Development of a SNP parentage assignment panel in some North-Eastern Spanish meat sheep breeds

Jorge H Calvo,Magdalena Serrano,Pilar Sarto,Stéphane Fabre,José Folch,Flavie Tortereau,Laura P Iguacel,Belén Lahoz,José L Alabart,María A Jiménez

doi:10.5424/sjar/2020184-16805

Abstract

Aim of study: To validate two existing single nucleotide polymorphism (SNP) panels for parentage assignment in sheep, and develop a cost effective genotyping system to use in some North-Eastern Spanish meat sheep populations for accurate pedigree assignment.Area of study: SpainMaterial and methods: Nine sheep breeds were sampled: Rasa Aragonesa (n=38), Navarra (n=39), Ansotana (n=41), Xisqueta (n=41), Churra Tensina (n=38), Maellana (39), Roya Bilbilitana (n=24), Ojinegra (n=36) and Cartera (n=39), and these animals were genotyped with the Illumina OvineSNP50 BeadChip array. Genotypes were extracted from the sets of 249 SNPs and 163 SNPs for parentage assignment designed in France and North America, respectively. Validation of a selected cost-effective genotyping panel of 158 SNPs from the French panel were performed by Kompetitive allele specific PCR (KASP). Additionally, some functional SNPs (n=15) were also genotyped.Main results: The set of 249 SNPs for parentage assignment showed better diversity, probability of identity, and exclusion probabilities than the set of 163 SNPs. The average minor allele frequency for the set of 249, 163 and 158 SNPs were 0.41 + 0.01, 0.39 + 0.01 and 0.42 + 0.01, respectively. The parentage assignment rate was highly dependent to the percentage of putative sires genotyped.Research highlights: The described method is a cost-effective genotyping system combining the genotyping of SNPs for the parentage assignment with some functional SNPs, which was successfully used in some Spanish meat sheep breeds.

Highlights

Breeding programs have the purpose to get sustainable genetic gains in one or several traits while controlling the loss of genetic variation
The objective of this study was to validate two existing single nucleotide polymorphism (SNP) panels for parentage assignment in sheep, including the French panel, and develop a cost-effective genotyping system of a reduced set of SNPs in an open platform to use in some North-Eastern Spanish meat sheep populations for accurate pedigree assignment
We selected two sets of SNPs for parentage assignment described in sheep

Summary

Introduction

Breeding programs have the purpose to get sustainable genetic gains in one or several traits while controlling the loss of genetic variation. Complete pedigree information is a prerequisite to get accurate EBVs, correctly rank parents and offspring and maximize the genetic gain (Israel & Weller, 2000; Raoul et al, 2016). In this sense, the proportion of known sires is very low in Spanish meat sheep populations because the management (extensive or semi-extensive farming) relies very little on artificial insemination (AI) or natural mating with a single ram per group of ewes. The implementation of a mating scheme based in pedigree information can control the inbreeding that is greatly affected by population structure (Gutiérrez et al, 2008)

Objectives

Methods

Results