Linkage disequilibrium analysis for microsatellite loci in six cattle breeds

Kiselyova, Tatyana; Kantanen, Juha; Vorobyov, N. I.; Podoba, B. E.; Terletsky, Valeriy P.

doi:10.1134/s1022795414040048

Cited by 10 publications

(8 citation statements)

References 22 publications

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“…Understanding the genetic diversity and population structure of local cattle breeds is necessary for their genetic improvement and the development of effective conservation programs as well as for understanding their capacity to survive under certain environmental conditions [ 54 , 55 ]. Numerous studies have been undertaken to characterize the Russian cattle breeds using mitochondrial DNA polymorphisms [ 19 ], single protein-coding genes [ 56 ] and multiple microsatellite loci [ 11 , 18 – 21 , 57 ]. To elucidate the origin of the Russian cattle population, we investigated the genetic diversity and population structure of nine Russian cattle breeds, including eight breeds from the European part of Russia and one breed native to Siberia (Yakut), and their relationship with the cattle breeds from around the world at the whole-genome level using a set of 35,874 polymorphic SNPs from the Bovine SNP50 K BeadChip (Illumina, Inc., San-Diego, USA).…”

Section: Discussionmentioning

confidence: 99%

Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

et al. 2018

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BackgroundThe origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references.ResultsThe observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337–0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource.ConclusionsWhole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0408-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

et al. 2018

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“…Based on microsatellite diversity, the hybrid origin of the Near East cattle breeds was verified [19,20] and the different histories of Mediterranean and Northern European cattle populations were proven [21]. Microsatellites were successfully applied to study genetic diversity, genetic structure and diversity of several Russian cattle breeds [22][23][24]. With the publication of the complete sequence of a cattle genome in 2009 [25,26], it became possible to trace the history of breed origins and to evaluate genetic relationships between modern breeds, based on the results of genome-wide SNP screening [27][28][29][30][31].…”

Section: Abstract: Russian Cattle Breeds Whole-genome Snp Screeningmentioning

confidence: 99%

Study of Genetic Diversity and Population Structure of Five Russian Cattle Breeds Using Whole-Genome SNP Analysis

Zinovieva¹,

Dotsev²,

Sermyagin³

et al. 2016

S-h. biol.

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With the publication of the complete sequence of a cattle genome, it became possible to trace the history of breed origins and to evaluate genetic relationships between modern breeds, based on the results of genome-wide SNP screening. Whilst numerous studies have been undertaken to characterize the commercial breeds and some local cattle breeds of Europe, North America, Asia and Africa at whole-genome level, little is known about genetic differences, relationships and population genetic structure of the Russian native cattle breeds. The aim of our work was to study the genetic diversity and population structure of five locally-developed Russian cattle breeds, based on genome-wide single nucleotide polymorphisms (SNPs) generated using Illumina Bovine SNP50 BeadChips (Illumina, San Diego, CA, USA). In total, 116 samples (sperm or tissue) collected from five breeds were analyzed, including Bestuzhev (BEST, n = 27), Kholmogor (KHLM, n = 25), Kostromsky (KSTR, n = 20), Red Gorbatov (RGBT, n = 23) and Yaroslavl breeds (YRSL, n = 21). Samples of Holstein cattle (HLST, n = 29) were used for comparison. Quality filtering of genetic markers was performed in PLINK v 1.07. Data processing was performed using software PLINK 1.

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“…Compared to human studies, likely due to smaller effective population size and intensive selection pressure, higher levels of LD have been found in livestock species [ 9 – 11 ]. Although, several studies have been conducted regarding linkage disequilibrium in cattle populations based on microsatellite markers [ 12 , 13 ], availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds [ 14 – 16 ]. Extensive LD along with different patterns on each chromosome observed in different cattle breeds, have confirmed that the LD maps can be used to characterize the cattle populations.…”

Section: Introductionmentioning

confidence: 99%

Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data

2015

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BackgroundKnowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data.ResultsA total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r2 criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r2 above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations.ConclusionsA wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.

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Linkage disequilibrium analysis for microsatellite loci in six cattle breeds

Cited by 10 publications

References 22 publications

Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

Study of Genetic Diversity and Population Structure of Five Russian Cattle Breeds Using Whole-Genome SNP Analysis

Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data

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