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

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posted on 2023-05-03, 16:04 authored by Vincent Prieur, Shannon ClarkeShannon Clarke, Luiz Brito, John McEwanJohn McEwan, Michael Lee, Ken Dodds, Rudiger BrauningRudiger Brauning, Benoit Auvray
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 (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 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).

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Rights statement

© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Language

  • English

Does this contain Māori information or data?

  • No

Publisher

BioMed Central

Journal title

BMC Genetics

ISSN

1471-2156

Citation

Prieur, V., Clarke, S. M., Brito, L. F., McEwan, J. C., Lee, M. A., Dodds, K. G., … Auvray, B. (2017). Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps. BMC Genetics, 18, 68. doi:10.1186/s12863-017-0534-2

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