Czech J. Anim. Sci., 2018, 63(2):61-69 | DOI: 10.17221/56/2017-CJAS

Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattleOriginal Paper

Mohamed Mahmoud Ibrahim Salem*,1, Gertrude Thompson2, Shanyuan Chen2, Albano Beja-Pereira2,3, Julio Carvalheira2,4
1 Department of Animal and Fish Production, Faculty of Agriculture, University of Alexandria, Alexandria, Egypt
2 Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Porto, Portugal
3 Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
4 Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal

The objectives of this study were to estimate linkage disequilibrium (LD), describe and scan a haplotype block for the presence of genes that may affect milk production traits in Portuguese Holstein cattle. Totally 526 animals were genotyped using the Illumina BovineSNP50 BeadChip, which contained a total of 52 890 single nucleotide polymorphisms (SNPs). The final set of markers remaining after considering quality control standards consisted of 37 031 SNPs located on 29 autosomes. The LD parameters historical recombinations through allelic association (D') and squared correlation coefficient between locus alleles frequencies ( r2) were estimated and haplotype block analyses were performed using the Haploview software. The averages of D' and r2 values were 0.628 and 0.122, respectively. The LD value decreased with increasing physical distance. The D' and r2 values decreased respectively from 0.815 and 0.283 at the distance of 0-30 kb to 0.578 and 0.090 at the distance of 401-500 kb. The identified total number of blocks was 969 and consisted of 4259 SNPs that covered 159.06 Mb (6.24% of the total genome) on 29 autosomes. Several genes inside the haplotype blocks were detected; CSN1S2 gene in haplotype block 51 on BTA 6, IL6 and B4GALT1 genes in haplotype blocks 6 and 33 on BTA 8, IL1B and ID2 genes in haplotype blocks 19 and 29 on BTA 11, and DGAT1 gene in haplotype block 1 on BTA 14. The extension of LD using BovineSNP50 BeadChip did not exceed 500 kb and its parameters r2 and D' were less than 0.2 and 0.70, respectively, after 70-100 kb. Consequently, the 50K BeadChip would have a poor power in genome wide association studies at distances between adjacent markers lower than 70 kb.

Keywords: single nucleotide polymorphism; GWAS; dairy cattle

Published: February 28, 2018  Show citation

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Salem MMI, Thompson G, Chen S, Beja-Pereira A, Carvalheira J. Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattle. Czech J. Anim. Sci.. 2018;63(2):61-69. doi: 10.17221/56/2017-CJAS.
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