Cristina Sartori

Direct and social genetic effects on body weight at 270 days and carcass and ham quality traits in heavy pigs

The aims of this study were to estimate covariance components for BW at 270 d (BW270) and carcass and ham quality traits in heavy pigs using models accounting for social effects and to compare the ability of such models to fit the data relative to models ignoring social interactions. Phenotypic records were from 9,871 pigs sired by 293 purebred boars mated to 456 crossbred sows. Piglets were born and reared at the same farm and randomly assigned at 60 d of age to groups (6.1 pigs per group on average) housed in finishing pens, each having an area of 6 m(2). The average additive genetic relationship among group mates was 0.11. Pigs were slaughtered at 277 ± 3 d of age and 169.7 ± 13.9 kg BW in groups of nearly 70 animals each. Four univariate animal models were compared: a basic model (M1) including only direct additive genetic effects, a model (M2) with nonheritable social group (pen) effects in addition to effects in M1, a model (M3) accounting for litter effects in addition to M2, and a model (M4) accounting for social genetic effects in addition to effects in M3. Restricted maximum likelihood estimates of covariance components were obtained for BW270; carcass backfat depth; carcass lean meat content (CLM); iodine number (IOD); and linoleic acid content (LIA) of raw ham subcutaneous fat; subcutaneous fat depth in the proximity of semimembranosus muscle (SFD1) and quadriceps femoris muscle (SFD2); and linear scores for ham round shape (RS), subcutaneous fat (SF), and marbling. Likelihood ratio tests indicated that, for all traits, M2 fit the data better than M1 and that M3 was superior to M2 except for SFD1 and SFD2. Model M4 was significantly better than M3 for BW270 (P < 0.001) and CLM, IOD, RS, and SF (P < 0.05). The contribution of social genetic effects to the total heritable variance was large for CLM and BW270, ranging from 33.2 to 35%, whereas the one for ham quality traits ranged from 6.8 (RS) to 11.2% (SF). Direct and social genetic effects on BW270 were uncorrelated, whereas there was a negative genetic covariance between direct and social effects on CLM, IOD, RS, and SF, which reduced the total heritable variance. This variance, measured relative to phenotypic variance, ranged from 21 (CLM) to 54% (BW270). Results indicate that social genetic effects affect variation in traits relevant for heavy pigs used in dry-cured hams manufacturing. Such effects should be exploited and taken into account in design of breeding programs for heavy pigs.

Genetics of fighting ability in cattle using data from the traditional battle contest of the Valdostana breed

The tendency to fight is a well-known behavior in Valdostana cattle, and non-cruel traditional contests are organized yearly by farmers to identify the most dominant cow. Cow battles consist of elimination matches that have important economic implications for both tourism and farmers. The aims of this study are 1) to validate a scoring system to express fighting ability, and 2) to carry out a genetic analysis for this trait using different data sets and models. A data set accounting for 16,509 fighting records of 5,981 cows relevant to contests over 6 yr was retained after editing (data set 1). Data on placements were used to compute a placement score accounting for wins, tournament size, and difficulty, and differentiating the 20 preliminary battles each year from the final match. A second data set was created using only the individual best yearly placement scores, that is, deleting repeats with a smaller placement score for the same animal within each year (data set 2; n = 10,367 records, corresponding to a single datum per year per cow). Compared with the placement or position of each cow, the placement score proved to be less skewed (-1.45 for placement position and 1.25 for placement score, respectively) and exhibited better coefficients for the probability of a normal distribution. An animal model REML method analysis (accounting for 13,456 animals in the pedigree) was carried out, with consideration given to different combinations of fixed and random nongenetic factors other than the random animal and permanent environmental effects. Results indicated that random factors other than additive genetic and permanent environment effects did not improve the model fit; therefore, it was not useful to take them into account. Heritability estimates obtained with the model showing the best fit were 0.078 (data set 1) and 0.098 (data set 2). Results of this study indicate that selection for fighting ability in Valdostana cattle using data on battle performance is possible.

Genetic parameters for body condition score, locomotion, angularity, and production traits in Italian Holstein cattle

The objectives of this research were to estimate genetic parameters for body condition score (BCS) and locomotion (LOC), and to assess their relationships with angularity (ANG), milk yield, fat and protein content, and fat to protein content ratio (F:P) in the Italian Holstein Friesian breed. The Italian Holstein Friesian Cattle Breeders Association collects type trait data once on all registered first lactation cows. Body condition score and LOC were introduced in the conformation scoring system in 2007 and 2009, respectively. Variance (and covariance) components among traits were estimated with a Bayesian approach via a Gibbs sampling algorithm and an animal model. Heritability estimates were 0.114 and 0.049 for BCS and LOC, respectively. The genetic correlation between BCS and LOC was weak (-0.084) and not different from zero; therefore, the traits seem to be genetically independent, but further investigation on possible departures from linearity of this relationship is needed. Angularity was strongly negatively correlated with BCS (-0.612), and strongly positively correlated with LOC (0.650). The genetic relationship of milk yield with BCS was moderately negative (-0.386), and was moderately positive (0.238) with LOC. These results indicate that high-producing cows tend to be thinner and tend to have better locomotion than low-producing cows. The genetic correlation of BCS with fat content (0.094) and F:P (-0.014) was very weak and not different from zero, and with protein content (0.173) was weak but different from zero. Locomotion was weakly correlated with fat content (0.071), protein content (0.028), and F:P (0.074), and correlations were not different from zero. Phenotypic correlations were generally weaker than their genetic counterparts, ranging from -0.241 (BCS with ANG) to 0.245 (LOC with ANG). Before including BCS and LOC in the selection index of the Italian Holstein breed, the correlations with other traits currently used to improve type and functionality of animals need to be investigated.

Effects of inbreeding on fighting ability measured in Aosta Chestnut and Aosta Black Pied cattle.

Aosta Black Pied (ABP) and Aosta Chestnut (AC) are dual-purpose cattle indigenous to the western Alps and famous for their fighting ability in traditional Italian Batailles de Reines. The present study aimed to investigate the influence of inbreeding on breeding values for fighting ability achieved in participants. Inbreeding (F) and average relatedness (AR) were obtained from the entire pedigree information available (19,554 and 87,967 records for ABP and AC, respectively). Data (n = 23,998) relating to 8,259 cows competing in years 2001-2009 were analyzed to obtain heritability (h(2)) estimates and breeding values for the trait. A placement score was chosen as a phenotype for fighting ability and both a classical quantitative model (NORM) and its implementation, used to identify its indirect genetic effects (COMP), were analyzed using the expectation maximization-REML (EM-REML) method. The F and AR trends in animals born between 1990 and 2009 were generally low and were greater for ABP (+0.06%/yr) than for AC (+0.03%/yr) populations, which also presented a greater mean F (about 2.8% ± 1.7% vs. 0.8% ± 1.5% for ABP and AC, respectively) and mean AR among individuals (about 1.0% ± 0.8% vs. 0.4% ± 0.3% for ABP and AC, respectively). Heritability estimates from 0.083 ± 0.036 to 0.120 ± 0.037 were obtained using the NORM model, accounting for or not accounting for F, respectively. Similar results were obtained also for the COMP model, with h(2) estimates of 0.12 ± 0.037, whether or not F was taken into consideration. Linear regression analyses carried out on the 33 major lineages to which most of participants belonged (n = 6,087) revealed an overall negative trend of EBV compared with the increase of either F (b = -21.3, P < 0.01) or AR (b = -50.1, P < 0.01). However, a great variability in the relationship between EBV and F or AR was found by analyzing data within lineages. Despite the variability, an unfavorable effect of inbreeding was detected in the fighting ability trait of both ABP and AC cattle, and this should be carefully considered in the breeding management of both breeds.

Test day-milk yields variance component estimation using repeatability or random regression models in the Rendena breed

Abstract This study has aimed to compare Repeatability (RP-TDm) and Random-Regression Test Day models (RR-TDm) in genetic evaluations of milk (M), fat (F) and protein (P) yields in Rendena breed. Variance estimations for Milk (M), Fat (F) and Protein (P) were obtained on a sample of 43,842 TD belonging to 2,692 animals controlled over 15 years (1990-2005). RP-TDm estimates of h2 were of 0.21 for M and 0.17 for both F and P, whereas RR-TDM provided a trend of h2 ranging from 0.15-0.34 for M, 0.15-0.31 for F and 0.10-0.24 for P. Both RP-TDm and RR-TDm results agreed with literature, even though RR-TDm provided a pattern of h2 along the lactation different from other studies, with the lowest h2 at the beginning and at the end of lactation. PSB, MAD and -2Log L parameters revealed lower power of RP-TDm as compare with the RR-TDm.

In vivo performance of Italian Heavy Draft Horse weanlings fed two protein levels and slaughtered at two ages.

This study aimed at evaluating in vivo performance, growth parameters, intakes, dressing percentage, and blood parameters in Italian Heavy Draft Horse (IHDH) weanlings fed 2 CP levels up to the 2 typical ages of slaughter. Forty-one weanlings were grouped in 8 pens according to sex, age, and BW. After a transition period, animals were randomly assigned to 2 isoenergetic diets containing different CP levels: 10.6 and 11.2% CP in DM for low protein (LP) and 13.2 and 14.7% CP in DM for high protein (HP) diets in the first and second phase, respectively. About half of the animals (n = 22) were slaughtered when aged 13 mo (end of first phase); the remaining animals (n = 19) were slaughtered at 18 mo (end of second phase). Animals were weighed, measured for withers height, and scored in vivo for fleshiness and BCS at 3 wk intervals. Feed intake in each pen was measured weekly, and feed samples were collected every 2 mo. Blood samples from venous jugular were collected in both phases to analyze plasma protein, urea, glucose, bilirubin, hepatic enzymes, and mineral content. Growth parameters were estimated within phase by modeling BW as a function of age using fourth-degree Legendre polynomials. During the first phase, a different linear coefficient (P = 0.051) for the growth curve was observed between females fed a HP or a LP diet, while males showed differences only on quadratic and cubic Legendre coefficients. However, no significant differences were detected in ADG between the CP levels and sexes. In the second phase, Legendre coefficients were not different between treatments for the remaining weanlings, and once again no differences were found on ADG. The DM intake was influenced by diets in both periods, greater in the HP diet as compared with the LP diet (P < 0.001). No differences due to diet were observed for fleshiness or BCS scores at the end of each phase or in the dressing percentage at slaughter. As expected, plasma urea was greater (P < 0.001) in animals fed the HP diet but was within a normal range for healthy horses. In conclusion, a small dietary protein restriction (i.e., on average 3% of DM) did not change the in vivo performance of IHDH weanlings up to 13 or up to 18 mo of age.

Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics

Biogas upgrading via carbon dioxide hydrogenation is an emerging technology for electrofuel production. The biomethanation efficiency is strongly dependent on a balanced microbial consortium, whose high- resolution characterization along with their functional potential and interactions are pivotal for process optimization. The present work is the first genome-centric metagenomic study on mesophilic and thermophilic biogas upgrading reactors aiming to define the metabolic profile of more than 200 uncultivated microbes involved in hydrogen assisted methanogenesis. The outcomes from predictive functional analyses were correlated with microbial abundance variations to clarify the effect of process parameters on the community. The operational temperature significantly influenced the microbial richness of the reactors, while the H2 addition distinctively alternated the abundance of the taxa. Two different Methanoculleus species (one mesophilic and one thermophilic) were identified as the main responsible ones for methane metabolism. Finally, it was demonstrated that the addition of H2 exerted a selective pressure on the concerted or syntrophic interactions of specific microbes functionally related to carbon fixation, propionate and butanoate metabolisms. Novel bacteria were identified as candidate syntrophic acetate oxidizers (e.g., Tepidanaerobacter sp. DTU063), while the addition of H2 favored the proliferation of potential homoacetogens (e.g., Clostridia sp. DTU183). Population genomes encoding genes of Wood-Ljungdahl pathway were mainly thermophilic, while propionate degraders were mostly identified at mesophilic conditions. Finally, putative syntrophic interactions were identified between microbes that have either versatile metabolic abilities or are obligate/facultative syntrophs.

Genetic correlations among milk yield, morphology, performance test traits and somatic cells in dual-purpose Rendena breed

Selection in native local breeds needs great carefulness due to the small population size and the risk of inbreeding. Furthermore, most breeds are dual-purpose, and milk and beef attitudes are antagonistic. For preservation purposes functional traits need to be considered. Focusing on the small local Rendena cattle, this study aimed to analyse the genetic correlations among milk, beef and udder health traits and the response to selection predicted under different scenarios. The study considered milk, fat and protein yields (MY), factor scores for udder volume (UV), conformation (UC) and muscularity obtained from type traits scored on primiparous cows, and performance test traits (PT) measured on young bulls at test station: average daily gain, in vivo SEUROP fleshiness, in vivo dressing percentage. Somatic cell score (SCS) was considered as a functional trait, with a possibility of restricting its genetic gain to zero. The study considered 281 497 MY test-day data collected on 16 974 cows, and data from linear type evaluation on 11 992 primiparous cows for factor scores. The PT data were recorded on 1428 young bulls, and SCS obtained from cell counts at milk recording. Bi-trait restricted maximum likelihood animal model analyses were performed to assess genetic parameters. Heritability varied from 0.157 (fat) to 0.442 (dressing percentage). Udder volume and MY resulted positively genetically correlated (average correlation 0.427), whereas the low-negative genetic correlation between MY and UC (-0.141) suggested a negative impact of milk gain on udder form. Beef traits of factor muscularity and PT showed medium-high favourable genetic correlations (from 0.357 to 0.984), excluding a null correlation between daily gain and muscularity. The genetic correlation MY v. muscularity was unfavourable (-0.328 on average), whereas null correlations were found in MY v. PT, apart from fat v. dressing percentage (-0.151). Somatic cell score showed low unfavourable correlations with protein (0.111) and UV (0.092), and favourable correlations with UC (-0.193). Response to selection in different scenarios indicated a good balanced gain for milk and beef when standardized economic weights of 0.66 and 0.34 are given to the two attitudes, and SCS genetic gain is restricted. Current genetic trends (MY and PT increasing, but muscularity lessening) reflect a stronger selection for milk, suggesting a slight progressive change towards a milk conformation. Aiming to preserve the dual-purpose characteristics of a breed, proper breeding policies taking into account the genetic relationships among traits and including functional traits should be applied in local dual-purpose populations.

Genetic correlations between type and test-day milk yield in small dual-purpose cattle populations: The Aosta Red Pied breed as a case study

This study aimed at estimating the relationships between linear type traits and milk production in the dual-purpose Aosta Red Pied (ARP) cattle breed, by expressing type traits as factor scores with the same biological meaning of the individual traits. Factor analysis was applied to individual type traits for muscularity and udder of 32,275 first-parity ARP cows, obtaining 3 factor scores for individual muscularity (F1), udder side (F2), and udder conformation (F3). Data from 169,008 test-day records of milk, fat, and protein yield (kg), belonging to the first 3 lactations of 16,605 cows, were also analyzed. After obtaining genetic parameters for both morphological factors and milk production traits through a series of AIREML single-trait models, bivariate analyses were performed on a data set accounting for 201,283 records of 35,530 cows, to assess the phenotypic and genetic correlations among all factor scores and milk yield traits. The heritability estimates obtained proved to be moderate for both groups of traits, ranging from 0.132 (fat) to 0.314 (F1). Muscularity factor showed moderate and negative genetic correlations (ra) with udder size (-0.376) and udder conformation (0.214) factors. A low and negative ra was found between udder factors. Strong and positive ra were found among all the 3 milk production traits and F 0010 (ra≥0.597). Negative ra with milk traits were obtained for both F 0005 and F3, ranging from -0.417 to -0.221. Phenotypic correlations were lower than the genetic ones, and sometimes close to zero. The antagonism between milk production and meat attitude traits suggests that great attention should be paid in assigning proper weight to the traits, comprising functional traits such as udder conformation, included in selection indices for the dual-purpose breed. The ra obtained for factor scores are consistent with previous estimates for the corresponding individual type traits, and this confirms the possible use of factor analysis to improve type traits relevant to beef attitude.

Factor analysis for genetic evaluation of linear type traits in dual-purpose autochthonous breeds.

Factor analysis was applied to individual type traits (TT) scored in primiparous cows belonging to two dual purpose Italian breeds, Rendena (REN; 20 individual type traits evaluated on 11 399 first parity cows), and Aosta Red Pied (ARP; 22 individual type traits evaluated on 36 168 primiparous cows). Six common latent factors (F1 to F6; eigenvalues ⩾1) which explained 63% (REN) and 58% (ARP) of the total variance were obtained. F1 included TT mainly related to muscularity, and F2 to body size. The F3 and F4 accounted for udder size and conformation, respectively. F5 included rear legs and feet. Biological significance for F6 was not readily obtained. Moderate to low heritability were estimated through REML single-trait analysis from factor scores (from 0.22 to 0.52 in REN, and from 0.08 to 0.37 in ARP). The greatest heritability values were estimated for body size and muscularity (0.52 and 0.37 for body size; and 0.40 and 0.32 for muscularity in REN and ARP, respectively). As expected, rank correlations, obtained considering estimated breeding values derived from best linear unbiased prediction analysis on the individual TT and factor score, showed similar coefficients to those observed in the factor analysis following loading of TT within each latent factor. These results suggest the possibility to implement the factor analysis in the morphological evaluation, simplifying the information given by the type traits into new variables useful for the genetic improvement of dual purpose cattle.