Estimation of effective population size (Ne) in Angus breed by 777K Bovine BeadChip

Effective population size (Ne) is an important population parameter that helps to explain how the populations evolved and expanded, and to improve the understanding and modeling of the genetic architecture underlying complex traits [2]. Traditionally, Ne has been estimated by comparing DNA sequences. However, Ne is unlikely to have been constant during the evolution of humans, and so DNA sequence heterozygosity estimates some average Ne over a long period of time. Ne can also be estimated from linkage disequilibrium (LD) data [4]. This approach will estimate Ne over more recent history than DNA sequence heterozygosity [1] and can therefore complement evolutionary studies of human populations. Until recently it has not been possible to estimate Ne from LD due to the large number of closely linked markers required to do so. The aim of this study was calculated Ne in genome of Angus Cattle. Blood samples were collected from 42 Angus bulls and Genomic DNA was extracted from samples. The samples were genotyped by using Illumina’s bovine HD BeadChip. Data were filtered by using PLINK v1.07. After filtering a total of 14219 loci with call rates <99% were pruned. After frequency and genotyping pruning, 535696 SNPs were remaind. Only SNPs located on chromosome 1 was used to calculate r2 and Ne. the ped and map file were analyzed by Haploview v3.1. In this study, the formulation Ne=(1/4c)(1/E(r^2 ) -1) was used to estimate Ne, where c is the marker distance in Morgan on autosomes assuming 100 Mb per Morgan [3]. And the age of Ne for any distance is calculated by 1/2c. We inferred Ne on autosomes at distance bins of 0.001> , 0.001-0.002, 0.002-0.003, 0.003-0.004, 0.004-0.005, 0.005-0.006, 0.006-0.007, 0.007-0.008, 0.008-0.009, 0.009-0.01 cM. In this study, that the average r2 decreased with the increasing distance of SNP pairs. Specifically, the average r2 was equal to 0.6 when the SNP pair distances were less than 10 kb. With the SNP pairs increase to 100 kb, the average r2 was only 0.02. This Result showed the estimated Ne decreased through time and Ne for Angus from 1666 at 5000 generation ago were decresed to 1065 animals in the last generation (500 generations ago).

Keywords:

effective population size , Genome , Angus cattle , BovinHD , r2