Genetic correlations of direct and indirect genetic components of social dominance with fitness and morphology traits in cattle.

BACKGROUND: Within the same species, individuals show marked variation in their social dominance. Studies on a handful of populations have indicated heritable genetic variation for this trait, which is determined by both the genetic background of the individual (direct genetic effect) and of its opponent (indirect genetic effect). However, the evolutionary consequences of selection for this trait are largely speculative, as it is not a usual target of selection in livestock populations. Moreover, studying social dominance presents the challenge of working with a phenotype with a mean value that cannot change in the population, as for every winner of an agonistic interaction there will necessarily be a loser. Thus, to investigate what could be the evolutionary response to selection for social dominance, it is necessary to focus on traits that might be correlated with it. This study investigated the genetic correlations of social dominance, both direct and indirect, with several morphology and fitness traits. We used a dataset of agonistic contests involving cattle (Bos taurus): during these contests, pairs of cows compete in ritualized interactions to assess social dominance. The outcomes of 37,996 dominance interactions performed by 8789 cows over 20 years were combined with individual data for fertility, mammary health, milk yield and morphology and analysed using bivariate animal models including indirect genetic effects. RESULTS: We found that winning agonistic interactions has a positive genetic correlation with more developed frontal muscle mass, lower fertility, and poorer udder health. We also discovered that the trends of changes in the estimated breeding values of social dominance, udder health and more developed muscle mass were consistent with selection for social dominance in the population. CONCLUSIONS: We present evidence that social dominance is genetically correlated with fitness traits, as well as empirical evidence of the possible evolutionary trade-offs between these traits. We show that it is feasible to estimate genetic correlations involving dyadic social traits.

Improvement of Genomic Predictions in Small Breeds by Construction of Genomic Relationship Matrix Through Variable Selection.

Genomic selection has been increasingly implemented in the animal breeding industry, and it is becoming a routine method in many livestock breeding contexts. However, its use is still limited in several small-population local breeds, which are, nonetheless, an important source of genetic variability of great economic value. A major roadblock for their genomic selection is accuracy when population size is limited: to improve breeding value accuracy, variable selection models that assume heterogenous variance have been proposed over the last few years. However, while these models might outperform traditional and genomic predictions in terms of accuracy, they also carry a proportional increase of breeding value bias and dispersion. These mutual increases are especially striking when genomic selection is performed with a low number of phenotypes and high shrinkage value-which is precisely the situation that happens with small local breeds. In our study, we tested several alternative methods to improve the accuracy of genomic selection in a small population. First, we investigated the impact of using only a subset of informative markers regarding prediction accuracy, bias, and dispersion. We used different algorithms to select them, such as recursive feature eliminations, penalized regression, and XGBoost. We compared our results with the predictions of pedigree-based BLUP, single-step genomic BLUP, and weighted single-step genomic BLUP in different simulated populations obtained by combining various parameters in terms of number of QTLs and effective population size. We also investigated these approaches on a real data set belonging to the small local Rendena breed. Our results show that the accuracy of GBLUP in small-sized populations increased when performed with SNPs selected via variable selection methods both in simulated and real data sets. In addition, the use of variable selection models-especially those using XGBoost-in our real data set did not impact bias and the dispersion of estimated breeding values. We have discussed possible explanations for our results and how our study can help estimate breeding values for future genomic selection in small breeds.

Genotype by Environment Interaction and Selection Response for Milk Yield Traits and Conformation in a Local Cattle Breed Using a Reaction Norm Approach.

Local breeds are often reared in various environmental conditions (EC), suggesting that genotype by environment interaction (GxE) could influence genetic progress. This study aimed at investigating GxE and response to selection (R) in Rendena cattle under diverse EC. Traits included milk, fat, and protein yields, fat and protein percentage, and somatic cell score, three-factor scores and 24 linear type traits. The traits belonged to 11,085 cows (615 sires). Variance components were estimated in a two-step reaction norm model (RNM). A single trait animal model was run to obtain the solutions of herd-EC effect, then included in a random regression sire model. A multivariate response to selection (R) in different EC was computed for traits under selection including beef traits from a performance test. GxE accounted on average for 10% of phenotypic variance, and an average rank correlation of over 0.97 was found between bull estimated breeding values (EBVs) by either including or not including GxE, with changing top ranks. For various traits, significantly greater genetic components and R were observed in plain farms, loose housing rearing system, feeding total mixed ration, and without summer pasture. Conversely, for beef traits, a greater R was found for mountain farms, loose housing, hay-based feeding and summer pasture.

Genomic Prediction in Local Breeds: The Rendena Cattle as a Case Study.

The maintenance of local cattle breeds is key to selecting for efficient food production, landscape protection, and conservation of biodiversity and local cultural heritage. Rendena is an indigenous cattle breed from the alpine North-East of Italy, selected for dual purpose, but with lesser emphasis given to beef traits. In this situation, increasing accuracy for beef traits could prevent detrimental effects due to the antagonism with milk production. Our study assessed the impact of genomic information on estimated breeding values (EBVs) in Rendena performance-tested bulls. Traits considered were average daily gain, in vivo EUROP score, and in vivo estimate of dressing percentage. The final dataset contained 1691 individuals with phenotypes and 8372 animals in pedigree, 1743 of which were genotyped. Using the cross-validation method, three models were compared: (i) Pedigree-BLUP (PBLUP); (ii) single-step GBLUP (ssGBLUP), and (iii) weighted single-step GBLUP (WssGBLUP). Models including genomic information presented higher accuracy, especially WssGBLUP. However, the model with the best overall properties was the ssGBLUP, showing higher accuracy than PBLUP and optimal values of bias and dispersion parameters. Our study demonstrated that integrating phenotypes for beef traits with genomic data can be helpful to estimate EBVs, even in a small local breed.

Selection Response Due to Different Combination of Antagonistic Milk, Beef, and Morphological Traits in the Alpine Grey Cattle Breed.

Selection in local dual-purpose breeds requires great carefulness because of the need to preserve peculiar traits and also guarantee the positive genetic progress for milk and beef production to maintain economic competitiveness. A specific breeding plan accounting for milk, beef, and functional traits is required by breeders of the Alpine Grey cattle (AG), a local dual-purpose breed of the Italian Alps. Hereditability and genetic correlations among all traits have been analyzed for this purpose. After that, different selection indexes were proposed to identify the most suitable for this breed. Firstly, a genetic parameters analysis was carried out with different datasets. The milk dataset contained 406,918 test day records of milk, protein, and fat yields and somatic cells (expressed as SCS). The beef dataset included performance test data conducted on 749 young bulls. Average daily gain, in vivo estimated carcass yields, and carcass conformation (SEUROP) were the phenotypes obtained from the performance tests. The morphological dataset included 21 linear type evaluations of 11,320 first party cows. Linear type traits were aggregated through factor analysis and three factors were retained, while head typicality (HT) and rear muscularity (RM) were analyzed as single traits. Heritability estimates (h2) for milk traits ranged from 0.125 to 0.219. Analysis of beef traits showed h2 greater than milk traits, ranging from 0.282 to 0.501. Type traits showed a medium value of h2 ranging from 0.238 to 0.374. Regarding genetic correlation, SCS and milk traits were strongly positively correlated. Milk traits had a negative genetic correlation with the factor accounting for udder conformations (-0.40) and with all performance test traits and RM. These latter traits showed also a negative genetic correlation with udder volume (-0.28). The HT and the factor accounting for rear legs traits were not correlated with milk traits, but negatively correlated with beef traits (-0.32 with RM). We argue that the consequence of these results is that the use of the current selection index, which is mainly focused on milk attitude, will lead to a deterioration of all other traits. In this study, we propose more appropriate selection indexes that account for genetic relationships among traits, including functional traits.

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification.

Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.

Flock-dependent exploitation of a limited resource in House Sparrow.

The performances of different social groups can depend on various characteristics, such as familiarity among their members or the presence of individuals with specific traits. However, it has rarely been investigated how groups perform during an encounter with other conspecifics, even if in the natural environment social groups often run into each other and compete for resources. We investigated whether a certain characteristic of the group (i.e., familiarity) could benefit its members when they are confronted with another group. We designed a novel experimental set-up, creating triads of captive house sparrows (Passer domesticus) and examining whether in a situation of competition for limited resources one triad could gain benefits over the other (consume more mealworms, Tenebrio molitor). While we did not find an effect of previous familiarity among triad members on the triads' performances, we discovered a group-based difference in the number of mealworms eaten per capita. Group-mates of the very first individual to eat a mealworm (first feeder) ate more mealworms than those in the opposing triad. First feeder individuals also foraged sooner and more than other birds in a subsequent prey consumption assay. Our results suggest that individual performances were influenced by group membership, even when groups were exploiting the same resource simultaneously.

Can house sparrows recognize familiar or kin-related individuals by scent?

In the last decades, higher attention has been paid to olfactory perception in birds. As a consequence, a handful of avian species have been discovered to use olfaction in different contexts. Nevertheless, we still have a very limited knowledge about the use of odor cues in avian social life, particularly, in the case of songbirds. Here, we investigate if female house sparrows Passer domesticus show any preference for the odor of kin and nonkin conspecifics and we also test a possible role of familiarity based on male scent in female choice. We performed the experiment with captive birds twice, during the nonbreeding and breeding seasons. Our results show that female house sparrows strongly avoided the odor of unrelated familiar (UF) males, both in the breeding and nonbreeding seasons. Our results suggest recognition for olfactory stimuli related to familiarity and kinship. We suggest that avoidance for UF males is associated with previous experience in this species. Also, we provided further evidence to the use of olfaction in passerine species by using a new experimental setup.

House sparrows' (Passer domesticus) behaviour in a novel environment is modulated by social context and familiarity in a sex-specific manner.

BACKGROUND: Exploratory behaviour is one of the best-investigated behavioural traits. However, little is known about how differences in familiarity, i.e. in the knowledge and previous experience with a companion can influence the exploration of a novel environment. However, to our knowledge, such a critical feature of the social environment has never been the target of a study relating it to exploratory behaviour in birds. Here we examined if familiarity with a conspecific could affect behavioural responses of individuals confronted with a novel environment. We recorded the latency to land on the ground, latency to feed, time spent feeding and number of sectors visited of 48 female and 48 male house sparrows (Passer domesticus) in an indoor aviary in three contexts: alone (individual context), with an unfamiliar and with a familiar same-sex companion. RESULTS: House sparrows landed sooner on the ground when in the familiar context than when in the individual context. Birds in unfamiliar pairs followed each other less than familiar birds, but this difference diminished with time spent exploring. Moreover, males and females differed in their behavioural responses in the unfamiliar context. Females with a familiar companion landed sooner than when they were paired with an unfamiliar conspecific, whereas only the presence of a companion but not familiarity reduced males latency to land on the ground. Finally, when considering the unfamiliar context males had shorter latencies to forage and thus spent more time eating than females. CONCLUSIONS: The presence or absence of a companion and its familiarity with the focal individual influenced differently the behavioural responses of male and female house sparrows in a novel environment. As house sparrows are strongly sociable, the influence of the social environment is likely to be of paramount importance to understand the selective pressures acting on them, particularly in recently colonized areas with ephemeral food sources. Our results shed light on the complex influence that the social environment has on the behavioural responses of a cosmopolitan bird.

The effect of social connections on the discovery of multiple hidden food patches in a bird species.

Social foraging is thought to provide the possibility of information transmission between individuals, but this advantage has been proved only in a handful of species and contexts. We investigated how social connections in captive flocks of house sparrows (Passer domesticus) affected the discovery of (i.e. feeding for the first time from) two hidden food patches in the presence of informed flock-mates. At the first-discovered and most-exploited food patch social connections between birds affected the order of discovery and presumably contributed to a greater exploitation of this patch. However, social connections did not affect discovery at the second food patch despite its close spatial proximity. Males discovered the food sources sooner than females, while feeding activity was negatively related to patch discovery. Age had no effect on the order of discovery. Birds that first discovered and fed at the food patches were characterized by higher level of social indifference, i.e. followed others less frequently than other birds in an independent context. Our findings provide experimental evidence for the importance of variable social connections during social foraging in house sparrow flocks, and suggest that social attraction can contribute differently to the exploitation of different patches when multiple food sources are present.