Luis Gomez-Raya

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 r ² 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.

Background Two individuals with a first-degree relationship share about 50 percent of their alleles. Parent-offspring relationships cannot be homozygotes for alternative alleles (genetic exclusion). Methods Applying the concept of genetic exclusion to HD arrays typed in animals for experimental purposes or genomic selection allows estimation of the rate of rejection of first-degree relationships as the rate at which two individuals typed for a large number of SNPs do not share at least one allele. An Expectation–Maximization algorithm is applied to estimate parentage. In addition, genotyping errors are estimated in true parent-offspring relationships due to the large number of SNPs. Nine candidate Duroc sires and 55 Iberian dams producing 214 Duroc × Iberian barrows were typed for the HD porcine Affymetrix array. Results We were able to establish paternity and maternity of 75 and 86 piglets, respectively. A lower bound of the genotyping error of 0.003345 was estimated based on the rate of rejection of true parent-offspring relationships among autosomal SNPs. The true genotyping error is estimated to be between twice and three times the average of the rate of rejection observed in true relationships, i.e., between approximately 0.0067 and 0.0100. A total of 8,558 SNPs were rejected in six or more true parent-offspring relationships facilitating identification of “problematic” SNPs with inconsistent inheritance. Conclusions This study shows that animal experiments and routine genotyping in genomic selection allow to establish or to verify first-degree relationships as well as to estimate genotyping errors for each batch of animals or experiment.

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.

We investigated the ability to predict production performance in Iberian pigs in an extensive production system from measurements of feed efficiency measured intensively. The second objective of this work was to study the relationship between feed efficiency and meat quality (composition, juiciness, tenderness, color, and subcutaneous fatty acid composition) and if cooked and cured quality properties can be predicted by properties in fresh meat. Thirty Iberian sows received successively a restricted diet of concentrate (P1concentrate) and acorns (P2acorn) intensively [...] ABSTRACT We investigated the ability to predict production performance in Iberian pigs in an extensive production system from measurements of feed efficiency measured intensively. The second objective of this work was to study the relationship between feed efficiency and meat quality (composition, juiciness, tenderness, color, and subcutaneous fatty acid composition) and if cooked and cured quality properties can be predicted by properties in fresh meat. Thirty Iberian sows received successively a restricted diet of concentrate (P1concentrate) and acorns (P2acorn) intensively

There is an interest in replacing soybean meal with locally produced ingredients in livestock feeds. Narbon vetch is resistant to unfavorable climatic and soil conditions, common pests, and has a favorable nutritional profile. The effect of substitution of soybean meal with 0% (V0), 5% (V5), 10% (V10), and 20% (V20) inclusion of Narbon vetch on growth curve parameters, daily body weight gain (DBWG), daily feed intake (DFI), feed conversion efficiency (FCE), and residual feed intake (RFI) was investigated in 47 Duroc × Iberian barrows in 16 periods (a total of 125 d). DFI and DBWG were reduced (p < 0.05) up to four weeks after introduction of the novel feed in V20 and V10. Small, mostly nonsignificant differences existed between treatments in FCE and RFI. However, because of accumulative small differences in feed efficiency between the four diets, pigs in V0 reached the highest BW, and pigs in V20 reached the lowest BW on a similar feed intake. Economic implications of Narbon vetch inclusion depend on the extra amount of feed required and associated feed costs, and on the costs of additional days on-farm required to reach a given slaughter weight.

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.

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} = T_24-24-21, T_19-19-19, and T_23-17-15) 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 T_23-17-15than in T_19-19-19(P < 0.001). Pigs in T_23-17-15reached a lower mature body weight (P < 0.05). During the growing stage, pigs in T_23-17-15had higher DFI than those in T_24-24-21and T_19-19-19(P < 0.05); during the fattening stage, DFI was lowest in T_24-24-21(P < 0.001). In the growing stage, pigs had highest DBWG in the warmest environments (T_24-24-21and T_23-17-15) and lowest in the coldest environment (T_19-19-19; P < 0.001). Feed efficiency was highest in warmer environments (P < 0.01). Temperature T_24-24-21favored loin yield, T_19-19-19favored ham yield, and T_23-17-15favored 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.

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 (F_L). Regions of differentiation between breeds were investigated using F_ST 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 F_ST across the genome was 0.038 (SD = 0.059). There were 2,949 SNPs with F_ST > 0.125. The correlation between estimates of F_L and estimates of F_ST 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 F_L and high F_ST 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 F_ST.

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. 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. 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.