Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect of the microbiota composition on the breeding value of an animal is the conditional expectation of its breeding value, given the vector with microbiota frequencies, that is The breeding value of an animal can therefore be decomposed into a heritable contribution that arises from an altered microbiota composition and a heritable contribution that arises from altered metabolic pathways within the animal, so Instead of selecting for breeding value , an index comprising the two components and with appropriate weights, that is , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.     

Performance of pedigree and various forms of marker-derived relationship coefficients in genomic prediction and their correlations

In recent years, with development and validation of different genotyping panels, several methods have been proposed to build efficient similarity matrices among individuals to be used for genomic selection. Consequently, the estimated genetic parameters from such information may deviate from their counterpart using traditional family information. In this study, we used a pedigree-based numerator relationship matrix ( A ) and three types of marker-based relationship matrices () including two identical by descent, that is and and one identical by state, as well as four Gaussian kernel () similarity kernels with different smoothing parameters to predict yet to be observed phenotypes. Also, we used different kinship matrices that are a linear combination of marker-derived IBD or IBS matrices with A, constructed as , where the weight () assigned to each source of information varied over a grid of values. A Bayesian multiple-trait Gaussian model was fitted to estimate the genetic parameters and compare the prediction accuracy in terms of predictive correlation, mean square error and unbiasedness. Results show that the estimated genetic parameters (heritability and correlations) are affected by the source of the information used to create kinship or the weight placed on the sources of genomic and pedigree information. The superiority of GK -based model depends on the smoothing parameters (θ) so that with an optimum θ value, the GK -based model statistically yielded better performance (higher predictive correlation, lowest MSE and unbiased estimates) and more stable correlations and heritability than the model with IBD, IBS or kinship matrices or any of the linear combinations.     

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 () 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 and were obtained from elements of additive genetics ( and ) or phenotypic ( and ) (co)variance matrices. In the first case, heritabilities were low (0.07 and 0.06 for and , 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 and , respectively) but the genetic correlation between and was moderate (0.58). Heritability of G_R was low (0.08). This trait was negatively correlated with and 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.     

A method to approximate the inverse of a part of the additive relationship matrix

Single‐step genomic predictions need the inverse of the part of the additive relationship matrix between genotyped animals ( A ₂₂). Gains in computing time are feasible with an algorithm that sets up the sparsity pattern of (SP algorithm) using pedigree searches, when is close to sparse. The objective of this study is to present a modification of the SP algorithm (RSP algorithm) and to assess its use in approximating when the actual is dense. The RSP algorithm sets up a restricted sparsity pattern of by limiting the pedigree search to a maximum number of searched branches. We have tested its use on four different simulated genotyped populations, from 10 000 to 75 000 genotyped animals. Accuracy of approximation is tested by replacing the actual by its approximation in an equivalent mixed model including only genotyped animals. Results show that limiting the pedigree search to four branches is enough to provide accurate approximations of , which contain approximately 80% of zeros. Computing approximations is not expensive in time but may require a great amount of memory (at maximum, approximately 81 min and approximately 55 Gb of RAM for 75 000 genotyped animals using parallel processing on four threads).     

Interplay between heritability,genetic correlation and economic weighting in a selection index with and without genomic information

The availability of genomic information demands proper evaluation on how the kind (phenotypic versus genomic) and the amount of information influences the interplay of heritability (h²), genetic correlation () and economic weighting of traits with regard to the standard deviation of the index (σ_I). As σ_I is directly proportional to response to selection, it was the chosen parameter for comparing the indices. Three selection indices incorporating conventional and genomic information for a two trait (i and j) breeding goal were compared. Information sources were chosen corresponding to pig breeding applications. Index I incorporating an own performance in trait j served as reference scenario. In index II, additional information in both traits was contributed by a varying number of full‐sibs (2, 7, 50). In index III, the conventional own performance in trait j was combined with genomic information for both traits. The number of animals in the reference population (N_P = 1000, 5000, 10 000) and thus the accuracy of GBVs were varied. With more information included in the index, σ_I became more independent of , and relative economic weighting. This applied for index II (more full‐sibs) and for index III (more accurate GBVs). Standard deviations of index II with seven full‐sibs and index III with N_P = 1000 were similar when both traits had the same heritability. If the heritability of trait j was reduced ( = 0.1), σ_I of index III with N_P = 1000 was clearly higher than for index II with seven full‐sibs. When enhancing the relative economic weight of trait j, the decrease in σ_I of the conventional full‐sib index was much stronger than for index III. Our results imply that N_P = 1000 can be considered a minimum size for a reference population in pig breeding. These conclusions also hold for comparing the accuracies of the indices.     

Founder representation and effective population size in old versus young breeds—genetic diversity of Finnish and Nordic Spitz

Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (f_a) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis () is 168, whereas the genetic effective population size (N_eg) computed the decay of linkage disequilibrium (r²) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had f_a of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz ( = 98 and N_eg = 49). Interestingly, the r² data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed.     

An insight into population structure and gene flow within pure‐bred cats

Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree‐based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, F_IS ranged between 0.96 and 1.83%, with this result being related to mating practices such as close inbreeding (on average 5% of individuals being inbred within two generations). Within the three groups of varieties studied, F_IT ranged from 1.59 to 3%, while values were estimated between 0.04 and 0.91%, which was linked to various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high individual inbreeding level caused by close inbreeding practices.     

Bioavailability of the dl-methionine and the calcium salt of dl-methionine hydroxy analog compared with l-methionine for nitrogen retention in starter pigs

Two nitrogen balance studies were conducted to evaluate the relative bioavailability values (RBV) of dl-methionine (dl-Met) and dl-methionine hydroxy analog calcium salt (MHA-Ca) to l-methionine (l-Met) as Met sources fed to pigs. In experiment 1, 42 pigs were assigned to 7 treatments feeding with basal diet (BD) formulated to be deficient in Met (0.22% standardized ileal digestible basis) but adequate in other amino acids. Diets included (1) BD, (2) BD + 0.025% dl-Met, (3) BD + 0.050% dl-Met, (4) BD + 0.075% dl-Met, (5) BD + 0.025% l-Met, (6) BD + 0.050% l-Met, and (7) BD + 0.075% l-Met. Increasing levels of l-Met and dl-Met enhanced N retained (g/d) and N retention (% of intake) linearly (P < 0.01). Using a linear slope ratio procedure, a product-to-product RBV of dl-Met compared with l-Met was 94% (95% confidence limits: 65% to 123%) based on N retained expressed as g/d and 99% (95% confidence limits: 70% to 128%) for N retention expressed as % of intake. In experiment 2, 42 pigs were allotted to 7 treatments in another N-balance trial. Diets included (1) BD, (2) BD + 0.025% l-Met, (3) BD + 0.050% l-Met, (4) BD + 0.075% l-Met, (5) BD + 0.030% MHA-Ca, (6) BD + 0.060% MHA-Ca, and (7) BD + 0.089% MHA-Ca. An increase in dietary inclusion rates of l-Met increased (P < 0.01) N retained (g/d) linearly while increasing levels of MHA-Ca had no effects (P > 0.05) on N retained (g/d) and N retention (% of intake). Using linear slope-ratio regression, the RBV of MHA-Ca compared with l-Met was 70% (95% confidence limits: 59% to 81%) on a product-to-product basis or 83% on equimolar basis based on N retained expressed as g/d. Overall, the mean RBV of dl-Met to l-Met of 97% (95% confidence limits cover 100%) indicated that dl-Met and l-Met are equally bioavailable as Met sources in pigs. Compared with l-Met, the RBV of MHA-Ca was lower at 70% (95% confidence limits: 59% to 81%) on a product-to-product basis or 83% on equimolar basis in starter pigs.     

Functional amino acids,growth and immunity

Open in a separate window

Functional amino acids (FAA) are those that elicit a metabolic response independent of their necessity for protein synthesis. Supplementation of FAA may offset growth deficits (Ji et al., 2019; Moreira et al., 2020), boost intestinal immunity (Ren et al., 2020) and improve blood flow to tissues and organs (Peine et al., 2020) through mechanisms that include activation of cellular signaling modules (DeBoer et al., 2018; Yan et al., 2018). The piglet often is faced with health challenges that include exposure to pathogens. A recent study reports that FAA can alleviate partially the negative impacts of Salmonella infection in weaned piglets (Rodrigues et al., 2020). These results provide further evidence of FAA as critical modifiers of intestinal health and antioxidant state.     

Environmental enrichment and stress relief in pigs

Open in a separate window

Animal welfare programs implement external stimuli to relieve stress which may promote health and growth of the animal. Effective design of enrichment programs rely upon an improved understanding of animal cognition (Nawroth et al., 2019). In piglets, early life socialization can modify their behavioral responses to food rewards and other cognitive tests later in life (Weller et al., 2019; Weller et al., 2020). While the mechanism underlying cognitive and behavioral responses to stimuli remain largely unresolved, the positive impact of enrichment on animal physiology is apparent. For example, music is a simple enrichment tool that dampens stress in dogs (Lindig et al., 2020), horses (Lansade et al., 2014; Wisniewska et al., 2019) and piglets (Li et al., 2019). In this issue, Angarita et al. (2021) and Li et al. (2021) examine feeding behavior and response to music in pigs. Results provide further insight into the social behavior of young pigs and their possible effects on health.     

Phytase activity in phosphorus deficient and adequate swine diets

Open in a separate window

Cereal grains found in swine diets contain phytate, a storage form of phosphorus that is largely unavailable for use by the animal. To improve phosphorous bioavailability, diets are supplemented with phytase, an enzyme that degrades phytate to inositol phosphate isomers and inorganic phosphorus (Kebreab et al., 2012; Rosenfelder-Kuon et al., 2020). Inclusion of the enzyme in swine diets can improve calcium and phosphorus digestibility in pigs as well as increase average daily gain and feed efficiency (Ren et al., 2020). Because many of the formative studies with phytase supplementation were performed with P deficient diets, a recent study examined phytase mediated phosphorus release in diets adequate for the mineral (Olsen et al., 2021). Results indicate that phytase behaves differently when supplemented into phosphorus deficient or adequate diets.     

A comparison of small noncoding RNA requirements in mice and cattle

Open in a separate window

Long noncoding RNA (lncRNA) molecules have gained attention in the field of livestock growth biology as modifiers of gene expression and regulatory participants during both muscle and adipose development (Gao et al., 2017; Wei et al., 2019). Similar to lncRNA, small noncoding RNAs (sncRNAs) play important roles during tissue development. For example, miRNAs, a class of snRNA molecules, suppress mRNA translation of mediators of bovine germ cell physiology. In this issue, Chukrallah et al. (2021) compare and contrast the regulatory actions of snRNAs that underpin germ cell biology in mice and cattle.     

Development of multiple cutaneous and follicular neoplasms associated with canine papillomavirus type 3 in a dog

A 12‐year‐old spayed English pointer dog developed multiple skin lesions including pigmented viral plaques, basal cell carcinomas, squamous cell carcinomas and trichoblastomas. Canine papillomavirus type 3 was detected in multiple lesions suggesting common aetiology.

     

Oral and pulmonary necrobacillosis in a juvenile reticulated giraffe

A 1-mo-old reticulated giraffe had progressive anorexia and died at the Ordos Zoo. Autopsy revealed necrotic stomatitis with severe bilateral necroulcerative lesions at the base of the tongue and of the cheeks near the commissures of the mouth. There was also severe bilateral confluent bronchopneumonia with a pronounced bronchial pattern and multifocal fibrinous pleuritis. Histologically, there was serofibrinous-suppurative bronchopneumonia with necrosuppurative bronchiolitis and necrotic arteritis. Filamentous bacteria with morphology consistent with Fusobacterium necrophorum were observed at the advancing edge of the necrotic tissue in the tongue and cheeks, as well as in the affected alveolar spaces and bronchioles. Aggregates of slender, gram-negative, rod-like or filamentous bacteria were identified in the lung impression smear. PCR results of 16S rDNA of the tongue and lung lesions had 100% homology to the F. necrophorum subsp. funduliforme B35 sequence ({"type":"entrez-nucleotide","attrs":{"text":"EF447425.1","term_id":"133753393"}}EF447425.1). The gross, histologic, Gram stain, and PCR product sequencing features in our case were consistent with oral and pulmonary necrobacillosis in ruminants, a rare disease of giraffes.     

Bioavailability of the calcium salt of dl-methionine hydroxy analog compared with dl-methionine for nitrogen retention and the preference of nursery pigs for diets based on the 2 forms of methionine

Experiments were conducted to determine the relative bioavailability (RBV) of the calcium salt of the hydroxy analog of dl-methionine (MHA-Ca, 84%) to dl-methionine (dl-Met, 99%) as Met sources fed to pigs. In experiment 1, 42 crossbred barrows (initial BW of 15.0 ± 0.7 kg) were allotted to 7 treatments in an N-balance study. The basal diet (BD) was formulated to contain 15.4% CP and 0.22% Met (70% of requirement). Diets included (1) BD, (2) BD + 0.025% dl-Met, (3) BD + 0.050% dl-Met, (4) BD + 0.075% dl-Met, (5) BD + 0.038% MHA-Ca, (6) BD + 0.077% MHA-Ca, and (7) BD + 0.115% MHA-Ca. An increase in dietary inclusion rates of both Met sources linearly increased (P < 0.01) N retained (g/d) and N retention (% of intake). Using linear slope-ratio regression, the RBV value of MHA-Ca to dl-Met for N retained (g/d) was 63.0% on a product-to-product basis (75.0% on an equimolar basis). In experiment 2, 40 crossbred barrows (initial BW of 15.5 ± 1.5 kg) were allotted to 5 treatments in another N-balance study. The BD was formulated to contain 17.0% CP and 0.22% Met (70% of requirement). Diets included (1) BD, (2) BD + 0.030% dl-Met, (3) BD + 0.060% dl-Met, (4) BD + 0.046% MHA-Ca, and (5) BD + 0.092% MHA-Ca. Increasing levels of dl-Met or MHA-Ca increased N retained (g/d) and N retention (% of intake) linearly (P < 0.001) and quadratically (P < 0.05). Using linear slope-ratio regression, a product-to-product RBV value of MHA-Ca to dl-Met was 68.4% (81.4% on an equimolar basis) for N retained (g/d). In experiment 3, 276 pigs (12 barrow and 11 gilt replicates; initial BW of 7.09 ± 1.1 kg) were used in 3 diet preference studies. Pigs were randomly allotted to 1 of 3 treatment comparisons of feed choice: (1) BD (0.23% Met) or BD + 0.07% dl-Met; (2) BD or BD + 0.0825% MHA-Ca, and (3) BD + 0.07% dl-Met or BD + 0.0825% MHA-Ca. Pigs consumed a higher percentage (55 vs. 45%; P = 0.008) of their total feed intake from the diet supplemented with 0.07% dl-Met in Comparison 1, but a lower percentage (45 vs. 55%; P = 0.003) of their total feed intake from the diet supplemented with 0.0825% MHA-Ca in Comparison 2. There was no diet preference for dl-Met or MHA-Ca in Comparison 3. The observed Met source preference differences occurred in the barrow replicates but not in the gilt replicates. These results demonstrated the mean RBV of MHA-Ca to dl-Met of 65.7% on a product-to-product (wt/wt) basis or 78.2% on an equimolar basis and that a preference for Met sources was observed in barrows but not in gilts.