Detection of SNP effects on feed conversion ratio in pigs based on entropy approach

© Slovak University of Agriculture in Nitra Faculty of Agrobiology and Food Resources


Introduction
The feed conversion ratio (FCR) is a measure of the amount of feed required to produce 1 kilogramme of pig live weight.The conversion of high quality feed into weight gain is importance in modern pig breeding as a broad indicator of efficiency and ecological-friendly pig production (Sahana et al. 2013, Do et al. 2014).More efficient use of feed has the potential to reduce greenhouse gas intensity and improve productivity (MacLeod M. et al. 2013).FCR is an index based on factors affecting the variables of growth rate and feed intake, like genetic background, feeding practice, environmental control or health status.Recently, several statistical approaches to detect the effects of SNPs on livestock performance traits have been described.The most common is the Genome-Wide Association Study method, so called genome scanning, applied to study the association between value of the trait and single nucleotide polymorphisms (SNPs) distributed throughout the genome.An alternative, new approach is entropy analysis addressed for categorical characters.Theoretical backgrounds of this methodology have been described among others by Shannon (1948).This methodology has been increasingly implemented in genetic studies especially in medicine (Moore et al. 2006) however the application of entropy analysis is still growing also in animal science (Borowska et al., 2014).
The objectives of the study were to classify SNPs according to their contribution to the feed conversion ratio, as well as to indicate interactions between the most informative SNPs using entropy analysis.

Material and methods
The records of 1296 pigs from the Hylean Maxgro™ line were included.The feed conversion ratio (FCR) was analysed.Entropy analysis requires discrete variables therefore the collected data wereclassified into four groups (according to the quartiles).In consequence, the traits can be treated s categorical.Molecular data included 61 565 SNPs.Two selection criteria of this data were applied: call rate 0.95 and minor allele frequency 0.05.After this, 50 951 SNPs were included into the entropy analysis.
The effects of studied loci were examined in two steps.Firstly, genotypes were classified according to their contribution to the traits.For each SNP, entropy and conditional entropy were estimated (see e.g.Borowska et al., 2014): The objectives of the study were to classify SNPs according to their contribution to the feed conversion ratio and to indicate interactions between the most informative SNPs using entropy analysis.The records of 1296 pigs were included.Two selection criteria for molecular data were applied: call rate 0.95 and minor allele frequency 0.05.After this, 50 951 SNPs were included into the entropy analysis.For each SNP entropy and conditional entropy were estimated.For interaction analyses the most informative SNPs were selected.For each pair of SNPs, the mutual information was assessed.A majority of the loci studied showed relatively small contributions.The most informative SNPs are mainly located on chromosomes: 1, 4, 7, 9 and 14.Whereas important interactions between SNP pairs were detected on chromosomes: 1, 14, 15 and 16.High mutual information was registered for SNPs located nearby.where: p(t|s) -the probability that analysed trait (T) obtain value of t under the condition that analysed SNP (S) obtain a genotype of s n -the number of classes of trait T under analysed SNP S

Keywords
In the second stage, interactions between SNPs were analysed.For this analysis the most informative SNPs were selected.In the first step, SNPs with the smallest values of conditional entropy (from first quartile) were chosen.Next, a quarter of the most informative SNPs for each chromosome were taken into interaction analysis.For each pair of selected SNPs, the mutual information (MI) were assessed: where: H(S 1 ), H(S 2 ) -the entropies of the SNP S 1 /S 2 H(S 1 , S 2 ) -the joint entropy between SNP S 1 and S 2 Analyses were performed by the use of the R 3.1 Statistical Software (2014).

Results and discussion
The participation of analysed loci in the feed conversion ratio varied.A majority of these loci showed relatively small contributions.Normed conditional entropy coefficients (ET -EC) for the most informative SNPs are visualized on a genome-wide scale in Figure 1.2014) identified TTC29 as candidate gene for residual feed intake based on their genome-wide association analysis in pigs.

Conclusions
The most informative SNPs are mainly located on chromosomes: 1, 4, 7, 9 and 14.Whereas important interactions between SNP pairs are detected on chromosomes: 1, 14, 15 and 16.High mutual information was registered for SNPs located nearby.Moreover, entropy analysis is able to elucidate informative regions at the genome-wide level.