Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

Vincent Prieur; Shannon M Clarke; Luiz F Brito; John C McEwan; Michael A Lee; Rudiger Brauning; Ken G Dodds; Benoît Auvray

doi:10.1186/s12863-017-0534-2

Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

BMC Genet. 2017 Jul 21;18(1):68. doi: 10.1186/s12863-017-0534-2.

Authors

Vincent Prieur^{1

2}, Shannon M Clarke¹, Luiz F Brito³, John C McEwan¹, Michael A Lee⁴, Rudiger Brauning¹, Ken G Dodds⁵, Benoît Auvray⁴

Affiliations

¹ AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.
² Current address: France Limousin Sélection, Pôle de Lanaud, 87220, Boisseuil, France.
³ Centre for Genetic Improvement of Livestock, University of Guelph, N1G2W1, Guelph, Canada.
⁴ Department of Mathematics and Statistics, University of Otago, Dunedin, 9058, New Zealand.
⁵ AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand. ken.dodds@agresearch.co.nz.

Abstract

Background: Investments 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 (N_e) 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 N _e 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 N _e . 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).

Results: The estimates obtained with M2 and M3 showed much less variability between autosomes than those with M1, which tended to give lower N _e results and higher LD decay. The results suggest that N _e has decreased since the development of sheep breeds in Europe and this reduction in N_e has been accelerated in the last three decades. The N _e 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.

Conclusions: M3 was considered the most accurate method to create genetic maps for the estimation of LD and N_e. 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.

Keywords: Genetic diversity; LD; Ovine 50 K SNP chip; Ovis aries; genetic maps.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Breeding
Chromosome Mapping*
Genetic Markers
Genome
Linkage Disequilibrium*
Polymorphism, Single Nucleotide*
Population Density
Sheep / genetics*

Substances

Genetic Markers