Single nucleotide polymorphisms between two lines of European bison (Bison bonasus) detected by the use of Illumina Bovine 50 K BeadChip

Kamiński, Stanisław; Olech, Wanda; Oleński, Kamil; Nowak, Zuzanna; Ruść, A.

doi:10.1007/s12686-011-9535-z

Cited by 14 publications

(17 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…For comparison, in studies by Tokarska et al (2009) the 50 Lowland European bison (LB) tested gave a reading of 52,978 SNPs, of which 960 markers were polymorphic. In contrast, Kamiński et al (2012), despite testing only 10 European bison (five LB and five LC specimens), obtained 1,337 polymorphic SNPs. The number of markers was higher due to inclusion of both genetic lines in the studies and LC is intrinsically more diverse than LB, which is also noticeable in the present study.…”

Section: Discussionmentioning

confidence: 89%

“…Oleński et al (2015) used for the first time the BovineHD microarray to find SNP markers associated with posthitis in the same genetic line. The first SNP analysis using the BovineSNP50 microarray which included both genetic lines (five individuals from LB and five individuals from LC) was performed by Kamiński et al in 2012. The aim of the present study was to identify a panel of SNP markers (among those assayed on the Illumina BovineSNP50 and BovineHD arrays) that could be used to analyse genetic structure, identify individuals and control the origin and relatedness of the European bison, as well as identify alleles specific to the two genetic lines: Lowland (LB) and Lowland-Caucasian (LC). This is the first study using BovineHD microarray to compare genetic structure of two genetic lines of European bison.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Panel of informative SNP markers for two genetic lines of European bison: Lowland and Lowland–Caucasian

Wojciechowska¹,

Nowak²,

Gurgul³

et al. 2017

Anim. Biodiv. Conserv.

Self Cite

View full text Add to dashboard Cite

Panel of informative SNP markers for two genetic lines of European bison: Lowland and Lowland-Caucasian.-As the result of a population bottleneck, the present population of European bison shows a high level of inbreeding, and a significant loss of genetic variability. In studies on such specific species there is a need to apply methods that obtain as much information about the genome as possible in a short time. The aim of the study was to define a panel of SNP (single nucleotide polymorphism) markers that could serve in genetic diversity analysis of European bison from two lines: Lowland (LB) and Lowland-Caucasian (LC). The study used 57 individuals from the LB line and 72 from the LC line. To identify well-performing SNPs in European bison, we used two microarrays with different markers densities: BovineSNP50 v2 BeadChip and BovineHD BeadChip. As a result of the adopted criteria, 1,421 and 22,122 markers, respectively, were selected. On the basis of statistical analysis (allele frequencies, Fisher's exact test, and the Z-test), a panel of 1,536 informative SNP markers was ultimately selected for further study; 26 of these with private alleles for the LB line and 611 with private alleles for the LC line. The data obtained in this study could further enrich and support breeding programs in the context of relatedness between particular specimens and herds from captive breeding centres. ResumenConjunto de marcadores de tipo PSN para dos líneas genéticas de bisonte europeo: Lowland y Lowland-Caucasiana.-Debido al cuello de botella demográfico, la población actual de bisonte europeo muestra un elevado grado de endogamia y una pérdida significativa de variabilidad genética. Es necesario que en los estudios realizados con estas especies específicas se apliquen métodos que permitan obtener tanta información genómica como sea posible en un tiempo breve. El objetivo de este estudio era definir un conjunto de marcadores de tipo PSN (polimorfismo de un solo nucleótido) que pudiera servir para analizar la diversidad genética de las dos líneas de bisontes europeos: Lowland (LB) y Lowland-Caucasiana (LC). En el estudio se analizaron 57 individuos de la línea LB y 72 de la línea LC. Para caracterizar bien el rendimiento de los PSN en el bisonte europeo, se usaron dos micromatrices multigénicas (genochip) con densidades diferentes de marcadores: BovineSNP50 v2 BeadChip y BovineHD BeadChip. Como consecuencia de los criterios adoptados, se seleccionaron 1.421 y 22.122 marcadores, respectivamente. Sobre la base del análisis estadístico (frecuencias alélicas, prueba exacta de Fisher y prueba Z), en última instancia se seleccionó un conjunto de 1.536 marcadores informativos de PSN para los estudios adicionales, 26 de los cuales tienen alelos privados para LB y 611, para la línea LC. La información obtenida en este estudio podría enriquecer aún más y apoyar a los programas de reproducción en un contexto de parentesco entre especímenes particulares y manadas que viven en cautividad en centros reproductivos.Palabras claves: Bison bonasu...

show abstract

Section: Discussionmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Panel of informative SNP markers for two genetic lines of European bison: Lowland and Lowland–Caucasian

Wojciechowska¹,

Nowak²,

Gurgul³

et al. 2017

Anim. Biodiv. Conserv.

Self Cite

View full text Add to dashboard Cite

show abstract

“…In a panel of a similarly large number of SNPs designed for cattle, only about 2.5 and 3% of the cross‐species amplifications were successful in two lines of European bison and two species of antelopes respectively (Kaminski et al . ; Ogden et al . ).…”

Section: Discussionmentioning

confidence: 99%

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

et al. 2013

View full text Add to dashboard Cite

The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.

show abstract

“…Performing GWAS in wild living species is usually difficult, as all the commercially available microarray sets are designed for model or domestic animals. It has been shown that cattle SNP microarrays work well in bison species [ 6 - 8 ]. The European Bison ( Bison bonasus ), (EB), after extinction in the wild before World War II, was restored based on progeny of just 12 individuals preserved in private collections and zoological gardens [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2015

View full text Add to dashboard Cite

BackgroundAbout 5–6% of the European bison (Bison bonasus) males are affected by posthitis (necrotic inflammation of the prepuce) and die in the wild forest. Despite many years of study, pathogenesis of this disease has not yet been determined. The main aim of the study was to find SNP markers significantly associated with the incidence of posthitis and mine the genome for candidate genes potentially involved in the development of the disease.ResultsIt was shown that relatively small number of SNPs effects reached genome-wide significance after false discovery rate (FDR) correction. Among 25 significant markers, the highest effects were found for two SNPs (rs110456748 and rs136792896) located at the distance of 23846 bp and 37742 bp, respectively, from OR10A3 gene (olfactory receptor genes), known to be involved in atopic dermatitis in humans. It was also observed that five other significant SNP markers were located in the proximity of candidate genes involved in severe diseases of skin tissue and cancer/tumour development of epithelial or testicular germ cells, which suggest their potential participation in the posthitis. The 25 investigated SNPs showed marked differences in allelic and genotypic frequencies between the healthy and affected bison groups.ConclusionsThe 2 Mb region of the BTA15 chromosome is involved in genetic background of posthitis and should be closer examined to find causal mutations helpful in better understanding of the disease ethology and to control its incidence in the future.ReviewersThis article was reviewed by Prof. Lev Klebanov and Dr. Fyodor Kondrashov.

show abstract

Single nucleotide polymorphisms between two lines of European bison (Bison bonasus) detected by the use of Illumina Bovine 50 K BeadChip

Cited by 14 publications

References 6 publications

Panel of informative SNP markers for two genetic lines of European bison: Lowland and Lowland–Caucasian

Panel of informative SNP markers for two genetic lines of European bison: Lowland and Lowland–Caucasian

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

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

Contact Info

Product

Resources

About