Abstract
BackgroundNew Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs. These composite breeds were developed based on crossing various Terminal Sire and Maternal breeds and, therefore, present high genetic diversity compared to other sheep breeds. Their breeding programs are focused on improving carcass and meat quality traits. There is an interest from the industry to implement genomic selection in this population to increase the rates of genetic gain. Therefore, the main objectives of this study were to determine the accuracy of predicted genomic breeding values for various growth, carcass and meat quality traits using a HD SNP chip and to evaluate alternative genomic relationship matrices, validation designs and genomic prediction scenarios. A large multi-breed population (n = 14,845) was genotyped with the HD SNP chip (600 K) and phenotypes were collected for a variety of traits.ResultsThe average observed accuracies (± SD) for traits measured in the live animal, carcass, and, meat quality traits ranged from 0.18 ± 0.07 to 0.33 ± 0.10, 0.28 ± 0.09 to 0.55 ± 0.05 and 0.21 ± 0.07 to 0.36 ± 0.08, respectively, depending on the scenario/method used in the genomic predictions. When accounting for population stratification by adjusting for 2, 4 or 6 principal components (PCs) the observed accuracies of molecular breeding values (mBVs) decreased or kept constant for all traits. The mBVs observed accuracies when fitting both G and A matrices were similar to fitting only G matrix. The lowest accuracies were observed for k-means cross-validation and forward validation performed within each k-means cluster.ConclusionsThe accuracies observed in this study support the feasibility of genomic selection for growth, carcass and meat quality traits in New Zealand Terminal Sire breeds using the Ovine HD SNP chip. There was a clear advantage on using a mixed training population instead of performing analyzes per genomic clusters. In order to perform genomic predictions per breed group, genotyping more animals is recommended to increase the size of the training population within each group and the genetic relationship between training and validation populations. The different scenarios evaluated in this study will help geneticists and breeders to make wiser decisions in their breeding programs.
Highlights
New Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs
The difference in number of records is because only genotyped animals were included in this study and not all of them were measured for all the traits, plus some traits were not recorded in all flocks (e.g. BWT) and a quality control of the raw data was done as previously described
Heritability estimates for traits measured in the live animal, carcass and meat quality traits ranged from 0.10 to 0.43, 0.14 to 0.28 and 0.04 to 0.31, respectively
Summary
New Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs These composite breeds were developed based on crossing various Terminal Sire and Maternal breeds and, present high genetic diversity compared to other sheep breeds. Their breeding programs are focused on improving carcass and meat quality traits. Increased production efficiency is directly related to profitability To maintain this change and to increase the proportion entering the premium markets, both meat presentation and quality have to be improved continuously. Genomic selection (GS) [4] is revolutionising livestock breeding programs worldwide and is one of the most promising tools to genetically improve quality and production of sheep meat
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