Heterophil/lymphocyte response of local Spanish breeds of laying hens to cold stress, heat stress, and water restriction.

Environmental challenges may adversely affect poultry production. Autochthonous breeds are particularly valuable in a climate change context because of adaptation to the local environment. The objective of the present study was to determine the impact of cold stress, water restriction, and heat stress on the stress response quantified by the heterophil to lymphocyte ratio (H/L) of ten local Spanish breeds of laying hens. Hens of these local breeds were consecutively subjected to three treatments: natural cold stress (2, 4, 6, 7, 9, and 13 °C), water restriction (with a duration of 2.5, 4.5, 7, 10, and 12 h, respectively), and natural heat stress (23, 26, 28, 30, 34, 38, 40, and 42 °C). During cold stress, H/L was higher at 9 and 13 °C than at 2, 4, and 6 °C, and higher at 9 °C than at 7 °C (P < 0.05). H/L values were similar during all water restriction levels. During heat stress, H/L was particularly elevated at temperatures higher than 40 °C (P < 0.05). Overall, Andaluza Azul, Andaluza Perdiz and Prat Codorniz showed lowest resilience to stress based on their H/L response, whereas Pardo de Leon, Villafranquina Roja, and Prat Leonada showed highest resilience.

Failing the four-gamete test enables exact phasing: the Corners' Algorithm.

BACKGROUND: Failing the four-gamete test for two polymorphic DNA markers is an indication that two or three rather than four haplotypes segregate in the population. The objective of this paper is to show that when just three haplotypes are segregating, all three haplotypes can be fully and unambiguously phase-resolved. THEORY AND METHODS: The Corners' Algorithm tests the four corners in a 3 × 3 table of two-locus genotypes. If one of the four corners is filled with zeroes, then the missing haplotype is identified and the phases of all three haplotypes can be unambiguously resolved for all individuals. Three applications of this method are proposed when the four-gamete test fails: (1) direct estimation of linkage disequilibrium (LD), (2) haplotype-based genome-wide association studies (GWAS) of three haplotypes (single-marker GWAS tests for two out of three haplotypes only), and (3) haplotyping of chromosomal regions that are comprised of pairs of single nucleotide polymorphisms (SNPs) that consist of just three haplotypes. An example based on 435 sows with performance records for total number of piglets born is used to illustrate the methods. RESULTS: Of 20,339 SNPs, approximately 50% of the pairs of flanking SNPs failed the four-gamete test. For those, the expectation maximization (EM) algorithm gave the same results. The average of the absolute value of the difference in r2 between flanking SNPs across the genome between the two methods was 0.00082. Single-marker GWAS (using two of three haplotypes) detected significant associations for total number of piglets born on chromosomes 1, 2, 6, 9, 10, 12, 13, 14, 15, and 18. Haplotype-based GWAS using the third haplotype resolved with the Corners' Algorithm detected additional significant associations for total number of piglets born on chromosomes 2, 5, 10, 13, 14, 15, and 18. Estimated substitution effects ranged from 0.40 to 1.35 piglets. Haplotyping of chromosomal regions that failed the four-gamete test for any pair of SNPs covered 961 Mb out of the 2249 Mb by the SNP array. CONCLUSIONS: The Corner's Algorithm allows to fully phase haplotypes when the four-gamete test fails. Longer haplotypes in chromosomal regions in which the four-gamete test fails for any pair of SNPs can be used as a multi-allelic marker with increased polymorphism information content.

Vector space algebra for scaling and centering relationship matrices under non-Hardy-Weinberg equilibrium conditions.

BACKGROUND: Scales are linear combinations of variables with coefficients that add up to zero and have a similar meaning to "contrast" in the analysis of variance. Scales are necessary in order to incorporate genomic information into relationship matrices for genomic selection. Statistical and biological parameterizations using scales under different assumptions have been proposed to construct alternative genomic relationship matrices. Except for the natural and orthogonal interactions approach (NOIA) method, current methods to construct relationship matrices assume Hardy-Weinberg equilibrium (HWE). The objective of this paper is to apply vector algebra to center and scale relationship matrices under non-HWE conditions, including orthogonalization by the Gram-Schmidt process. THEORY AND METHODS: Vector space algebra provides an evaluation of current orthogonality between additive and dominance vectors of additive and dominance scales for each marker. Three alternative methods to center and scale additive and dominance relationship matrices based on the Gram-Schmidt process (GSP-A, GSP-D, and GSP-N) are proposed. GSP-A removes additive-dominance co-variation by first fitting the additive and then the dominance scales. GSP-D fits scales in the opposite order. We show that GSP-A is algebraically the same as the NOIA model. GSP-N orthonormalizes the additive and dominance scales that result from GSP-A. An example with genotype information on 32,645 single nucleotide polymorphisms from 903 Large-White × Landrace crossbred pigs is used to construct existing and newly proposed additive and dominance relationship matrices. RESULTS: An exact test for departures from HWE showed that a majority of loci were not in HWE in crossbred pigs. All methods, except the one that assumes HWE, performed well to attain an average of diagonal elements equal to one and an average of off diagonal elements equal to zero. Variance component estimation for a recorded quantitative phenotype showed that orthogonal methods (NOIA, GSP-A, GSP-N) can adjust for the additive-dominance co-variation when estimating the additive genetic variance, whereas GSP-D does it when estimating dominance components. However, different methods to orthogonalize relationship matrices resulted in different proportions of additive and dominance components of variance. CONCLUSIONS: Vector space methodology can be applied to measure orthogonality between vectors of additive and dominance scales and to construct alternative orthogonal models such as GSP-A, GSP-D and an orthonormal model such as GSP-N. Under non-HWE conditions, GSP-A is algebraically the same as the previously developed NOIA model.

Prospects for sustainability of pig production in relation to climate change and novel feed resources.

Pig production systems provide multiple benefits to humans. However, the global increase in meat consumption has profound consequences for our earth. This perspective describes two alternative scenarios for improving the sustainability of future pig production systems. The first scenario is a high input-high output system based on sustainable intensification, maximizing animal protein production efficiency on a limited land surface at the same time as minimizing environmental impacts. The second scenario is a reduced input-reduced output system based on selecting animals that are more robust to climate change and are better adapted to transform low quality feed (local feeds, feedstuff co-products, food waste) into meat. However, in contrast to the first scenario, the latter scenario results in reduced predicted yields, reduced production efficiency and possibly increased costs to the consumer. National evaluation of the availability of local feed and feedstuff co-product alternatives, determination of limits to feed sourced from international markets, available land for crop and livestock production, desired production levels, and a willingness to politically enforce policies through subsidies and/or penalties are some of the considerations to combine these two scenarios. Given future novel sustainable alternatives to livestock animal protein, it may become reasonable to move towards an added general premium price on 'protein from livestock animals' to the benefit of promoting higher incomes to farmers at the same time as covering the extra costs of, politically enforced, welfare of livestock animals in sustainable production systems. © 2020 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Extent of third-order linkage disequilibrium in a composite line of Iberian pigs.

BACKGROUND: Previous studies on linkage disequilibrium have investigated second order linkage disequilibrium in animal and plant populations. The objective of this paper was to investigate the genome-wide levels of third order linkage disequilibrium in a composite line founded by admixture of four Iberian pig strains. A model for the generation of third order linkage disequilibrium by population admixture is proposed. A computer Expectation-Maximization algorithm is developed and applied to the estimation of third order linkage disequilibrium at inter- and intra-chromosomal level using 26,347 SNPs typed in 306 sows. The relationship of third order linkage disequilibrium with physical distance was investigated over 35 million triplets in SSC12. Basic and normalized estimates of inter and intra-chromosomal third order linkage disequilibrium are reported. RESULTS: Genome-wide analyses revealed that third order linkage disequilibrium is rather common among linked loci in this Iberian pig line. It is shown that population admixture of multiple populations may explain the observed levels of third order linkage disequilibrium although it could be generated by genetic drift. Third order linkage disequilibrium decreases rapidly up to 4 Mb and then declines slowly. The short distances between consecutive markers explain the maintenance of the observed third order linkage disequilibria levels when using a model incorporating the break-up of disequilibrium by recombination. Genome-wide testing also revealed that only 3.6% of the normalized estimates were different from 1, - 1, 0, or from a not well-defined situation in which there is only one possible value for the third order linkage disequilibrium parameter, given allele frequencies and pairwise linkage disequilibria parameters. CONCLUSIONS: Third order linkage disequilibrium is common among linked markers in the analyzed pig line and may have been generated by population admixture of multiple populations or by genetic drift. As with second order linkage disequilibrium, the absolute value of the third order linkage disequilibrium decreases with physical distance. Normalization of third order linkage disequilibrium should be avoided for closely linked bi-allelic loci.

Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs.

BACKGROUND: The increasing availability of DNA markers provides new metrics of inbreeding based on single nucleotide polymorphisms (SNPs), i.e. molecular inbreeding or the proportion of runs of homozygosity (ROH), as alternatives to traditional pedigree-based inbreeding coefficients. However, none of these metrics incorporate the length of ROH as an indicator of recent inbreeding. Novel inbreeding coefficients that incorporate length of ROH as a random variable with an associated density are investigated. METHODS: New inbreeding metrics based on the distribution of the length of ROH are proposed: (1) the Kolmolgorov-Smirnov test, (2) a function of the quantiles of the cumulative distribution function of an individual versus the population, and (3) fitting of an exponential distribution to ROH lengths (mean, variance, and the probability of drawing at random a ROH larger than a given threshold). The new inbreeding and pedigree-based metrics were compared using 217 sows of an Iberian line that belong to three groups: C1 (conservation), C2 (conservation derived from C1), and S (selected and derived from C1), with complete pedigrees and genotyped for 35,023 SNPs. RESULTS: Correlations between pedigree-based and the new genomic inbreeding coefficients ranged from 0.22 to 0.72 but most ranged from 0.60 to 0.70. The correlation between quantile chromosomal inbreeding coefficients (using molecular information of just one chromosome at the time) and chromosomal length was 0.84 (SE = 0.14), supporting the hypothesis that these coefficients incorporate information on ROH length as an indication of recent inbreeding. Kolmogorov-Smirnov and exponential chromosomal inbreeding coefficients were also correlated with chromosomal length (0.57). Chromosome 1 had the largest quantile ROH inbreeding coefficient (largest ROH sizes), whereas chromosome 10 had the lowest (shortest ROH sizes). Selection for lean growth increased ROH-based inbreeding coefficients for group S when compared to unselected groups C1 and C2. At the chromosomal level, this comparison showed that the level of autozygosity and the length of ROH for most of the autosomes increased in the selection line. CONCLUSIONS: Quantile and exponential probability inbreeding coefficients using ROH length as a random variable provide additional information about recent inbreeding compared to existing inbreeding coefficients such as molecular, pedigree-based or total ROH content inbreeding coefficients.

Impact of environmental temperature on production traits in pigs.

There is an urgent need to identify the effects of temperature on production traits. This study aimed to determine the impact of pig production in three environments (T°Cgrowing-°Cfattening-°Cfinishing = T24-24-21, T19-19-19, and T23-17-15) on growth curve parameters, body weight gain (DBWG), feed intake (DFI), and feed efficiency during the growing, fattening and finishing stages, and on carcass yield of primal cuts (ham, shoulder, and loin) in 158 Duroc × Iberian pigs. Maturation rate was higher in T23-17-15 than in T19-19-19 (P < 0.001). Pigs in T23-17-15 reached a lower mature body weight (P < 0.05). During the growing stage, pigs in T23-17-15 had higher DFI than those in T24-24-21 and T19-19-19 (P < 0.05); during the fattening stage, DFI was lowest in T24-24-21 (P < 0.001). In the growing stage, pigs had highest DBWG in the warmest environments (T24-24-21 and T23-17-15) and lowest in the coldest environment (T19-19-19; P < 0.001). Feed efficiency was highest in warmer environments (P < 0.01). Temperature T24-24-21 favored loin yield, T19-19-19 favored ham yield, and T23-17-15 favored shoulder yield (P < 0.01). The results imply a favorable effect of temperature on feed efficiency, however, possible negative implications for animal health and welfare should be considered.

Autozygosity and Genetic Differentiation of Landrace and Large White Pigs as Revealed by the Genetic Analyses of Crossbreds.

Genomic information from crossbreds is routinely generated for genomic evaluations. The objective of this study is to investigate autozygosity and genetic differentiation in Landrace by Large-White breeds by using the genotypic information of SNP arrays in 1,173 crossbreds. A maximum likelihood approach was developed to estimate the probability of autozygosity (FL ). Regions of differentiation between breeds were investigated using FST and the difference in allele frequencies between the two parental breeds (릌Δ) at each single-nucleotide polymorphism (SNP) position. A maximum likelihood approach was proposed to estimate allele frequencies in the parental populations. The average length of runs of homozygosity (ROH) across the genome was 3.91, 2.3, and 0.7 Mb for segments with at least 25, 15, and 5 SNPs, respectively. Average age to coalesce was 46, 414, and 388 years for segments with at least 25, 15, and 5 SNPs, respectively. The probability of autozygosity was not uniform along the crossbred genome, being higher at the center for most chromosomes. The correlation between autozygosity and distance to the closest telomere was positive and significant in most chromosomes, which could be attributed to the higher recombination rate near telomeres. We also report a relatively high negative correlation between probability of recombination (from a published map) and probability of autozygosity. It supports that structural characteristics of the chromosomes related to recombination rate determine autozygosity at each chromosomal position of the pig genome. The average is Δ across the genome was 0.17 (SD = 0.16). After testing for differences in allele frequencies between the parental breeds, there were 4,184 SNPs with a likelihood ratio test, LRT ≥ 32.02. The average FST across the genome was 0.038 (SD = 0.059). There were 2,949 SNPs with FST > 0.125. The correlation between estimates of FL and estimates of FST across the genome was -0.10 (SE = 0.006). Analysis of the gene content of the genomic regions with the 2000 SNPs with highest LRT for FL and high FST showed overrepresentation of genes with a regulatory function. Genes with biological functions associated with production, such as tissue development, anatomical structure, and animal organ development, were also overrepresented in regions with a high FST .

Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs.

A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation maximization algorithm has been proposed for estimating these parameters in half-sibs without phasing the progeny. It, however, overlooks the fact that the underlying likelihood function may have two maxima. The magnitudes of the maxima depend on the maternal allele frequencies at the investigated marker pair. Which maximum the algorithm converges to depends on the chosen start values. We present a stepwise procedure in which the relationship between the two modes is exploited. The expectation maximization algorithm for the parameter estimation is applied twice using different start values, followed by a decision process to assess the most likely estimate. This approach was validated using simulated genotypes of half-sibs. It was also applied to a dairy cattle dataset consisting of multiple half-sib families and 39,780 marker genotypes, leading to estimates for 12,759,713 intrachromosomal marker pairs. Furthermore, the proper order of markers was verified by studying the mean of estimated recombination rates in a window adjacent to the investigated locus as well as in a window at its most distant chromosome end. Putatively misplaced markers or marker clusters were detected by comparing the results with the revised bovine genome assembly UMD 3.1.1. In total, 40 markers were identified as candidates of misplacement. This outcome may help improving the physical order of markers which is also required for refining the bovine genetic map.

A Hypothesis and Review of the Relationship between Selection for Improved Production Efficiency, Coping Behavior, and Domestication.

Coping styles in response to stressors have been described both in humans and in other animal species. Because coping styles are directly related to individual fitness they are part of the life history strategy. Behavioral styles trade off with other life-history traits through the acquisition and allocation of resources. Domestication and subsequent artificial selection for production traits specifically focused on selection of individuals with energy sparing mechanisms for non-production traits. Domestication resulted in animals with low levels of aggression and activity, and a low hypothalamic-pituitary-adrenal (HPA) axis reactivity. In the present work, we propose that, vice versa, selection for improved production efficiency may to some extent continue to favor docile domesticated phenotypes. It is hypothesized that both domestication and selection for improved production efficiency may result in the selection of reactive style animals. Both domesticated and reactive style animals are characterized by low levels of aggression and activity, and increased serotonin neurotransmitter levels. However, whereas domestication quite consistently results in a decrease in the functional state of the HPA axis, the reactive coping style is often found to be dominated by a high HPA response. This may suggest that fearfulness and coping behavior are two independent underlying dimensions to the coping response. Although it is generally proposed that animal welfare improves with selection for calmer animals that are less fearful and reactive to novelty, animals bred to be less sensitive with fewer desires may be undesirable from an ethical point of view.

A multistage testing strategy for detection of quantitative trait Loci affecting disease resistance in Atlantic salmon.

A multistage testing strategy to detect QTL for resistance to infectious salmon anemia (ISA) in Atlantic salmon is proposed. First, genotyping of amplified fragment length polymorphisms (AFLP) and a transmission disequilibrium test (TDT) were carried out using dead offspring from a disease resistance challenge test. Second, AFLP genotyping among survivors followed by a Mendelian segregation test was performed. Third, within-family survival analyses using all offspring were developed and applied to significant TDT markers with Mendelian inheritance. Maximum-likelihood methodology was developed for TDT with dominant markers to exploit linkage disequilibrium within families. The strategy was tested with two full-sib families of Atlantic salmon sired by the same male and consisting of 79 offspring in total. All dead offspring from the two families were typed for 64 primer combinations, resulting in 340 scored markers. There were 26 significant results out of 401 TDTs using dead offspring. In the second stage, only 17 marker families showed Mendelian segregation and were tested in survival analysis. A permutation test was performed for all survival analyses to compute experimentwise P-values. Two markers, aaccac356 and agccta150, were significant at P < 0.05 when accounting for multiple testing in the survival analyses. The proposed strategy might be more powerful than current mapping strategies because it reduces the number of tests to be performed in the last testing stage.

The use of genetic markers to measure genomic response to selection in livestock.

A method to measure genomic response to natural and artificial selection by means of genetic markers in livestock is proposed. Genomic response through several levels of selection was measured using sequential testing for distorted segregation of alleles among selected and nonselected sons, single-sperm typing, and a test with records for growth performance. Statistical power at a significance level of 0.05 was >0.5 for a marker linked to a QTL with recombination fractions 0, 0.10, and 0.20 for detecting genomic responses for gene effects of 0.6, 0.7, and 1.0 phenotypic standard deviations, respectively. Genomic response to artificial selection in six commercial bull sire families comprising 285 half-sib sons selected for growth performance was measured using 282 genetic markers evenly distributed over the cattle genome. A genome-wide test using selected sons was significant (P < 0.001), indicating that selection induces changes in the genetic makeup of commercial cattle populations. Markers located in chromosomes 6, 10, and 16 identified regions in those chromosomes that are changing due to artificial selection as revealed by the association of records of performance with alleles at specific markers. Either natural selection or genetic drift may cause the observed genomic response for markers in chromosomes 1, 7, and 17.

Genotype by environment interaction and breeding for robustness in livestock.

The increasing size of the human population is projected to result in an increase in meat consumption. However, at the same time, the dominant position of meat as the center of meals is on the decline. Modern objections to the consumption of meat include public concerns with animal welfare in livestock production systems. Animal breeding practices have become part of the debate since it became recognized that animals in a population that have been selected for high production efficiency are more at risk for behavioral, physiological and immunological problems. As a solution, animal breeding practices need to include selection for robustness traits, which can be implemented through the use of reaction norms analysis, or though the direct inclusion of robustness traits in the breeding objective and in the selection index. This review gives an overview of genotype × environment interactions (the influence of the environment, reaction norms, phenotypic plasticity, canalization, and genetic homeostasis), reaction norms analysis in livestock production, options for selection for increased levels of production and against environmental sensitivity, and direct inclusion of robustness traits in the selection index. Ethical considerations of breeding for improved animal welfare are discussed. The discussion on animal breeding practices has been initiated and is very alive today. This positive trend is part of the sustainable food production movement that aims at feeding 9.15 billion people not just in the near future but also beyond.

Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations.

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 (SD 0.00) and 0.19 (SD 0.03) for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by: a) estimation of the recombination fraction and LD in consecutive SNPs using family information, b) linkage analyses between fragments, c) phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual (sire level). SNPs for which the sire and calf were heterozygotes became informative (over 90%) after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes (with at least 20 SNP) in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.

Swine leukocyte antigen (SLA) diversity in Sinclair and Hanford swine.

The swine leukocyte antigen (SLA) haplotype B is associated with increased penetrance of the tumor traits in Sinclair swine cutaneous melanoma (SSCM). We established a series of SinclairxHanford swine crosses to facilitate genetic mapping of the tumor-associated loci. In this study, the SLA diversity in the founding animals was characterized for effective selection of maximum tumor penetrance in the pedigrees. Using the sequence-based typing (SBT) method we identified a total of 29 alleles at five polymorphic SLA loci (SLA-1, SLA-3, SLA-2, DRB1 and DQB1) representing six class I and five class II haplotypes. We subsequently developed a rapid PCR-based typing assay using sequence-specific primers (PCR-SSP) to efficiently follow the SLA types of the crossbred progeny. In a total of 469 animals we identified three crossovers within the class I region and three between the class I and class II regions, which corresponded to recombination frequencies of 0.39% and 0.56%, respectively. We also confirmed the presence of two expressed SLA-1 loci in three of the class I haplotypes and were able to determine the relative chromosomal arrangement of the duplicated loci in two haplotypes. This study furthers our understanding of the allelic architecture and polymorphism of the SLA system and will facilitate the mapping of loci associated with the expression of SSCM.