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Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

Makina SO, Taylor JF, van Marle-Köster E, Muchadeyi FC, Makgahlela ML, MacNeil MD, Maiwashe A - Front Genet (2015)

Bottom Line: We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20).Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner).Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Research Council-Animal Production Institute Pretoria, South Africa ; Department of Animal and Wildlife Sciences, University of Pretoria Pretoria, South Africa.

ABSTRACT
Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

No MeSH data available.


Related in: MedlinePlus

Average r2 estimates at different genetic distances for three different minor allele frequency (MAF) thresholds. Average LD estimates are pooled over all autosomal chromosomes: (A) Afrikaner, (B) Nguni, (C) Drakensberger, (D) Bonsmara, (E) Angus and, (F) Holstein.
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Figure 4: Average r2 estimates at different genetic distances for three different minor allele frequency (MAF) thresholds. Average LD estimates are pooled over all autosomal chromosomes: (A) Afrikaner, (B) Nguni, (C) Drakensberger, (D) Bonsmara, (E) Angus and, (F) Holstein.

Mentions: Three different minimum MAF thresholds (0.05, 0.1, and 0.2) were used to study the effect of MAF on the extent of LD. Figure 4 shows that MAF had an effect on the average value of r2, especially over short inter-marker distances (< 100 kb). The average r2 increased with MAF, for example, for markers with MAF ≥ 0.05 and separated by 0–10 kb, the average r2 was 0.47, 0.37, 0.37, 0.37, 0.46, and 0.45. For markers with MAF ≥ 0.1, the r2 estimates increased to 0.55, 0.42, 0.46, 0.42, 0.50, and 0.50; these estimates further increased to 0.61, 0.45, 0.49, 0.52, 0.60, and 0.57 with MAF ≥ 0.2, for Afrikaner, Nguni, Drakensberger, Bonsmara, Angus, and Holstein, respectively.


Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

Makina SO, Taylor JF, van Marle-Köster E, Muchadeyi FC, Makgahlela ML, MacNeil MD, Maiwashe A - Front Genet (2015)

Average r2 estimates at different genetic distances for three different minor allele frequency (MAF) thresholds. Average LD estimates are pooled over all autosomal chromosomes: (A) Afrikaner, (B) Nguni, (C) Drakensberger, (D) Bonsmara, (E) Angus and, (F) Holstein.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4664654&req=5

Figure 4: Average r2 estimates at different genetic distances for three different minor allele frequency (MAF) thresholds. Average LD estimates are pooled over all autosomal chromosomes: (A) Afrikaner, (B) Nguni, (C) Drakensberger, (D) Bonsmara, (E) Angus and, (F) Holstein.
Mentions: Three different minimum MAF thresholds (0.05, 0.1, and 0.2) were used to study the effect of MAF on the extent of LD. Figure 4 shows that MAF had an effect on the average value of r2, especially over short inter-marker distances (< 100 kb). The average r2 increased with MAF, for example, for markers with MAF ≥ 0.05 and separated by 0–10 kb, the average r2 was 0.47, 0.37, 0.37, 0.37, 0.46, and 0.45. For markers with MAF ≥ 0.1, the r2 estimates increased to 0.55, 0.42, 0.46, 0.42, 0.50, and 0.50; these estimates further increased to 0.61, 0.45, 0.49, 0.52, 0.60, and 0.57 with MAF ≥ 0.2, for Afrikaner, Nguni, Drakensberger, Bonsmara, Angus, and Holstein, respectively.

Bottom Line: We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20).Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner).Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Research Council-Animal Production Institute Pretoria, South Africa ; Department of Animal and Wildlife Sciences, University of Pretoria Pretoria, South Africa.

ABSTRACT
Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

No MeSH data available.


Related in: MedlinePlus