Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle

Abstract

Linkage disequilibrium (LD) and the persistence of its phase across populations are important for genomic selection as well as fine scale mapping of quantitative trait loci (QTL). However, knowledge of LD in beef cattle, as well as the persistence of LD phase between crossbreds (C) and purebreds, is limited. The objective of this study was to understand the patterns of LD in Angus (AN), Charolais (CH), and C beef cattle based on 31,073, 32,088, and 33,286 SNP in each population, respectively. Amount of LD decreased rapidly from 0.29 to 0.23 to 0.19 in AN, 0.22 to 0.16 to 0.12 in CH, 0.21 to 0.15 to 0.11 in C, when the distance range between markers changed from 0–30 kb to 30–70 kb and then to 70–100 kb, respectively. Breeds and chromosomes had significant effects (P < 0.001) on LD decay. There was significant interaction between breeds and chromosomes (P < 0.001). Correlations of LD phase were high between C and AN (0.84), C and CH (0.81), as well as between AN and CH (0.77) for distances less than or equal to 70 kb. These dropped when the distance increased. Estimated effective population sizes for AN and CH were 207 and 285, respectively, for 10 generations ago. Given a useful LD of at least 0.3 between pairs of SNPs, the LD phase between any pair of the three breed groups was highly persistent. The current SNP density would allow the capture of approximately 49% of useful LD between SNP and marker QTL in AN, and 38% in CH. A higher density SNP panel or redesign of the current panel is needed to achieve more of useful LD for the purpose of genomic selection beef cattle.

Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattle

“…Therefore, selection to improve milk traits would increase LD on BTA 14. In contrast, Lu et al (2012) reported higher LD on BTA 5 in Angus beef cattle, because several QTLs and genes like IGF-1 and myf5, which affect birth weight and carcass traits, were found on it. However, comparisons between LD values estimated in previous studies showed differences depending on marker type, sample size, and density.…”

“…Information concerning the structure of LD at the population level is crucial for interpretation and application of the results of genome wide association studies (Meuwissen and Goddard 2000;Khatkar et al 2006a;Bohmanova et al 2010;Lu et al 2012) and for determination of the statistical doi: 10.17221/56/2017-CJAS power of association studies (Khatkar et al 2007;Kim and Kirkpatrick 2009). Characterization of the empirical patterns of LD across the genome is important to improve our understanding the biological pathway of recombinations and selection results in the bovine genome (Khatkar et al 2006a;Bohmanova et al 2010).…”

Genome-wide linkage disequilibrium analysis of indigenous cattle breeds of Ethiopia and Korea using different SNP genotyping BeadChips

“…Although the values were not consistent across the chromosomes, LD estimates were slightly greater for longer chromosomes compared to shorter chromosomes. Differences in LD among chromosomes have been reported in cattle (Khatkar et al 2008;Lu et al 2012) and sheep (García-Gámez et al 2012). These differences might be attributed to variation in autosomal recombination rates, genetic drift and selection influences (Arias et al 2009;Qanbari et al 2010).The variation in LD across autosomal chromosomes implies that LD estimates based on a limited number of chromosomes are likely to be inaccurate (Khatkar et al 2008).…”

“…Estimation of the extent of linkage disequilibrium between markers is becoming increasingly critical for quantitative trait loci (QTL) mapping, association studies, and application of marker-assisted selection (Goddard and Hayes 2012;Kim et al 2009). Additionally, information on LD is useful for identifying genomic regions under selection (Hayes et al 2009;Prasad et al 2008) and estimating effective population sizes (The Bovine HapMap Consortium 2009;Lu et al 2012;Zhu et al 2013).…”

Evaluation of the genome in bird breeding

“…Так, чип Illumina SNP60K BeadChip для кур состоит из панели 57 636 SNP (Groenen et al, 2011), которые нашли применение в анализе различных коммерческих (Qanba ri et al, 2010) и генофондных популяций кур (Wragg et al, 2012). Оценка LD полезна в анализе малочисленных по-пуляций кур для определения эволюционной истории и расчета генетических параметров популяций, особенно при отсутствии племенных записей (Andreescu et al, 2007;Lu et al, 2012). Точная характеристика неравновесия по сцеплению внутри и между популяциями играет важную роль в генетических исследованиях домашних птиц, так как лежит в основе всех форм картирования генов и явля-ется важным параметром при проектировании маркерных панелей.…”