Linkage disequilibrium compared between five populations of domestic sheep

Jennifer Rs Meadows,James W Kijas,Eva Kf Chan

doi:10.1186/1471-2156-9-61

Jennifer Rs Meadows, James W Kijas + Show 1 more

Open Access

https://doi.org/10.1186/1471-2156-9-61

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Abstract

BackgroundThe success of genome-wide scans depends on the strength and magnitude of linkage disequilibrium (LD) present within the populations under investigation. High density SNP arrays are currently in development for the sheep genome, however little is known about the behaviour of LD in this livestock species. This study examined the behaviour of LD within five sheep populations using two LD metrics, D' and x2'. Four economically important Australian sheep flocks, three pure breeds (White Faced Suffolk, Poll Dorset, Merino) and a crossbred population (Merino × Border Leicester), along with an inbred Australian Merino museum flock were analysed.ResultsShort range LD (0 – 5 cM) was observed in all five populations, however the persistence with increasing distance and magnitude of LD varied considerably between populations. Average LD (x2') for markers spaced up to 20 cM exceeded the non-syntenic average within the White Faced Suffolk, Poll Dorset and Macarthur Merino. LD decayed faster within the Merino and Merino × Border Leicester, with LD below or consistent with observed background levels. Using marker-marker LD as a guide to the behaviour of marker-QTL LD, estimates of minimum marker spacing were made. For a 95% probability of detecting QTL, a microsatellite marker would be required every 0.1 – 2.5 centimorgans, depending on the population used.ConclusionSheep populations were selected which were inbred (Macarthur Merino), highly heterogeneous (Merino) or intermediate between these two extremes. This facilitated analysis and comparison of LD (x2') between populations. The strength and magnitude of LD was found to differ markedly between breeds and aligned closely with both observed levels of genetic diversity and expectations based on breed history. This confirmed that breed specific information is likely to be important for genome wide selection and during the design of successful genome scans where tens of thousands of markers will be required.

Highlights

The success of genome-wide scans depends on the strength and magnitude of linkage disequilibrium (LD) present within the populations under investigation
Comparison between metrics in this study revealed the average magnitude of D' was higher than x2' for a given genetic distance (Table 2 and Additional file 3) and many more marker pairs had elevated values (LD > 0.60) using D'
Knowledge concerning the behaviour of LD is important for performing genome wide association analysis and the emerging objective of genomic selection

Summary

Introduction

The success of genome-wide scans depends on the strength and magnitude of linkage disequilibrium (LD) present within the populations under investigation. A faster and more economical way to narrow the genetic interval surrounding a gene of interest is through whole genome scans and linkage disequilibrium (LD) mapping. The extent of LD serves to inform the number of markers required for a whole genome scan. A population with extensive LD will require a lower marker density as large tracts of the genome will be redundant to those surrounding it. Recombination events, population dynamics including drift and admixture as well as breed selection bottlenecks all serve to influence the extent of LD. With this in mind, it is important to quantify the extent of LD within different breeds as this is likely to have an impact on the success of gene mapping experiments

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