Development of a standardized multiplex SSR kit for genotyping both goats and sheep
2022
Spanoghe, M.C. | Whannou, H.R.V. | Dekuijper, C. | Dossa, L.H. | Lanterbecq, D.
In this technical note, we report the development of a reliable standardized protocol based on the multiplex SSR-PCR approach for genotyping the two small ruminant species, goats and sheep. The method is based on PCR conditions optimization allowing 12 informative microsatellites (SSR) markers to be co-amplified in two multiplex sets of 6 SSR markers, followed by a co-migration into one run onto a genetic analyzer. The performance of the assay was tested on a total of 207 goats and 197 sheep, originating from different breeds and localities sampled mainly in Benin, but also to lesser extent in Belgium. The optimized assay showed that the 12 selected markers were suited to amplify all the loci distributed between the two species with valuable genetic information, specific-species allelic patterns and similar polymorphism information content. The validated loci were polymorphic with high allele numbers for the two species, ranging from 6 to 21 for goats and 7 to 15 for sheep, with average 10.58 alleles per locus for goats and 11.33 for sheep, respectively. The Polymorphic Information Content (PIC) of selected markers averaged a value of 0.712 for goats and 0.751 for sheep. The differentiation of SSR alleles at an intraspecific resolution level allowed different heterotic groups to be detected, such as geographical or breeding groups. The newly developed genotyping kit could be successfully applied in diverse genetic variability studies and relatedness analyses, as well as for population structure assessment, parentage determination and traceability concerns, within and among sheep and goat species.
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