Estimating the genetic merit of sires by using pooled DNA from progeny of undetermined pedigree

Amy M Bell,Sigrid A Lehnert,Russell Mcculloch,Sonja Dominik,John M Henshall,Laercio R Porto-Neto,James Kijas

doi:10.1186/s12711-017-0303-8

Amy M Bell, Sigrid A Lehnert + Show 5 more

Open Access

https://doi.org/10.1186/s12711-017-0303-8

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Abstract

BackgroundDNA-based predictions for hard-to-measure production traits hold great promise for selective breeding programs. DNA pooling might provide a cheap genomic approach to use phenotype data from commercial flocks which are commonly group-mated with parentage unknown. This study on sheep explores if genomic breeding values for stud sires can be estimated from genomic relationships that were obtained from pooled DNA in combination with phenotypes from commercial progeny.MethodsPhenotypes used in this study were categorical data. Blood was pooled strategically aiming at even pool sizes and within sex and phenotype category. A hybrid genomic relationship matrix was constructed relating pools to sires. This matrix was used to determine the contribution of sires to each of the pools and therefore phenotype category by using a simple regression approach. Genomic breeding values were also estimated using the hybrid genomic relationship matrix.ResultsWe demonstrated that, using pooled DNA, the genetic performance of sires can be illustrated as their contribution to phenotype categories and can be expressed as a regression coefficient. Genomic estimated breeding values for sires were equivalent to the regression coefficients and are a commonly used industry tool.ConclusionsGenotyping of DNA from pooled biological samples offers a cheap method to link phenotypic information from commercial production animals to the breeding population and can be turned into information on the genetic value of stud sires for traits that cannot be measured in the stud environment.

Highlights

DNA-based predictions for hard-to-measure production traits hold great promise for selective breed‐ ing programs
Allele frequencies can be estimated from pooled genotype data and subsequently estimated effects of single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) have been demonstrated to be equivalent to effects of SNPs from individual genotyping [4, 5]
The dag score phenotype was assessed on a scale of 1 to 5 based on Visual Sheep Scores, a commercial guide for visually assessed traits developed by Australian Wool Innovation Limited (AWI) and Meat and Livestock Australia (MLA) [11]

Summary

Introduction

DNA-based predictions for hard-to-measure production traits hold great promise for selective breed‐ ing programs. Allele frequencies can be estimated from pooled genotype data and subsequently estimated effects of single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) have been demonstrated to be equivalent to effects of SNPs from individual genotyping [4, 5]. This approach reduces the cost of GWAS [6–8]. It has been demonstrated that the genetic merit of sires can be estimated from pooled DNA in combination with phenotype information collected on commercial properties during routine husbandry procedures [5, 9]

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