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Linkage disequilibrium compared between five populations of domestic sheep.

Meadows JR, Chan EK, Kijas JW - BMC Genet. (2008)

Bottom Line: Sheep 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Livestock Industries, Level 5 Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia. Jennifer.Meadows@csiro.au

ABSTRACT

Background: The 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 x Border Leicester), along with an inbred Australian Merino museum flock were analysed.

Results: Short 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 x 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.

Conclusion: Sheep 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.

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Cluster analysis of five sheep populations. Analysis of White Faced Suffolk (WFS), Poll Dorset (PD), Merino (MER), Merino × Border Leicester (MxB) and the Macarther Merino using STRUCTURE v2.2 [14] reveals the total genetic variation was explained with four sub-populations.
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Figure 1: Cluster analysis of five sheep populations. Analysis of White Faced Suffolk (WFS), Poll Dorset (PD), Merino (MER), Merino × Border Leicester (MxB) and the Macarther Merino using STRUCTURE v2.2 [14] reveals the total genetic variation was explained with four sub-populations.

Mentions: The level of relatedness between ovine populations was investigated by calculation of pair-wise FST (Table 1). The smallest value was observed between the White Faced Suffolk (WFS) and Poll Dorset (PD) (FST = 0.035), indicating of the five groups analysed, these two are the most closely related. The next lowest FST was observed between the MER and MxB (FST = 0.043). This is likely a reflection of the common Merino contribution to both populations. The highest FST values were observed for every pair-wise combination of populations which included the EMAI animals. A cluster based method was used to estimate the minimum number of sub-populations (K) required to explain the total sum of genetic variation observed [14]. Figure 1 illustrates four sub-populations (K = 4) differentiated the MER, MxB and EMAI as distinct populations, however the fourth cluster contains both the WFS and PD. The undifferentiated genetic unit containing both the WFS and PD is in keeping with the low FST reported for these breeds and is also consistent with breed history, as the White Faced Suffolk was founded in part by the Poll Dorset. Cluster analysis also illustrated subpopulation diversity. Figure 1 shows the EMAI group as a solid green block which is almost completely free from contribution of other sub-populations whilst MER appears to be a more heterogeneous subpopulation.


Linkage disequilibrium compared between five populations of domestic sheep.

Meadows JR, Chan EK, Kijas JW - BMC Genet. (2008)

Cluster analysis of five sheep populations. Analysis of White Faced Suffolk (WFS), Poll Dorset (PD), Merino (MER), Merino × Border Leicester (MxB) and the Macarther Merino using STRUCTURE v2.2 [14] reveals the total genetic variation was explained with four sub-populations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2572059&req=5

Figure 1: Cluster analysis of five sheep populations. Analysis of White Faced Suffolk (WFS), Poll Dorset (PD), Merino (MER), Merino × Border Leicester (MxB) and the Macarther Merino using STRUCTURE v2.2 [14] reveals the total genetic variation was explained with four sub-populations.
Mentions: The level of relatedness between ovine populations was investigated by calculation of pair-wise FST (Table 1). The smallest value was observed between the White Faced Suffolk (WFS) and Poll Dorset (PD) (FST = 0.035), indicating of the five groups analysed, these two are the most closely related. The next lowest FST was observed between the MER and MxB (FST = 0.043). This is likely a reflection of the common Merino contribution to both populations. The highest FST values were observed for every pair-wise combination of populations which included the EMAI animals. A cluster based method was used to estimate the minimum number of sub-populations (K) required to explain the total sum of genetic variation observed [14]. Figure 1 illustrates four sub-populations (K = 4) differentiated the MER, MxB and EMAI as distinct populations, however the fourth cluster contains both the WFS and PD. The undifferentiated genetic unit containing both the WFS and PD is in keeping with the low FST reported for these breeds and is also consistent with breed history, as the White Faced Suffolk was founded in part by the Poll Dorset. Cluster analysis also illustrated subpopulation diversity. Figure 1 shows the EMAI group as a solid green block which is almost completely free from contribution of other sub-populations whilst MER appears to be a more heterogeneous subpopulation.

Bottom Line: Sheep 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Livestock Industries, Level 5 Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia. Jennifer.Meadows@csiro.au

ABSTRACT

Background: The 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 x Border Leicester), along with an inbred Australian Merino museum flock were analysed.

Results: Short 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 x 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.

Conclusion: Sheep 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.

Show MeSH
Related in: MedlinePlus