Abstract
Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine (n = 24) and Saanen (n = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: CAST, CLEC4E, DES, GHRHR, HSP90AA1, IL15RA, IL1RN, IL8, MITF, PPRC1, SOCS3, TNF and TNFSF13. The studied Alpine population was in Hardy-Weinberg disequilibrium at the g.62894878A>G locus (rs671391101) (P < 0.05). The results showed that four SNPs rs671391101 (GHRHR), rs640582069 (IL1RN) rs635583012 (SOCS3) and rs635969404 (IL15RA) out of the 13 polymorphic markers were significantly associated with milk production, protein, fat and lactose content in the Alpine breed. However, no significant effect was recorded in the Saanen population regarding milk yield or milk chemical composition. The current results provide new insights for the development of SNP marker-assisted selection technology in the goat industry and confirm the potential of using SNPs for the GHRHR, IL1RN, SOCS3, and IL15RA genes as candidate genes for selection, highlighting the direct implications of such genes for farm production outputs. The results from this study are relevant for future goat genomic studies and the inclusion of the associated traits into up-to-date selection schemes.
Highlights
The goat sector within the European Union accounts for 12.3 million head (EUROSTAT, 2016), concentrated geographically in Greece, Spain, Romania, France and Italy (10.68 million altogether), with the farmers essentially focused on dairy production
The aim of the current pilot research was to investigate the polymorphism of 48 single nucleotide polymorphisms (SNPs) of 40 genes on dairy production and major milk components using genotyping methods in French Alpine and Saanen goats reared in Romania
For all investigated SNPs the KASP assays produced 2,230 identified allele calls and 122 unidentified allele calls with an allele call rate of 94,81% and a mean of unidentified allele calls of 5.19%
Summary
The goat sector within the European Union accounts for 12.3 million head (EUROSTAT, 2016), concentrated geographically in Greece, Spain, Romania, France and Italy (10.68 million altogether), with the farmers essentially focused on dairy production (milk and cheese production). As in other European countries, the main focus of the sector is milk and cheese production, with goat meat being considered a marginal product. There are significant differences in the average milk production of goats between regions, mostly due to management and feeding systems and to genetic background (breed, selection). In Romania, goats are reared predominantly in extensive low-input production systems (Raducuta, Calin & Purdoiu, 2012), and the unimproved indigenous Carpatina breed represents over 90% of the population. The breed has modest production outputs, with milk yields estimated at 220 to 350 kg/lactation (Padeanu, 2001, Pascal et al, 2011)
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