access were found to be good indicators of an animal's dominant or subordinate status within the cage. Based on results obtained in R animals (results were similar in AL animals), the most efficient animals were those that ate less frequently (phenotypic correlation with feed conversion ratio, rho = 0.6), and consumed smaller amounts per meal (rho = 0.7), spent less time at the feeder (rho = 0.4), and appeared to be subordinate, as they did not have priority access to the feeder (rho = -0.3), and had the smallest share of resources (range of rho = 0.2-0.6). We conclude that quantifying feeding and social behaviour traits can enhance the understanding of the mechanisms through which individuals exert their effects on the performance of their cage mates.

Survival analysis of productive life in Florida dairy goats using a Cox proportional hazards model

Longevity is an economically important trait, since extending the functional life of a doe would allow us to keep the most productive females in the herd as long as possible, and this could result in the increased profitability of dairy farms. Thus, the objectives of this study were to determine the most important factors that influence the length of productive life (LPL) of female Florida goats and to estimate its genetic additive variance using a Cox proportional hazards model. The data consisted of 70,695 productive life records from 25,722 Florida females kidding between 2006 and 2020. A total of 19,495 does had completed their productive life while 6227 (24.2%) does had censored information. The pedigree contained information on 56,901 animals. The average censoring age and average failure age after first kidding for LPL were 36 and 47 months respectively. The model included, as time-independent effects, the age at first kidding and the interaction between herd, year and season of birth of the doe, and as time-dependent effects, the age at kidding, the interaction between herd, year and season of kidding, the within-herd class of milk production deviation, and the interaction between the lactation number and the stage of lactation. All fixed effects had a significant effect on LPL (p < 0.05). Does with older ages at the first kidding and an earlier age at kidding were at higher risk of being culled. A large difference among herds was observed in terms of culling risk, which highlighted the importance of adequate management practices. Also, high-producing does were less likely to be culled. The estimate of the additive genetic variance was 1.844 (in genetic standard deviation), with a heritability estimate of 0.58 ± 0.012. The results of this study are expected to contribute to the development of a genetic model for genetic evaluation of the length of the productive life of Spanish dairy goat breeds.

Inbreeding depression on growth and prolificacy traits in two lines of rabbit

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 improved by inbreeding in a process called purging. This research aimed to quantify inbreeding depression on growth and prolificacy traits in two lines of rabbits selected for just one growth (Caldes line) or prolificacy (Prat line) trait, and also to find some evidence of purging of deleterious alleles by selection. Caldes line comprised 51 generations and 124,371 animals in the pedigree. Prat line comprised 34 generations and 161,039 animals in the pedigree. The effects of old, intermediate, and new inbreeding (Fold, Fint, and Fnew), as well as total cumulated classical inbreeding (F) and 3 measurements of ancestral inbreeding (AHC, Fa.K, and Fa.B) were estimated for average daily gain (ADG), slaughter weight (SW), weaning weight (WW), born alive (BA), the total number of kits (NT), and the number of weaned kits (NW). There was a clear inbreeding depression for all growth and prolificacy traits in the Caldes line (-7.19 g/d, -0.45 kg, -0.25 kg, -6 kits, -4 kits, and -4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively) and also in Prat line (-7.48 g/d, -0.31 kg, -0.11 kg, -4 kits, -5 kits, and -4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively). The inbreeding partition appears to be a reliable alternative for assessing inbreeding depression and purging. Thus, for example, in the Caldes line and for ADG the regression coefficients were -7.61, -5.41, and 7.76 g/d per unit of increase in Fnew, Fint, and Fold, respectively. In addition, AHC and Fa.B may provide more accurate evidence of purging than Fa.K. This study confirms the existence of inbreeding depression for growth and prolificacy traits in both lines of rabbits and shows evidence of purging of deleterious recessive alleles involved both in growth and prolificacy, independently of the selection criteria established in the line.

Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues

BACKGROUND

In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.

RESULTS

More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.

CONCLUSIONS

The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.

Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models

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 such a complex interplay by decomposing the effect on a production trait into direct host genetics effects and indirect host genetic effects that are exerted through microbiota effects. These indirect effects can be estimated via structural coefficients that measure the effect of the microbiota on growth while the effects of the host genetics are kept constant. In this study, we applied the SEM approach to infer causal relationships between the cecal microbiota and growth of rabbits fed under ad libitum (ADG_AL) or restricted feeding (ADG_R).

RESULTS

We identified structural coefficients that are statistically different from 0 for 138 of the 946 operational taxonomic units (OTU) analyzed. However, only 15 and 38 of these 138 OTU had an effect greater than 0.2 phenotypic standard deviations (SD) on ADG_AL and ADG_R, respectively. Many of these OTU had a negative effect on both traits. The largest effects on ADG_R were exerted by an OTU that is taxonomically assigned to the Desulfovibrio genus (- 1.929 g/d, CSS-normalized OTU units) and by an OTU that belongs to the Ruminococcaceae family (1.859 g/d, CSS-normalized OTU units). For ADG_AL, the largest effect was from OTU that belong to the S24-7 family (- 1.907 g/d, CSS-normalized OTU units). In general, OTU that had a substantial effect had low to moderate estimates of heritability.

CONCLUSIONS

Disentangling how direct and indirect effects act on production traits is relevant to fully describe the processes of mediation but also to understand how these traits change before considering the application of an external intervention aimed at changing a given microbial composition by blocking/promoting the presence of a particular microorganism.

Analysis of the causal structure of traits involved in sow lactation feed efficiency

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 selection strategies. Structural equation models can be used to infer the magnitude of the different causes of such interrelationships. The causal network necessary to fit structural equation models can be inferred using the inductive causation (IC) algorithm. By implementing these statistical tools, we inferred the causal association between the main energy sources and sinks involved in sow lactation feed efficiency for the first time, i.e., daily lactation feed intake (dLFI) in kg/day, daily sow weight balance (dSWB) in kg/day, daily litter weight gain (dLWG) in kg/day, daily back fat thickness balance (dBFTB) in mm/day, and sow metabolic body weight (SMBW) in kg^0.75. Then, we tested several selection strategies based on selection indices, with or without dLFI records, to improve sow efficiency during lactation.

RESULTS

The IC algorithm using 95% highest posterior density (HPD_95%) intervals resulted in a fully directed acyclic graph, in which dLFI and dLWG affected dSWB, the posterior mean of the corresponding structural coefficients (PM_λ) being 0.12 and - 0.03, respectively. In turn, dSWB influenced dBFTB and SMBW, with PM_λ equal to 0.70 and - 1.22, respectively. Multiple indirect effects contributed to the variances and covariances among the analyzed traits, with the most relevant indirect effects being those involved in the association between dSWB and dBFTB and between dSWB and SMBW. Selection strategies with or without phenotypic information on dLFI, or that hold this trait constant, led to the same pattern and similar responses in dLFI, dSWB, and dLWG.

CONCLUSIONS

Selection based on an index including only dBFTB and dLWG records can reduce dLFI, keep dSWB constant or increase it, and increase dLWG. However, a favorable response for all three traits is probably not achievable. Holding the amount of feed provided to the sows constant did not offer an advantage in terms of response over the other strategies.

Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota

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. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota.

Results

Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects.

Conclusions

This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00738-2.

Genotype by feeding regimen interactions for slaughter traits in rabbit and expected responses under restricted and full feeding

The interaction between the genotype and feeding regimen (G×FR) for slaughter traits was estimated from data corresponding to 2557 animals under full (FF) and 2424 with restricted feeding (RF). Expected responses to selection under different scenario regarding feeding regimen were also calculated. Body weight at slaughter (SW), carcass weight (CW) and dressing out percentage (DoP) were analysed by using linear animal models in which records obtained under different feeding regimes were treated as different traits. Animals belonged to Caldes line, selected for average daily gain (G) under ad libitum feeding. The selection process information was included in the analyses. Marginal posterior mean of heritabilities were 0.102 for G, and 0.364, 0.257 and 0.167 for SW, CW and DoP under FF feeding. The corresponding values for animals fed on RF were 0.243, 0.203 and 0.379 for SW, CW and DoP, respectively. Genetic correlations between G and CW were positive and moderate, and those between G and DoP were low. The estimated genetic correlation between SW, CW and DoP under different feeding regimens were: 0.73, 0.69 and 0.87, respectively. These correlations cannot be said to be far enough from one to generate relevant G×FR interaction variance, which were estimated to be only 11.1%, 8.6% and 5.3% of the mean of the phenotypic variance for SW, CW and DoP, respectively. This lack of G×FR interaction variance, jointly with the higher heritability of DoP under RF, explains that the genetic improvement of DoP can be done more efficiently recording traits on animals under RF, even if the interest is on the performances under FF, i.e. by indirect selection.

Improvement preclinical and clinical skills for dental preparations using assisted training software

INTRODUCTION

Digital workflow is currently available for different fields of dentistry. Additionally, to clinical use, digital technology is focused on the education and training of students. The objective of this study was to show the potential benefit of the use of digital CAD / CAM technology and assisted training software in the evaluation and improvement of student skills in preclinical and clinical environments.

MATERIALS AND METHODS

30 models of dental preparations were digitalised and analysed by PrepCheck software, after that was used the PrepCheck Report tool, gathering the results of the analysis in an automatically created report and containing the following parameters: analysis of the conicity, distance between a preparation and the opposing jaw, analysis of the type of preparation, quality of the margin and total occlusal convergence.

RESULTS

The use of the PrepCheck Pro 2.1 software makes evident the errors made by the students during the biomechanical preparation, since they generally change the inclination, in order to have less difficulties to comply with the parameters established in the preparations. Regarding the evaluated parameters for anterior and posterior fixed prosthesis) such as: 'Conicity', 'Type of preparation' and 'Distance to the antagonist', the preparations, in their majority, were classified within the tolerance range with of 50-60%, 80-93% and 53-67%, respectively.

CONCLUSION

This pilot study demonstrated the benefits of using software and CAD/CAM technology in both preclinical and clinical environments for teaching and learning. Its use on preclinical environments allows the student observe qualitatively and quantitatively a preparation flaws when compared to a master's preparation. Lastly, the ease of visualising errors associated with magnification would allow students to improve their skills.

Evaluation of trueness and precision of two intraoral scanners and a conventional impression: an in vivo clinical study

OBJECTIVE

To evaluate, in vivo, trueness and precision of two intraoral scanners, CEREC Omnicam (OMNI) and CEREC Primescan (PRIM), compared to a conventional impression serving as a master model.

METHOD AND MATERIALS

Impressions were performed for seven participants. For each participant, conventional polyvinylsiloxane impression and digital impressions using two intraoral scanners, OMNI (software 4.6; CEREC ORTHO Protocol) and PRIM (10 digital impressions per participant, per scanner), were made. Conventional impression was digitized with a laboratory scanner (INEOS X5), and used as reference model. .STL files were superimposed with software (Geomagic Control X) using the tools Initial Alignment and Best Fit Alignment, and trueness and precision were evaluated. Statistical evaluation was performed with Shapiro-Wilk and Mann-Whitney tests (P < .05).

RESULTS

Total mean trueness for the OMNI system was 56.45 ± 7.80 µm, and 47.29 ± 5.47 µm for the PRIM system. Regarding precision, values from the OMNI system were 42.47 ± 6.91 µm and from the PRIM system 21.86 ± 4.40 µm. PRIM presented better results for both trueness (P = .000) and precision (P = .000) when compared to OMNI.

CONCLUSIONS

PRIM provided a better combination of trueness and precision than its predecessor OMNI. However, both PRIM and OMNI performed acceptably when performing indirect restorations, according to the current acceptable thresholds, considering both trueness and precision.

CLINICAL IMPLICATIONS

Full-arch impressions with Primescan presented more precision and trueness than Omnicam; however, compared to previous reported values of conventional impressions, they still presented lower accuracy.

Molecular detection of Rickettsia in ectoparasites (Siphonaptera and Phthiraptera) of domestic and feral pigs from Argentina

Rickettsioses are distributed among a variety of hematophagous arthropods, and represent an emergent threat. The presence of rickettsial bacteria in ectoparasites collected from pigs from Argentina is still unknown. This study investigated the presence and identity of Rickettsia spp. in fleas, Pulex irritans, and sucking lice, Haematopinus suis, of domestic and feral pigs, Sus scrofa, from Central-Northern Argentina, through the genes gltA and ompB. Rickettsial bacteria were detected in 50% of fleas and 24% of lice. The BLASTn analysis of the ompB gene fragments in P. irritans samples showed identities 99% and 100% with R. felis. Positive samples of H. suis were 99% similar with species from the spotted fever group, future amplifications of a more polymorphic fragment of the ompB gene will allow to corroborate the identity of the Rickettsia species present in these lice samples. The Rickettsia spp. reported in the present study are having eventually been associated with cases of human diseases, and the circulation of these agents in arthropods has already been reported in several countries. Therefore, the identification of circulating pathogenic agents, such as reported in this study, is crucial for development of preventive measures for the control of ectoparasite-borne rickettsiosis diseases. Further studies, using serology techniques, will be allow to explore the ability of pigs as a possible Rickettsia reservoir and its role as part of transmission cycle of Rickettsia spp. in the studied scenarios.

Functional longevity in five rabbit lines founded on different criteria: Comparison at foundation and at fixed times after selection

The enhancement of rabbit female functional longevity, that is the ability to avoid voluntary culling, is a paramount aspect for the sustainability of meat rabbit production; this trait represents a direct indicator of female robustness. The objective of our study was to compare the functional longevity of five rabbit lines at their foundation and at fixed times during their selection processes. Four of them are maternal lines (A, V, H and LP) selected for litter size at weaning. The fifth line is the paternal line R, founded and selected for post-weaning daily gain from 28 to 63 days. The comparison at foundation involved the complete data set (from March 1980 to March 2013; records of 15,670 does) and pedigree (19,405 animals). Latter comparisons were made when all lines shared the same environmental and management conditions, from March 1997 to September 1998 and from March 2011 to September 2012. In these second comparisons, the same model as that used in the comparison at foundation was used, but now the additive effect was excluded, only data from the corresponding periods were considered. At their foundation, lines V, H and LP showed larger functional longevity than lines A and R, being LP line that with the longest productive life. In the latter comparisons, lines A and R still showing the lowest functional longevities. However, as the selection process evolves, the differences between these two lines and the others were reduced. It could be concluded that the average longevity of a population greatly depends on the criteria followed for its foundation. In addition, along the selection for litter size, the differences of longevity between lines tend to decrease, this is due to an unintended selection for functional longevity, since only offspring from females reaching three parturitions are selected as breeding animals for the next generation.

Social Network Analysis of Agonistic Behaviour and Its Association with Economically Important Traits in Pigs

Simple Summary

Aggression behaviour has several negative consequences on the performance and welfare of pigs. Here, a Social Network Analysis (SNA) approach was employed to (1) identify individual traits that describe the role of each animal in the aggression; (2) investigate the association of these traits with performance and feeding behaviour traits. The study was conducted on 326 Duroc pigs reared in 29 pens. Several individual centrality traits were identified and used to calculate the Social Rank Index. The Dominant, Subordinate, and Isolated animals represented 21.1%, 57.5% and 21.4%, respectively. No significant correlations were observed between out-degree (number of initiated agonistic behaviours) and growth traits, indicating the similarity of growth patterns for dominant and non-dominant animals. Furthermore, out-degree was correlated positively with average daily occupation time (time at the feeder/day) and average daily feeding frequency (number of visits to the feeder/day), but negatively with average daily feeding rate (gr/min). This may indicate the ability of non-dominant pigs to modify their behaviour to obtain their requirements. The Hamming distances between networks showed that there is no common behaviour pattern between pens. In conclusion, SNA showed potential for extracting behaviour traits that could be used to improve pig performance and welfare.

Abstract

Aggression behaviour has several negative consequences on the performance and welfare of pigs. Here, the Social Network Analysis (SNA) approach was employed to (1) identify individual traits that describe the role of each animal in the aggression; (2) investigate the association of these traits with performance and feeding behaviour traits. The study was conducted on 326 Duroc pigs reared in 29 pens. Several individual centrality traits were identified and used to calculate the Social Rank Index. The Dominant, Subordinate, and Isolated animals represented 21.1%, 57.5% and 21.4%, respectively. No significant correlations were observed between out-degree (number of initiated agonistic behaviours) and growth traits, indicating the similarity of growth patterns for dominant and non-dominant animals. Furthermore, out-degree was correlated positively with average daily occupation time (time at the feeder/day) and average daily feeding frequency (number of visits to the feeder/day) but negatively with average daily feeding rate (gr/min). This may indicate the ability of non-dominant pigs to modify their behaviour to obtain their requirements. The Hamming distances between networks showed that there is no common behaviour pattern between pens. In conclusion, SNA showed the potential for extracting behaviour traits that could be used to improve pig performance and welfare.

Genetic analysis of functional longevity in a complete diallel crossing experiment involving four maternal rabbit lines

In a diallel cross between four maternal lines of rabbits, the four maternal lines and the corresponding crossbred females (does) were evaluated concerning functional longevity, estimating their crossbreeding components. Sixteen genetic groups were produced by using four maternal lines of rabbit (A, V, H and LP (L)). The groups were distributed over 4 Spanish farms. In all farms, the V line was present as the reference group. A total of 7,211 does' longevity records were recorded. Using a Cox proportional hazard model of fixed effects, survival analysis was performed to study longevity analysing the hazard of death or culling. Does from lines A, H and V had similar risks of death or of being culled, and they were more susceptible compared with those from line L. The lowest hazard was associated with L line does. No significant differences were found between the average of all crosses and the V line except when comparing the V line to the cross between A and H lines, favouring the former (1.30 higher risk of replacement for AH animals). Significant differences between reciprocal crosses were observed between VH and HV, in favour of HV (0.72 of relative risk of replacement) and between LH and HL, in favour of HL (0.76 of relative risk). Line V had the highest risk due to the direct genetic effects, and these differences were significant with the lines H (1.40 of relative risk) and L (1.43 of relative risk). The differences in maternal genetic effects were small and not significant except between lines H and V in favour of V line (0.75 of relative risk). The estimated direct heterosis effects do not always follow the same trend but they showed the importance of the crossing between specialized lines to produce crossbred does for intensive meat rabbit production.

Selection for feed efficiency using the social effects animal model in growing Duroc pigs: evaluation by simulation

BACKGROUND

Traits recorded on animals that are raised in groups can be analysed with the social effects animal model (SAM). For multiple traits, this model specifies the genetic correlation structure more completely than the animal model (AM). Our hypothesis was that by using the SAM for genetic evaluation of average daily gain (ADG) and backfat thickness (BF), a high rate of improvement in feed conversion ratio (FCR) might be achieved, since unfavourable genetic correlations between ADG and BF reported in a Duroc pig line could be partially avoided. We estimated genetic and non-genetic correlations between BF, ADG and FCR on 1144 pigs using Bayesian methods considering the SAM; and responses to selection indexes that combine estimates of indirect (IGE) and direct (DGE) genetic effects for ADG and BF by stochastic simulation.

RESULTS

Estimates of the ratio of the variance of DGE to the phenotypic variance were 0.31, 0.39 and 0.25 and those of the total genetic variance to the phenotypic variance were 0.63, 0.74 and 0.93 for ADG, BF and FCR, respectively. In spite of this, when the SAM was used to generate data and for the genetic evaluations, the average economic response was worse than that obtained when BV predictions from the AM were considered. The achieved economic response was due to a direct reduction in BF and not to an improvement in FCR.

CONCLUSIONS

Our results show that although social genetic effects play an important role in the traits studied, their proper consideration in pig breeding programs to improve FCR indirectly is still difficult. The correlations between IGE and DGE that could help to overcome the unfavourable genetic correlations between DGE did not reach sufficiently high magnitudes; also, the genetic parameters estimates from the SAM have large errors. These two factors penalize the average response under the SAM compared to the AM.

Anticipating the Impact of the USMLE Step 1 Pass/Fail Scoring Decision on Underrepresented-in-Medicine Students

Three-digit United States Medical Licensing Examination (USMLE) Step 1 scores have assumed an outsized role in residency selection decisions, creating intense pressure for medical students to obtain a high score on this exam. In February 2020, the Federation of State Medical Boards and the National Board of Medical Examiners announced that Step 1 would transition to pass/fail scoring beginning in 2022.The authors discuss the potential advantages and disadvantages of the pass/fail scoring change for underrepresented-in-medicine (UiM) trainees. UiM students may benefit from this change because it reduces the effect of an inequitable exam; helps correct for students who attend medical schools with a curriculum heavier on nontested formative elements; and decreases stress, improves quality of life, and undermines imposter syndrome. However, this change may also precipitate unforeseen challenges, such as increased discrimination toward UiM trainees, an increase in high-stakes test failures due to a reduced focus on preparing for standardized exams, or the development of new (e.g., subject exams) or overreliance on existing (e.g., school ranking) metrics that would make UiM residency candidates less competitive.To enhance UiM representation in the future health care workforce, it is imperative that national organizations (e.g., accrediting, licensing, regulatory, professional, honor, student, and faculty), hospitals, residency programs, and patient advocacy groups undertake a shared, rigorous approach in assessing the impact of the pass/fail scoring change on UiM applicants' selection to specialty and subspecialty residencies.

Genome-wide association study for feed efficiency in collective cage-raised rabbits under full and restricted feeding

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 collected from cage groups, using 114 604 autosome SNPs segregating in 438 rabbits. Two different models were implemented: (1) an animal model with a linear regression on each SNP allele for growth trait; and (2) a two‐trait animal model, jointly fitting the performance trait and each SNP allele content, for FE traits. This last modeling strategy is a new tool applied to GWAS and allows information to be considered from non‐genotyped individuals whose contribution is relevant in the group average traits. A total of 189 SNPs in 17 chromosomal regions were declared to be significantly associated with any of the five analyzed traits at a chromosome‐wide level. In 12 of these regions, 20 candidate genes were proposed to explain the variation of the analyzed traits, including genes such as FTO, NDUFAF6 and CEBPA previously associated with growth and FE traits in monogastric species. Candidate genes associated with behavioral patterns were also identified. Overall, our results can be considered as the foundation for future functional research to unravel the actual causal mutations regulating growth and FE in rabbits.

Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

BACKGROUND

Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used a systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expression data to identify candidate genes, biological pathways, and potential predictors of FE in a Duroc pig population.

RESULTS

We applied an association weight matrix (AWM) approach to analyse the results from genome-wide association studies (GWAS) for nine FE associated and production traits using 31K SNPs by defining residual feed intake (RFI) as the target phenotype. The resulting co-association network was formed by 829 SNPs. Additive effects of this SNP panel explained 61% of the phenotypic variance of RFI, and the resulting phenotype prediction accuracy estimated by cross-validation was 0.65 (vs. 0.20 using pedigree-based best linear unbiased prediction and 0.12 using the 31K SNPs). Sixty-eight transcription factor (TF) genes were identified in the co-association network; based on the lossless approach, the putative main regulators were COPS5, GTF2H5, RUNX1, HDAC4, ESR1, USP16, SMARCA2 and GTF2F2. Furthermore, gene expression data of the gluteus medius muscle was explored through differential expression and multivariate analyses. A list of candidate genes showing functional and/or structural associations with FE was elaborated based on results from both AWM and gene expression analyses, and included the aforementioned TF genes and other ones that have key roles in metabolism, e.g. ESRRG, RXRG, PPARGC1A, TCF7L2, LHX4, MAML2, NFATC3, NFKBIZ, TCEA1, CDCA7L, LZTFL1 or CBFB. The most enriched biological pathways in this list were associated with behaviour, immunity, nervous system, and neurotransmitters, including melatonin, glutamate receptor, and gustation pathways. Finally, an expression GWAS allowed identifying 269 SNPs associated with the candidate genes' expression (eSNPs). Addition of these eSNPs to the AWM panel of 829 SNPs did not improve the accuracy of genomic predictions.

CONCLUSIONS

Candidate genes that have a direct or indirect effect on FE-related traits belong to various biological processes that are mainly related to immunity, behaviour, energy metabolism, and the nervous system. The pituitary gland, hypothalamus and thyroid axis, and estrogen signalling play fundamental roles in the regulation of FE in pigs. The 829 selected SNPs explained 61% of the phenotypic variance of RFI, which constitutes a promising perspective for applying genetic selection on FE relying on molecular-based prediction.

Effect of feed restriction on the environmental variability of birth weight in divergently selected lines of mice

BACKGROUND

Selection of mice for decreased environmental variability of birth weight has achieved higher survivability and larger litter size as a correlated response to canalized selection, which suggests higher welfare and robustness, and animals that are more homogeneous. However, in these studies, animals were not exposed to an environmental challenge. To demonstrate the advantages of this mouse line with a low environmental variability of birth weight, animals from two divergent lines (high and low variability of birth weight) were subjected to feed restriction. The objective of this study was to use these divergent lines to compare their response in terms of robustness against an environmental challenge. At weaning, 120 females, i.e. four full-sib females from 10 random litters of three consecutive generations of selection, were chosen from these divergent lines. The total number of females was divided into four groups, which were subjected to a feeding regimen by imposing different levels of feed restriction (i.e. 75, 90 and 85% of full ad libitum feed across three generations, respectively) in different combinations during the growth and reproduction periods.

RESULTS

Animals from the "low" line were less sensitive to a change in feed level than those from the "high" line. Regarding reproduction, the "low" line performed better in terms of number of females having parturitions, number of parturitions, and litter size. Imposing a feed restriction on female mice during their growth period did not affect the birth weight of their pups. The "low" line was preferred because of its higher reproductive efficiency and survival under an environmental challenge.

CONCLUSIONS

Selection for decreased environmental variability of birth weight produces animals that are less sensitive to environmental conditions, which can be interpreted as having greater robustness.

Use of group records of feed intake to select for feed efficiency in rabbit

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 ( FI ¯ F ) and individual records of growth rate (G_F ) and metabolic weight (M_F ). Growth rate (G_R ) as FE measurement on R was used. Data corresponded to 5,336 kits from a rabbit sire line, from 1,255 litters in 14 batches and 667 cages. A five-trait mixed model (also with metabolic weight on R, M_R ) was implemented including, for each trait, the systematic effects of batch, body weight at weaning, parity order and litter size; and the random effects of litter, additive genetic and individual. A Bayesian analysis was performed. Conditional traits such as FI ¯ F | M F , G F and G F | M F , FI ¯ F were obtained from elements of additive genetics ( FI ¯ F | M F , G F g and G F | M F , FI ¯ F g ) or phenotypic ( FI ¯ F | M F , G F p and G F | M F , FI ¯ F p ) (co)variance matrices. In the first case, heritabilities were low (0.07 and 0.06 for FI ¯ F | M F , G F g and G F | M F , FI ¯ F g , respectively) but null genetic correlation between the conditional and conditioning traits is guaranteed. In the second case, heritabilities were higher (0.22 and 0.16 for FI ¯ F | M F , G F p and G F | M F , FI ¯ F p , respectively) but the genetic correlation between FI ¯ F | M F , G F p and G F was moderate (0.58). Heritability of G_R was low (0.08). This trait was negatively correlated with G F | M F , FI ¯ F p and G F | M F , FI ¯ F g of animals on F, which indicate a different genetic background. The correlation between G_R and G_F was also low to moderate (0.48) and the additive variance of G_F was almost four times that of G_R , suggesting the presence of a substantial genotype by feeding regimen interaction.

Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs

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 (RNA-Seq) data from pigs that are phenotypically extreme for RFI.

Methods

RFI was computed by considering within-sex regression on mean metabolic body weight, average daily gain, and average backfat gain. RNA-Seq analyses were performed on liver and duodenum tissue from 32 high and 33 low RFI pigs collected at 153 d of age. Machine-learning algorithms were used to predict RFI class based on gene expression levels in liver and duodenum after adjusting for batch effects. Genes were ranked according to their contribution to the classification using the permutation accuracy importance score in an unbiased random forest (RF) algorithm based on conditional inference. Support vector machine, RF, elastic net (ENET) and nearest shrunken centroid algorithms were tested using different subsets of the top rank genes. Nested resampling for hyperparameter tuning was implemented with tenfold cross-validation in the outer and inner loops.

Results

The best classification was obtained with ENET using the expression of 200 genes in liver [area under the receiver operating characteristic curve (AUROC): 0.85; accuracy: 0.78] and 100 genes in duodenum (AUROC: 0.76; accuracy: 0.69). Canonical pathways and candidate genes that were previously reported as associated with FE in several species were identified. The most remarkable pathways and genes identified were NRF2-mediated oxidative stress response and aldosterone signalling in epithelial cells, the DNAJC6, DNAJC1, MAPK8, PRKD3 genes in duodenum, and melatonin degradation II, PPARα/RXRα activation, and GPCR-mediated nutrient sensing in enteroendocrine cells and SMOX, IL4I1, PRKAR2B, CLOCK and CCK genes in liver.

Conclusions

ML algorithms and RNA-Seq expression data were found to provide good performance for classifying pigs into high or low RFI groups. Classification was better with gene expression data from liver than from duodenum. Genes associated with FE in liver and duodenum tissue that can be used as predictive biomarkers for this trait were identified.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0453-y) contains supplementary material, which is available to authorized users.

Pedigree-based estimation of covariance between dominance deviations and additive genetic effects in closed rabbit lines considering inbreeding and using a computationally simpler equivalent model

Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software. Third, we present a new method to refer the estimated variance components to meaningful parameters in a particular population, i.e., final partially inbred generations as opposed to outbred base populations. We applied these developments to three closed rabbit lines (A, V and H) selected for number of weaned at the Polytechnic University of Valencia. Pedigree and phenotypes are complete and span 43, 39 and 14 generations, respectively. Estimates of broad-sense heritability are 0.07, 0.07 and 0.05 at the base versus 0.07, 0.07 and 0.09 in the final generations. Narrow-sense heritability estimates are 0.06, 0.06 and 0.02 at the base versus 0.04, 0.04 and 0.01 at the final generations. There is also a reduction in the genotypic variance due to the negative additive-dominance correlation. Thus, the contribution of dominance variation is fairly large and increases with inbreeding and (over)compensates for the loss in additive variation. In addition, estimates of the additive-dominance correlation are -0.37, -0.31 and 0.00, in agreement with the few published estimates and theoretical considerations.

Role of inbreeding depression, non-inbred dominance deviations and random year-season effect in genetic trends for prolificacy in closed rabbit lines

In closed rabbit lines selected for prolificacy at the Polytechnic University of Valencia, genetic responses are predicted using BLUP. With a standard additive BLUP model and year-season (YS) effects fitted as fixed, genetic trends were overestimated compared to responses estimated using control populations obtained from frozen embryos. In these lines, there is a confounding between genetic trend, YS effects and inbreeding, and the role of dominance is uncertain. This is a common situation in data from reproductively closed selection lines. This paper fits different genetic evaluation models to data of these lines, aiming to identify the source of these biases: dominance, inbreeding depression and/or an ill-conditioned model due to the strong collinearity between YS, inbreeding and genetic trend. The study involved three maternal lines (A, V and H) and analysed two traits, total born (TB) and the number of kits at weaning (NW). Models fitting YS effect as fixed or random were implemented, in addition to additive genetic, permanent environment effects and non-inbred dominance deviations effects. When YS was fitted as a fixed effect, the genetic trends were overestimated compared to control populations, inbreeding had an apparent positive effect on litter size and the environmental trends were negative. When YS was fitted as random, the genetic trends were compatible with control populations results, inbreeding had a negative effect (lower prolificacy) and environmental trends were flat. The model fitting random YS, inbreeding and non-inbred dominance deviations yielded the following ratios of additive and dominance variances to total variance for NW: 0.06 and 0.01 for line A, 0.06 and 0.00 for line V and 0.01 and 0.08 for line H. Except for line H, dominance deviations seem to be of low relevance. When it is confounded with inbreeding as in these lines, fitting YS effect as random allows correct estimation of genetic trends.

Genetic analysis of meat quality traits in maternal lines of rabbit and their diallel cross

Young rabbits, the dams of which came from a full diallel cross among four maternal lines (A, V, H and LP) and the sires from a single paternal line (R), that produce sixteen genetic groups, was carried out to evaluate the genetic groups and to estimate the crossbreeding genetic parameters of meat quality. The meat quality traits were recorded by NIRS from a sample of 285 longissimus lumborum muscles. Crossbreeding parameters were estimated according to Dickerson model. No differences in protein were found. The line A had significant differences with V line for intramuscular fat, and fatty acids groups. Significant differences for these traits appeared between the crossbred AH and VV (in favor of AH). As conclusion, the significant contrasts between genetic types for chemical composition of the meat are mainly consequence of direct-maternal genetic effects, having grandmaternal and maternal heterosis effects a less relevant role.

Expected responses to different strategies of selection to increase heat tolerance assessed by changes in litter size in rabbit

Response on litter size (LS) to selection based on EBV of the own trait and several indexes including EBV of 1 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 animal-specific temperature threshold (i.e., it had 3 parameters: intercept [Int], slope [Slp], and threshold [Thr]). Litter size data were generated assuming this model under 2 environmental conditions (comfort [CC] and comfort-to-heat [CtHC]). Variance components for Int, Slp, Thr, and LS were taken from literature. The initial base population consisted of 125 females and 25 males. Ten generations of selection were conducted keeping constant the population size. Eight different selection criteria were considered, depending on both the evaluation model and the index combining EBV for 1 or more parameters of the RNM. In 1 case selection was based on EBV of the own trait predicted by using a repeatability animal model. In the other 7 cases the genetic evaluation was conducted using the same model as that used in the simulation. For each scenario 25 replicates were conducted and response to selection was assessed within replicate as the difference between generations in the average of trait. Results indicate that, under the studied conditions and for the used genetic parameters, selection based on the observed trait seems to have the same effect as selection based on some index, including EBV of the RNM parameters. In addition, response to selection could be greater under CtHC rather than CC. Animals selected exclusively for EBV of the Slp and Thr are not expected to have good performance under CC. Under CtHC, selection for LS has a major response on those parameters, whereas response on Int was very small. Under CC, response to selection on LS is mainly determined by a change in Int, whereas Slp does not change and Thr slightly increases. Selection based on EBV of Slp, Thr, or on an index including both seems to have the same effect on the trait and it was doubly effective in modifying the shape of the RNM under CtHC than under CC. Selection based on EBV of Thr and Slp does not seem to lead to any response in LS. Selection based on EBV of Int seems to have no effect on the trait or on animal's tolerance to heat under CtHC, but it would lead to a positive response in LS under CC.

Effective population size and inbreeding depression on litter size in rabbits. A case study

The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47,794 l and a pedigree of 14,622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection.

Racial and ethnic minority medical students' perceptions of and interest in careers in academic medicine

PURPOSE

To describe diverse medical students' perceptions of and interest in careers in academic medicine.

METHOD

In 2010, the authors invited students attending three national medical student conferences to respond to a survey and participate in six focus groups. The authors identified trends in data through bivariate analyses of the quantitative dataset and using a grounded theory approach in their analysis of focus group transcripts.

RESULTS

The 601 survey respondents represented 103 U.S. medical schools. The majority (72%) were in their first or second year; 34% were black and 17% were Hispanic. Many respondents (64%) expressed interest in careers in academic medicine; teaching and research were viewed as positive influences on that interest. However, black and Hispanic respondents felt they would have a harder time succeeding in academia. The 73 focus group participants (25% black, 29% Hispanic) described individual- and institutional-level challenges to academic medicine careers and offered recommendations. They desired deliberate and coordinated exposure to academic career paths, research training, clarification of the promotion process, mentorship, protected time for faculty to provide teaching and research training, and an enhanced infrastructure to support diversity and inclusion.

CONCLUSIONS

Medical students expressed an early interest in academic medicine but lacked clarity about the career path. Black and Hispanic students' perceptions of having greater difficulty succeeding in academia may be an obstacle to engaging them in the prospective pool of academicians. Strategic and dedicated institutional resources are needed to encourage racial and ethnic minority medical students to explore careers in academic medicine.

Comparison of immune response to lipopolysaccharide of rabbit does selected for litter size at weaning or founded for reproductive longevity

To evaluate differences in maternal lines to the immune response of reproductive rabbit does, a total of 64 animals of two different lines: (1) founded for hyper-longevity and litter size criteria (LP) and (2) selected for litter size at weaning (V) were used. Females were subjected to three different reproductive efforts: post-partum (PP) mating at first lactation and 9 kits during the second; post-weaning (PW) mating at first lactation and 9 kits during the second; and PW mating at first lactation and 5 kits during the second. At second weaning (30 days PP), an acute response was induced by intravenous infusion of lipopolysaccharide (LPS). LP females seemed to be lower affected during the hyper-acute phase than V females, showing lower plasma glucose content at 1.5 h post infusion (pi) and rectal temperature at 6 h pi; and showed higher ulterior immune response, with higher levels of C-reactive protein at 48 h pi and haptoglobin in plasma from 24 h pi. Survival test conferred a higher risk of culling for V than for LP females during the first hours after challenge. These results may suggest that, regarding immune response to LPS challenge, foundation by hyper-longevity productive criteria lead to obtain a more robust population of rabbit does, characterized by improved response ability.

Sources of individual variation to heat tolerance in a rabbit line

The objective of the present study was to quantify the extent of the interaction between temperature and animal-specific effects on prolificacy and average weaning weight in rabbit does and to assess to what extent this interaction has a genetic determination. For this purpose, 18,491 total born (TB) records from 5,929 Caldes does, as well as 16,868 weaned kits (NW) and average weaning weight (AvgWW) records from 5,353 does of the same line were used. Four models were considered, ranging from the simplest, which assumed no effect of temperature on the traits studied, to the most complex, which allowed for different slopes of response and thresholds for heat tolerance for each animal. Deviance information criteria (DIC) were adopted as model choice criteria. The model postulating that each animal is subjected to a linear change in its performance when the temperature reaches a certain animal-specific threshold was preferred for all the considered traits. This interaction has the greatest effect for AvgWW; the ratio between the variance associated to the intercept and the total variance declined from 29.1% at 19°C to 19.4% at 25°C. This decline results from the increase in the variation associated with the interaction of the individual effects with temperature and also from the covariance between this interaction term and the intercepts. An important part of this interaction has a genetic origin, particularly for AvgWW and NW, for which the estimated heritability increased from 0.11 to 0.24 and 0.06 to 0.10, respectively, from 19 to 25°C. Similarly, it was found that the proportion of the total variance for the individual effects involved in the interaction with temperature which have a genetic origin is high for all the traits, around one-half for the variation on the linear changes in the performance and more than one-third for the variation on the onsets for heat stress. However, the error associated with these estimates is large and results must be considered with caution. Thus, in conclusion the extent of the interaction between individual variation and in farm temperature seems to be important and has a genetic origin. Nevertheless, the accuracy of the estimated genetic parameters is low.

Health and body condition of lactating females on rabbit farms

The aim was to study relationships between morbidity, defined through prevalence of diseases of rabbit females, and BCS, and to assess the effect of several risk factors on both morbidity and BCS. Our study was based on individual examinations of 18,510 does in lactation on 103 farms. We evaluated BCS on a linear scale from 1 to 9, with 5 being the optimum. Prevalence of major diseases were 22.7%, 4.0%, and 6.4% for coryza, mastitis, and ulcerative pododermatitis, respectively. In addition, prevalence was 3.0% for diseases of minor presentation, including mange, which had a prevalence of 1.9%. The BCS of the R line (selected for growth) was 5.55 ± 0.14, whereas for the A line (selected for litter size) it was 4.40 ± 0.11. Females with more than 20 kindlings had on average a BCS 0.25 ± 0.07 units less than those in the 12th lactation (P = 0.0002). Optimal BCS 4.60 ± 0.11 was reached during the third lactation week. Sick females had a BCS of 0.6 ± 0.01 units less than healthy females. Females with a footrest had on average a BCS 0.19 ± 0.05 units greater than those without. The absence of footrests was an enabling risk factor for ulcerative pododermatitis, the prevalence of which increased by 53%. Ulcerative pododermatitis was associated (P = 0.045) with diet; females consuming a rich energy diet were prone to having this disorder; 1 SD increase in DE (0.32 MJ) determined an increase in ulcerative pododermatitis prevalence of 0.8 percentage points. Diet was not an enabling risk factor for the other diseases. The genetic type to which a female belongs is a predisposing risk factor of disease; P, V and H were also maternal lines, while S group was exclusively formed by maternal lines. With regard to coryza, the S group had the greatest prevalence (44.0%), followed by A, P, R (19.0 to 21.0%); the V line, selected for prolificacy, showed the least prevalence (12.0%). For the case of mastitis although significant (P < 0.05), the magnitude of the differences between disease prevalence was less; R line had a mastitis prevalence of 11.0% while the least prevalence was observed for V does (4.0%). Simultaneous evaluation of both BCS and morbidity on the rabbit farm is recommended for the right assessment of welfare conditions. In this study, the relationships between both variables have been shown, as well as how other intrinsic and extrinsic risk factors modulate these variables; and thus, these factors should be considered during a welfare assessment.

Replication and refinement of a quantitative trait locus influencing milk protein percentage on ovine chromosome 3

A previous genome scan that was conducted in Spanish Churra sheep identified a significant quantitative trait locus (QTL) for milk protein percentage (PP) on chromosome 3 (OAR3), between markers KD103 and OARVH34. The aim of this study was to replicate these results and to refine the mapped position of this QTL. To accomplish this goal, we analysed 14 new half-sib families of Spanish Churra sheep including 1661 ewes from 29 different flocks. These animals were genotyped for 21 microsatellite markers mapping to OAR3. In addition to a classical linkage analysis (LA), a combined linkage disequilibrium and linkage analysis (LDLA) was performed with the aim of enhancing the resolution of the QTL mapping. The LA that was performed in this sheep population identified the presence of a highly significant QTL for PP near marker KD103 (P(c) < 0.001; P(exp) < 0.001). The phenotypic variance that was owing to the QTL was 2.74%. Two segregating families for the target QTL were identified in this population with QTL effect estimates of 0.47 and 0.95 SD. The LDLA identified the same QTL as the previous analyses with a high level of statistical significance (P = 9.184 E-11) and narrowed the confidence interval (CI) to a 13 cM region. These results confirm the segregation of the previously identified OAR3 QTL that influences PP in Spanish Churra sheep. Future research will aim to increase the marker density across the refined CI and to analyse the corresponding candidate genes to identify the allelic variant or variants that underlie this genetic effect.

The role of bovine causal genes underlying dairy traits in Spanish Churra sheep

In dairy cattle, quantitative trait nucleotides (QTNs) underlying quantitative trait loci (QTL) for milk production traits have been identified in bovine DGAT1, GHR and ABCG2 genes. The SPP1 gene has also been proposed to be a regulator of lactation. In sheep, QTL underlying milk production traits have been reported only recently, and no proven QTN has been identified. Taking into account the close phylogenetic relationship between sheep and cattle, this study examined the possible effects of the aforementioned genes on sheep milk production traits. We first studied the genetic variability of the DGAT1, GHR, ABCG2 and SPP1 genes in 15 rams of the Spanish Churra dairy sheep breed. Second, we performed an association analysis between SNPs identified in these genes and three milk production traits recorded in a commercial population of Churra sheep. This analysis revealed only three significant associations at the nominal level (P-value <0.05) involving allelic variants of the ABCG2 gene, whereas no significant association was found for the DGAT1, GHR and SPP1 genes. When the Bonferroni correction was applied to take into account the multiple tests performed, none of the associations identified at the nominal level remained significant. Nevertheless, taking into account the high level of false-negative findings that can arise when applying the stringent Bonferroni correction, we think that our results provide a valuable primary assessment of strong candidate genes for milk traits in sheep.

Detection of quantitative trait loci affecting the milk fatty acid profile on sheep chromosome 22: role of the stearoyl-CoA desaturase gene in Spanish Churra sheep

Sheep milk fat contains several components that may provide human health benefits, such as monounsaturated fatty acids and conjugated linoleic acid (CLA). Most of the CLA in ruminant milk is synthesized in the mammary gland by the action of the enzyme stearoyl-CoA desaturase (SCD) on circulating vaccenic acid (trans-11 C18:2; VA). Previous studies have found significant associations between polymorphisms in the SCD gene and the fatty acid composition of ruminant products, including sheep milk. Based on this, we performed a quantitative trait loci (QTL) analysis of an ovine chromosome (22) that harbors the SCD gene for effects on milk fatty acid composition traits and classical milk production traits. We identified a suggestive QTL influencing the CLA/VA ratio with the maximum statistic at position 26 cM of the studied chromosome, whereas the SCD gene has been mapped to position 41.6 cM. The individual introduction of 4 SCD single nucleotide polymorphisms in the QTL model did not cause a reduction of the variance explained by the QTL, which suggests that the SCD gene is not directly responsible for the detected effect in the Churra population studied herein. This conclusion was supported by the lack of any significant association identified between the 4 SCD single nucleotide polymorphisms and the CLA/VA ratio. This association analysis suggested a possible effect of the SCD gene on milk fat percentage in Churra sheep. An independent confirmation of these primary results will be required before attempting its practical implementation in selection programs.

The identification of QTL that affect the fatty acid composition of milk on sheep chromosome 11

In this work, we analysed 11 genetic markers localized on OAR11 in a commercial population of Spanish Churra sheep to detect QTL that underlie milk fatty acid (FA) composition traits. Following a daughter design, we analysed 799 ewes distributed in 15 half-sib families. Eight microsatellite markers and three novel SNPs identified in two genes related to fatty acid metabolism, acetyl-CoA carboxylase alpha (ACACA) and fatty acid synthase (FASN), were genotyped in the whole population under study. The phenotypic traits considered in the study included 22 measurements related to the FA composition of the milk and three other milk production traits (milk protein percentage, milk fat percentage and milk yield). Across-family regression analysis revealed four significant QTL at the 5% chromosome-wise level influencing contents of capric acid (C10:0), lauric acid (C12:0), linoleic conjugated acid (CLA) and polyunsaturated fatty acids (PUFA) respectively. The peaks of the QTL affecting C10:0 and PUFA contents in milk map close to the FASN gene, which has been evaluated as a putative positional candidate for these QTL. The QTL influencing C12:0 content reaches its maximum significance at 58 cM, close to the gene coding for the glucose-dependent insulinotropic polypeptide. We were not able to find any candidate genes related to fat metabolism at the QTL influencing CLA content, which is located at the proximal end of the chromosome. Further research efforts will be needed to confirm and refine the QTL locations reported here.

Genetic determination of the onset of heat stress on daily milk production in the US Holstein cattle

Existence of individual variation in the onset of heat stress for daily milk yield of dairy cows was assessed. Data included 353,376 test-day records of 38,383 first-parity Holsteins from a random sample of US herds. Three hierarchical models were investigated. Model 1 inferred the value of a temperature-humidity index (THI) at which mean yield began to decline as well as the extent of that decline. Model 2 assumed individual variation in yield decline beyond a common THI threshold. Model 3 additionally assumed individual variation for the onset of heat stress. Deviance information criteria indicated the superiority of model 3 over model 2. For model 2, genetic correlation between milk yield in the absence of heat stress and the THI threshold for heat stress was -0.4 (0.11) [marginal posterior mean (marginal posterior standard deviation)]. For model 3, genetic correlations were -0.53 (0.05) between milk yield and THI threshold and -0.62 (0.08) between milk yield and yield decay beyond the THI threshold. Total standard deviation (sum of additive genetic and permanent environmental standard deviations) for the THI threshold was 3.95 (0.06), and more than half of that variation had an additive genetic origin [56% (5%)]. Because of the high genetic correlation [0.95 (0.03)] between yield decay and THI threshold with model 3, using only one of them as a selection criterion for heat tolerance would modify the other in the desired direction.

Model for fitting longitudinal traits subject to threshold response applied to genetic evaluation for heat tolerance

A semi-parametric non-linear longitudinal hierarchical model is presented. The model assumes that individual variation exists both in the degree of the linear change of performance (slope) beyond a particular threshold of the independent variable scale and in the magnitude of the threshold itself; these individual variations are attributed to genetic and environmental components. During implementation via a Bayesian MCMC approach, threshold levels were sampled using a Metropolis step because their fully conditional posterior distributions do not have a closed form. The model was tested by simulation following designs similar to previous studies on genetics of heat stress. Posterior means of parameters of interest, under all simulation scenarios, were close to their true values with the latter always being included in the uncertain regions, indicating an absence of bias. The proposed models provide flexible tools for studying genotype by environmental interaction as well as for fitting other longitudinal traits subject to abrupt changes in the performance at particular points on the independent variable scale.

Multi-breed genetic evaluation in a Gelbvieh population

A multi-breed model was presented for the genetic evaluation of growth traits in beef cattle. In addition to the fixed effects, random direct and maternal genetic effects, and random maternal permanent environmental effects are considered; the model also fits direct and maternal heterosis and direct and maternal breed-of-founder (BOF) x generation group effects using a Bayesian approach that weights prior literature estimates relative to information supplied by the dataset to which the model will be applied. The multi-breed evaluation procedures also allow the inclusion of external evaluations for animals of other breeds. The multi-breed model was applied to a dataset provided by the American Gelbvieh Association. Different analyses were conducted by varying the weights given to the prior literature relative to the information provided by the dataset. Large differences were observed for the heterosis estimates, the BOF x generation group effect estimates, and the predicted breeding values across breeds due to the weights posed on prior literature estimates versus estimates derived directly from data. However, the rankings within breed were observed to be relatively robust to the different weights on prior information.

Late reproductive senescence in a rabbit line hyper selected for reproductive longevity, and its association with body reserves

The aim of the present study was to investigate differences in reproductive and body traits during successive parities between two genetic lines. The LP line was constituted by means of selection of animals having an extremely high number of parities (at least 25) and an average reproductive performance compared to the V line selected for litter size at weaning during 31 generations. The two lines were found to have an equal reproductive performance in the first three parities, but the LP line had higher reproductive performance from the fourth parturition onwards. The low reproductive performance after the third parity in the V line was suggested to be caused by constrained environmental conditions in the test station. A line by parity interaction was also observed for body weight, since body weight declined going from the third to the fourth parity in the LP line but not the V line. Thus, it was concluded that hyper selection for reproductive longevity and average prolificacy successfully delayed reproductive senescence, and that this newly founded line showed less environmental sensitivity, which might have been mediated by a higher body reserve.

Genetic and environmental correlations between longevity and litter size in rabbits

An estimation of the genetic and environmental correlations between prolificacy (kits born alive and number of kits at weaning) and functional longevity in a population selected for litter size at weaning since 1992 was carried out. The method is only an approximation, but suggests that genetically longevity and litter size are not antagonistic objectives in breeding programmes, because the estimated genetic correlations are not significantly different from zero.

Analysis of rabbit doe longevity using a semiparametric log-Normal animal frailty model with time-dependent covariates

Data on doe longevity in a rabbit population were analysed using a semiparametric log-Normal animal frailty model. Longevity was defined as the time from the first positive pregnancy test to death or culling due to pathological problems. Does culled for other reasons had right censored records of longevity. The model included time dependent covariates associated with year by season, the interaction between physiological state and the number of young born alive, and between order of positive pregnancy test and physiological state. The model also included an additive genetic effect and a residual in log frailty. Properties of marginal posterior distributions of specific parameters were inferred from a full Bayesian analysis using Gibbs sampling. All of the fully conditional posterior distributions defining a Gibbs sampler were easy to sample from, either directly or using adaptive rejection sampling. The marginal posterior mean estimates of the additive genetic variance and of the residual variance in log frailty were 0.247 and 0.690.

Regulation of Arabidopsis thaliana 4-coumarate:coenzyme-A ligase-1 expression by artificial zinc finger chimeras

The use of artificial zinc finger chimeras to manipulate the expression of a gene of interest is a promising approach because zinc finger proteins can be engineered to bind any given DNA sequence in the genome. We have previously shown that a zinc finger chimera with a VP16 activation domain can activate a reporter gene in transgenic Arabidopsis thaliana (Sánchez, J.P., Ullman, C., Moore, M., Choo, Y. and Chua, N.H. (2002) Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43, 1465-1472). Here, we report the use of artificial zinc finger chimeras to specifically regulate the 4-coumarate:coenzyme-A ligase-1 (At4CL1) gene in A. thaliana. At4CL1 is a key enzyme in lignin biosynthesis and the down-regulation of At4CL1 can lead to a decrease in lignin content, which has a significant commercial value for the paper industry. To this end, we designed zinc finger chimeras containing either an activation or a repression domain, which bind specifically to the At4CL1 promoter region. Transgenic lines expressing a zinc finger chimera with the VP16 activation domain showed an increase in At4CL1 expression and enzyme activity. In contrast, transgenic lines expressing a chimera with the KOX (KRAB) repression domain displayed repression of At4CL1 expression and enzyme activity. The activation of At4CL1 expression produced an increase in lignin content, and transgenic plant stems showed ectopic lignin distribution. Repression of the At4CL1 gene resulted in reduced lignin content, and lignin distribution in transgenic stems was severely diminished. Our results confirm and extend previous studies of gene regulation using various artificial zinc finger chimeras in animal and plant systems, and show that this system can be used to up- and down-regulate the expression of an endogenous plant gene such as At4CL1.

Crossbreeding parameter estimation for functional longevity in rabbits using survival analysis methodology

A complete diallel cross involving 3 maternal lines of rabbit was performed to estimate cross-breeding parameters for functional longevity. This trait was defined as the ability to delay involuntary culling. The lines considered, A, V, and Prat, had all been selected by litter size at weaning for a long period. Data were related to a total of 653 does belonging to the 9 genetic types from the diallel cross; does were reared and bred on the same commercial farm. Survival analysis was performed using a Cox proportional hazard model. The model incorporated time-dependent factors, such as year-season, litter size, and the interaction between cycle and physiological status of the female; time-independent factors, such as the genetic type of the doe; and sire and dam random factors. Crossbreeding parameters were estimated from the solutions obtained for the type of doe and its estimated variance-covariance matrix, using a generalized least squares procedure. The estimated parameters were the differences between lines in direct genetic effects and maternal genetic effects and individual heterosis. Relevant differences were observed in direct genetic effects between lines A and Prat but not in any maternal effects. Heterosis was found to be significant and favorable between lines A and Prat, and between the lines V and Prat. The magnitude of this effect was variable but important, especially in the first cross. Results stress the importance of using crosses between specialized lines to produce does for intensive meat rabbit production.

Effect of changing female stimulus on intensive semen collection in young Murciano-Granadina male goats1

The aim of this research was to study the effect of changing female stimulus on libido and semen characteristics from young Murciano-granadina male goats submitted to intensive semen collection using females not in estrus as teasers. Males were submitted to two different sexual stimulation procedures. In the first procedure, the same doe was used as the female stimulus for three consecutive presentations. In the second, the doe was replaced after the second presentation by a new female. Semen volume, concentration, forward progressive motility, and live spermatozoa were scored. To analyze reaction time (RT), three types of analysis were performed. In the first one, RT was analyzed by multifactor ANOVA, taking as a missing value 300 s when a buck did not ejaculate. In the second, RT also was analyzed by multifactor ANOVA, but data from males that did not ejaculate were removed. In the third, a Cox Survival analysis was carried out by censoring data when a buck did not ejaculate within 5 min of entering the test arena. A decrease in semen volume and sperm concentration in the successive ejaculations was observed, being highly marked in the third ejaculation independent of the stimulation procedure (0.62 vs. 0.38 and 0.43 mL, and 2,828 vs. 2,183 and 2,223 million spermatozoa/mL to the first and third ejaculation respectively; P < 0.05). No significant differences were observed either in forward progressive motility or live sperm rate. Changing the female stimulus in the third presentation had no significant effect on any seminal characteristic. Regarding libido and mounting behavior variables, there was a substantial decrease in RT in the third service when the female was changed (with both types of ANOVA). When censored data were taken into account, the relative risk showed that the probability of a male ejaculating in the third presentation increased almost fourfold when the female was replaced than when the female was the same in all services (P < 0.05). In conclusion, young Murciano-granadina bucks can be used as semen donors because none of the most important semen variables used to reject or accept an ejaculate before freezing process decreased after intensive semen collection. We also recommend changing the female stimulus to make the semen collection procedure more efficient and using survival analysis methodology to analyze time data, mainly when a high rate of censored data are scored.

[Biotechnological aspects in "loco" larvae]

The biology of planktotrophic larvae of Concholepas concholepas is the main bottleneck towards developing biotechnologies to rear this muricid. Data concerning planktonic larvae development, diets and environmental signals triggering larval settlement and recruitment is scarce. We have begun the study of the molecular and cell biology of embryos, larvae and recruits having as a final goal, the development of appropriate biotechnologies to rear this gastropod. First, an inverse ratio between BuChE and AChE enzyme activities was established. This ratio may be a precise developmental marker for this species. Second, for the first time a phosphoinositide related regulatory pathway is reported in a muricid, opening a new approach to the biotechnological management of larvae. Third, the relation between sulfate in sea water and larval motility was studied. Concentrations below 125 microM sulfate decreases larval motility. The sulfate is incorporated in proteoglycans which participate in different developmental phenomena. Lastly, a genomic Concholepas concholepas DNA sequence, similar to that of a human growth hormone probe was detected. This is very interesting since growth factors are key molecules during development, growth and are involved in food conversion rates in fish and also, in a variety of marine invertebrates.