Abstract
BackgroundInvestments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of linkage disequilibrium (LD) and ancestral effective population size (Ne) through quantifying this diversity and comparison between populations allows for more informed decisions with regards to selective breeding taking population genetic diversity into account. The estimation of Ne can be determined via genetic markers and requires knowledge of genetic distances between these markers. Single nucleotide polymorphisms (SNP) data from a sample of 12,597 New Zealand crossbred and purebred sheep genotyped with the Illumina Ovine SNP50 BeadChip was used to perform a genome-wide scan of LD and Ne. Three methods to estimate genetic distances were investigated: 1) M1: a ratio fixed across the whole genome of one Megabase per centiMorgan; 2) M2: the ratios of genetic distance (using M3, below) over physical distance fixed for each chromosome; and, 3) M3: a genetic map of inter-SNP distances estimated using CRIMAP software (v2.503).ResultsThe estimates obtained with M2 and M3 showed much less variability between autosomes than those with M1, which tended to give lower Ne results and higher LD decay. The results suggest that Ne has decreased since the development of sheep breeds in Europe and this reduction in Ne has been accelerated in the last three decades. The Ne estimated for five generations in the past ranged from 71 to 237 for Texel and Romney breeds, respectively. A low level of genetic kinship and inbreeding was estimated in those breeds suggesting avoidance of mating close relatives.ConclusionsM3 was considered the most accurate method to create genetic maps for the estimation of LD and Ne. The findings of this study highlight the history of genetic selection in New Zealand crossbred and purebred sheep and these results will be very useful to understand genetic diversity of the population with respect to genetic selection. In addition, it will help geneticists to identify genomic regions which have been preferentially selected within a variety of breeds and populations.
Highlights
Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness
This can be achieved using genomic information and for this purpose, we utilized a dataset of 12,597 animals genotyped with the Illumina OvineSNP50 BeadChip; a single nucleotide polymorphisms (SNP) array developed by the International Sheep Genomics Consortium (ISGC) in conjunction with Illumina [4, 7]
The results show clearly that using M2 or M3 affects the estimates of linkage disequilibrium (LD) and Effective population size (Ne) compared to M1
Summary
Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Sheep have spread throughout the whole world and have been raised and genetically improved for various purposes such as meat, wool, fiber, skin and milk [1, 2] The footprints of this selection remain in the sheep genome and can be used to investigate the history of the species and its spread across the world [3, 4]. Natural selection combined with recent breed creation has led to an overall decrease of the genetic diversity observed within isolated populations [5]. It is crucial to understand the genetic structure of the selected populations and to assess its genetic diversity This can be achieved using genomic information and for this purpose, we utilized a dataset of 12,597 animals genotyped with the Illumina OvineSNP50 BeadChip; a SNP array developed by the International Sheep Genomics Consortium (ISGC) in conjunction with Illumina [4, 7]
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