Genomic Association between SNP Markers and Diseases in the “Curraleiro Pé-Duro” Cattle

Susceptibility to diseases is inherited and can be transmitted between populations. Single-nucleotide polymorphism (SNPs) in genes related to immune response is associated with diseases in cattle. This study investigated SNPs in the genomic region of cytokines in 702 samples of Curraleiro Pé-Duro cattle and associated them with the occurrence of antibodies in brucellosis, leptospirosis, neosporosis, leukosis, infectious bovine rhinotracheitis (IBR), and bovine viral diarrhea (BVD) tests. DNA samples were evaluated by the kompetitive allele-specific polymerase chain reaction (KASP) method to identify polymorphisms. The gametic phase and SNP haplotypes were determined with the help of PHASE 2.1.1 software. Haplotypes were associated with serological results against Brucella abortus, Leptospira sp., Neospora caninum, leukosis, infectious rhinotracheitis, and BVD using univariate analysis followed by logistic regression. Haplotype 2 of TLR2 was present in 70% of the animals that tested positive for N. caninum infection. Haplotypes of TLR10 and TLR6 and IL10RA were more common in seronegative animals. Haplotypes related to the gene IL10RA were associated with animals negative to all infections. Curraleiro Pé-Duro cattle presented polymorphisms related to resistance to bacterial, viral, and N. caninum infections.

On the logic of Fisherian sexual selection

In Fisher’s model of sexual selection, a female preference for a male trait spreads together with the trait because their genetic bases become correlated. This can be interpreted as a ‘greenbeard’ system: a preference gene, by inducing a female to mate with a trait-bearing male, favors itself because the male is disproportionately likely also to carry the preference gene. Here, we use this logic to argue that Fisherian sexual selection in diploids proceeds via two channels, corresponding to two reasons that trait-bearing males disproportionately carry preference genes: (i) trait-bearing males are disproportionately the product of matings between preference-bearing mothers and trait-bearing fathers, and thus trait and preference genes are correlated ‘in trans’; (ii) trait and preference genes come into gametic phase disequilibrium, and thus are correlated ‘in cis’. Gametic phase disequilibrium is generated by three distinct mechanisms: a ‘recombination mechanism’, a ‘dominance mechanism’, and a ‘sexual admixture mechanism’. The trans channel does not operate when sexual selection is restricted to the haploid phase, and therefore represents a fundamental difference between haploid and diploid models of sexual selection. We use simulation experiments to artificially eliminate the cis channel, and show that a preference gene can spread in its absence in the diploid model, but not in the haploid model. We further show that the cis and trans channels contribute equally to the spread of the preference when recombination between the preference and trait loci is free, but that the trans channel becomes substantially more important when linkage is tight.

Genomic data reveals large similarities among Canadian and French maternal pig lines

Combining reference populations from different countries and breeds could be an affordable way to enlarge the size of the reference populations for genomic prediction of breeding values. Therefore, the main objectives of this study were to assess the genetic diversity within and between two Canadian and French pig breeds (Landrace and Yorkshire) and the genomic relatedness among populations to evaluate the feasibility of an across-country reference population for pig genomic selection. A total of 14 756 pigs were genotyped on two single nucleotide polymorphism (SNP) chip panels (∼65K SNPs). A principal component analysis clearly discriminated Landrace and Yorkshire breeds, and also, but to a lesser extent, the Canadian and French purebred pigs of each breed. Linkage disequilibrium (LD) between adjacent SNPs was similar within Yorkshire populations. However, levels of LD were slightly different for Landrace populations. The consistency of gametic phase was very high between Yorkshire populations (0.96 at 0.05 Mb) and high for Landrace (0.88 at 0.05 Mb). Based on consistency of gametic phase, Canadian and French pig maternal lines are genetically close to each other. These results are promising, as they indicate that the accuracy of estimated genomic breeding values may increase by combining reference populations from the two countries.

Number of recombinations and genetic properties of a maize population undergoing recurrent selection

In maize recurrent selection programs, selected genotypes were recombined once to generate genetic variability for the next selection cycle. Selection generates negative gametic phase disequilibrium which reduces genetic variances, and this disequilibrium is not significantly reduced with only one generation of recombination. The objective of this research was to assess the effects of one additional generation of recombination on phenotypic and genotypic parameters in a maize population undergoing recurrent selection. Selected progenies of the EPB-4 population were subjected to one and two generations of recombination, and from each generation half- and full-sib progenies were developed and evaluated at three environments for grain yield, plant and ear heights, prolificacy, and ear placement. There were no significant changes between each progeny type with one and two generations of recombination for the means, ranges, phenotypic distribution of the traits, genetic variances, heritability coefficients, and genetic correlations for the traits assessed. The results suggest that an additional generation of recombination will not increase the effectiveness of maize recurrent selection programs.