Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in <scp>E</scp>thiopia

Edea, Zewdu; Dadi, Hailu; Kim, S.W.; Park, Jun Hyung; Shin, Ga-Hee; Dessie, Tadelle; Kim, K.S.

doi:10.1111/jbg.12083

Cited by 36 publications

(40 citation statements)

References 31 publications

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“…Similarly, the differences in LD between Hanwoo and Ethiopian cattle could Genes Genom be attributed to ascertainment bias. In the 50 K BeadChip, SNPs were mainly discovered from Bos taurus breeds and they were more common in the Bos taurus cattle breeds compared to Ethiopian cattle populations,which have significant ancestry from zebu (Bos indicus) (Edea et al 2014). Both measures of LD tended to decrease with increasing physical distances between adjacent SNPs.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a higher SNP density 80 K BeadChip, which is mainly derived from Bos indicus breeds, has become commercially available (GeneSeek Genomic Profiler HD BeadChip). In a recent study, we employed this BeadChip to analyze Ethiopian cattle breeds and obtained higher minor allele frequencies and diversity indices for most breeds (Edea et al 2014) than in earlier studies using Illumina 9 and 50 K BeadChips (Edea et al 2015;Edea et al 2013). The extent of LD influences both genome-wide association studies and the accuracy of genomic predictions.…”

Section: Introductionmentioning

confidence: 94%

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

et al. 2015

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Knowledge of the extent of linkage disequilibrium (LD) between markers is crucial for determining the number of markers required for quantitative trait loci mapping, genome-wide association studies, and application of marker-assisted selection. In this study, we surveyed genome-wide LD using three genotyping BeadChips (9, 50, and 80 K) in 11 indigenous Ethiopian cattle populations and the Korean (Hanwoo) cattle breed. The overall mean r 2 values were 0.05 ± 0.12, 0.12 ± 0.20, and 0.20 ± 0.24 in the Ethiopian cattle populations for the 9, 50, and 80 K genotyping BeadChips, respectively. In Hanwoo cattle, these values were respectively 0.06 ± 0.13, 0.15 ± 0.23, and 0.15 ± 0.26. The level of LD was significantly affected by breed, genotyping BeadChip, and chromosome (P \ 0.0001). For Ethiopian cattle populations, a moderate level of LD (r 2 = 0.22) extended at marker distances of 20-40 kb for the indicine-derived 80 K BeadChip, whereas it was only 0.14 for the 50 K BeadChip. As a consequence of the moderate r 2 , genome-wide association studies in Ethiopian cattle populations require 75,000-150,000 indicine-derived SNPs (with a MAF C 0.05). We suggest that indicine-derived SNPs maybe more suitable for genomewide association studies and genomic selection in indigenous Ethiopian (or African) cattle populations.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 94%

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

et al. 2015

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“…Similarly, metabolic genes of cattle living in the Ethiopian highlands bear strong signatures of selection (Edea et al . ). Pigs living in the Tibetan Plateau also bear signatures of selection for genes involved in angiogenesis, response to hypoxia and nucleic acid metabolism (Dong et al .…”

Section: A Survey Of Empirical Gwssmentioning

confidence: 97%

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

2015

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Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example FST, cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.

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“…Selection signature analyses in cattle also revealed novel potential selection targets. A genetic comparison of cattle populations from low and high altitude in Ethiopia revealed novel potential selection targets involved in hypoxia response ( BDNF , TFRC , PML ), metabolism ( ATP2A3 , CA2 , MYO18B , SIK3 , INPP4A , IREB2 ) and heat stress ( PRKDC , CDK1 , TFDC ) (Edea et al ). In an analysis of whole‐genome sequence data from Pakistani‐indicine cattle native to high‐altitude regions, enrichment analyses of the genes with predicted high‐impact variants resulted in a significant overrepresentation of the HIF‐1, VEGF (vascular endothelial growth factor) and VSMC (vascular smooth muscle cell) signalling pathways, highlighting the role of the cardiovascular system in altitude adaptation (Iqbal et al ).…”

Section: Genetic Background Of High‐altitude Adaptationmentioning

confidence: 99%

Selection signatures for high‐altitude adaptation in ruminants

Friedrich

Wiener

2020

Animal Genetics

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Summary High‐altitude areas are important socio‐economical habitats with ruminants serving as a major source of food and commodities for humans. Living at high altitude, however, is extremely challenging, predominantly due to the exposure to hypoxic conditions, but also because of cold temperatures and limited feed for livestock. To survive in high‐altitude environments over the long term, ruminants have evolved adaptation strategies, e.g. physiological and morphological modifications, which allow them to cope with these harsh conditions. Identification of such selection signatures in ruminants may contribute to more informed breeding decisions, and thus improved productivity. Moreover, studying the genetic background of altitude adaptation in ruminants provides insights into a common molecular basis across species and thus a better understanding of the physiological basis of this adaptation. In this paper, we review the major effects of high altitude on the mammalian body and highlight some of the most important short‐term (coping) and genetically evolved (adaptation) physiological modifications. We then discuss the genetic architecture of altitude adaptation and target genes that show evidence of being under selection based on recent studies in various species, with a focus on ruminants. The yak is presented as an interesting native species that has adapted to the high‐altitude regions of Tibet. Finally, we conclude with implications and challenges of selection signature studies on altitude adaptation in general. We found that the number of studies on genetic mechanisms that enable altitude adaptation in ruminants is growing, with a strong focus on identifying selection signatures, and hypothesise that the investigation of genetic data from multiple species and regions will contribute greatly to the understanding of the genetic basis of altitude adaptation.

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Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia

Cited by 36 publications

References 31 publications

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

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

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

Selection signatures for high‐altitude adaptation in ruminants

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