Genome-wide association study for posthitis in the free-living population of European bison (Bison bonasus)

Oleński, Kamil; Tokarska, Małgorzata; Hering, Dorota; Puckowska, Paulina; Ruść, A.; Pertoldi, Cino; Kamiński, Stanisław

doi:10.1186/s13062-014-0033-6

Cited by 11 publications

(10 citation statements)

References 30 publications

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“…For the European bison, however, large regions of the genome had a 100% (or near 100%) frequency of SNPs falling within a ROH. This suggests high levels of inbreeding, which is consistent with earlier studies and known population history involving a severe bottleneck [17, 18]. However, even limited inbreeding can cause detrimental effects [1, 19] and should be monitored.…”

Section: Discussionsupporting

confidence: 86%

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

Iacolina

Strønen

Pertoldi

et al. 2016

International Journal of Genomics

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Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.

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Section: Discussionsupporting

confidence: 86%

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

Iacolina

Strønen

Pertoldi

et al. 2016

International Journal of Genomics

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“…The differences in heterozygosity levels observed among populations, especially for YAK, can be partially explained by the SNP array design, which did not include all the cattle populations evaluated in this study and therefore, ascertainment bias might have influenced the estimates. It is worth noting that cattle SNP chip panels have been used for genotyping animals from other Bovidae species (e.g., bison, water buffalo, YAK), which generated very relevant results (e.g., Michelizzi et al, 2011 ; Wu et al, 2012 ; Oleński et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

et al. 2021

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Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (FST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

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“…However, by contrast, Paris et al (2017) [ 18 ] recovered a higher number of loci using de novo pipeline in comparison to a reference pipeline in RAD-Seq processing. In our case, we presume that the decreased number of SNPs from the de novo pipeline when compared to the reference pipeline might be explained by the extremely low level of heterozygosity of the European bison, which was reported in previous studies [ 24 , 27 ].…”

Section: Discussionmentioning

confidence: 59%

“…Previous genomic studies on the European bison (Bison bonasus) mainly utilized the genomic resources available for cattle. This approach turned out to be successful in a num- ber of studies [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ] but also leaves doubt that the evolutionarily acquired changes of the species might have remained unknown due to the application of non-specific tools [ 30 ]. There is a dramatic demographic history of the species: extinction in the wild, recovery based on just seven founders with extremely unequal gene shares, and high inbreeding resulted in one of the lowest known genetic diversity in wild mammals.…”

Section: Introductionmentioning

confidence: 99%

In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Kunvar

Czarnomska

Pertoldi

et al. 2021

Animals

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The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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Genome-wide association study for posthitis in the free-living population of European bison (Bison bonasus)

Cited by 11 publications

References 30 publications

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

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