Genomic scan for identifying candidate genes for paratuberculosis resistance in sheep

Abstract

Abstract. Breeding objectives relating to health, functional traits and welfare need to receive priority in the research programs and selection schemes, but very few reports are available on natural resistant genotypes in livestock, where some important diseases cause severe economic losses and pose serious zoonotic threats. In this study, diagnosis of paratuberculosis was performed on 759 adult sheep, from a single flock, with the serum antibody enzyme-linked immunosorbent assay; 100 sheep were selected among the extreme divergent animals for the S/P ratio obtained from the test, and were genotyped on the Illumina Ovine SNP50K BeadChip. A genome-wide scan was then performed on the individual marker genotypes, in the attempt to identify genomic regions associated with disease resistance in sheep. For each marker, the allelic substitution effect was calculated by regressing the S/P value on the number of copies of the reference allele. The position on the OARv3.1 Genome Assembly was searched for 32 markers, which showed a statistically significant allelic substitution effect (Raw P < 0.0006 and FDR P < 0.09). All markers were located within, or close to, annotated genes. Five of these genes, SEMA3, CD109, PCP4, PRDM2 and ITFG2 are referred in literature to play a role in either disease resistance or cell-mediated immune response.

Identification of missense mutations in the PCP4 and CD109 genes to validate the effect of neutral genetic markers

“…Furthermore, no LD was registered between the mutation and the anonymous marker OAR1_278884883.1. In conclusion, for the PCP4 gene, the suggestive association proposed by Moioli et al (2015) might have been simply probabilistic, due to the limited size of the analyzed sample and the possible relationship between individuals of the same flock.…”

“…Genotyping results at the OvineSNP50 BeadChip for 100 sheep of the Sarda breed were available from the previous study (Moioli et al 2015); the sheep represented the two tails of the distribution of the serological assessment for MAP diagnose, that had been performed on 759 sheep of the same flock using the ELISA test. DNA of 42 genotyped Sarda sheep for the present study was provided by the Animal Health Institute of Viterbo, Italy.…”

“…Because Moioli et al (2015) had hypothesized that OAR1_278980576.1 and OAR8_270360, located in proximity of the PCP4 and the CD109 genes, were potential markers of MAP resistance, the genotyping results of the 100 Sarda sheep of the previous study were used to perform a χ 2 test of significance of differences of the allele frequencies between the 50 serologically positive and 50 negative sheep. The χ 2 test was performed on the genomic scaffolds encompassing the PCP4 and the CD109 genes, in order to restrain the genomic region to be submitted to direct DNA sequencing, because the average distance between markers of the OvineSNP50 BeadChip ranges from 60 to 200K.…”

“…The present study was conceived to search for the presence of further polymorphisms in the coding or regulatory region of PCP4 and CD109 genes that might explain and corroborate the effect of the two anonymous markers identified by Moioli et al (2015) in influencing disease resistance.…”

“…It causes substantially reduced production, higher susceptibility to acquire other diseases and infertility (Kennedy and Benedictus 2001). In a flock of MAP-infected sheep, Moioli et al (2015) performed a Genome Wide Association Analysis (GWAS) with the OvineSNP50 BeadChip on 100 ewes representing the extreme divergent animals for the optical density (S/P) ratio obtained from MAP serological assay, assessed on about 700 sheep. The authors hypothesized the presence of 30 putative candidate genes of disease susceptibility, these genes being in close proximity of the polymorphic markers which showed a significant effect on the obtained serological value.…”