scholarly journals Whole genome studies of origin, selection and adaptation of the Russian cattle breeds

2019 ◽  
Vol 23 (5) ◽  
pp. 559-568
Author(s):  
N. S. Yudin ◽  
D. M. Larkin
Keyword(s):  
Russian Federation ◽  
Association Studies ◽  
Coat Colour ◽  
Whole Genome ◽  
Cattle Breeds ◽  
Genome Association ◽  
Whole Genome Association ◽  
The Russian Federation ◽  
Signatures Of Selection ◽  
Cattle Domestication

Our review presents several recent studies on the genetic history and signatures of selection in genomes of the native Russian cattle breeds. Most of these works are not easily accessible for the Russian-speaking audience. We describe the origins of appearance of the Russian cattle breeds from the genetics perspective. We point to the links between most of the Russian breeds with the taurine breeds of the European origin and for some Russian breeds with the breeds of the Asian origin. We describe major phylogenetic clusters of the Russian breeds and point to those that still maintain their unique genetics, meaning that their preservation is a priority. In addition, we review the results of the search for signatures of selection in genomes of the Russian cattle breeds. Some unique signatures of selection present in the genomes of so-called “turano-mongolian” cattle (i. e. the Yakut cattle) are described which allowed the Yakut cattle to adapt to harsh environments found above the Polar Circle. Signatures of selection which could help other cattle breeds of the Russian origin to adapt to various climatic condition of the Russian Federation are reviewed. The Russian cattle genomes also contain known signatures of selection related to cattle domestication about 8–10 thousand years ago. The most profound ones include genes related to changes of the coat colour. This phenotype in many cases could be related to the distinction of the first domesticated populations and lead to the formation of so-called land races (primitive breeds). Whole-genome association studies of Russian cattle breeds pointed to a novel gene which could be related to the “white-faced” phenotype and to a gene which is related to body temperature support under the acute cold stress. The data presented in our review could be used for identification of genetic markers to focus on in future efforts on designing new highly productive cattle breeds adapted to climates of the Russian Federation and other countries with similar climates.

scholarly journals Sampling strategies for whole genome association studies in aquaculture and outcrossing plant species

2009 ◽  
Vol 91 (6) ◽  
pp. 367-371 ◽  
Author(s):  
B. J. HAYES ◽  
I. M. MACLEOD ◽  
M. BARANSKI
Keyword(s):  
Plant Species ◽  
Association Studies ◽  
Whole Genome ◽  
Minimal Effect ◽  
Sampling Strategies ◽  
False Discovery ◽  
Breeding Populations ◽  
Genome Association ◽  
Whole Genome Association ◽  
Sib Families

SummaryA number of farmed species are characterized by breeding populations of large full-sib families, including aquaculture species and outcrossing plant species. Whole genome association studies in such species must account for stratification arising from the full-sib family structure to avoid high rates of false discovery. Here, we demonstrate the value of selective genotyping strategies which balance the contribution of families across high and low phenotypes to greatly reduce rates of false discovery with a minimal effect on power.

scholarly journals Calibrating the Performance of SNP Arrays for Whole-Genome Association Studies

PLoS Genetics ◽  
2008 ◽  
Vol 4 (6) ◽  
pp. e1000109 ◽  
Author(s):  
Ke Hao ◽  
Eric E. Schadt ◽  
John D. Storey
Keyword(s):  
Association Studies ◽  
Whole Genome ◽  
Snp Arrays ◽  
Genome Association ◽  
Whole Genome Association

Exploring Genetic Basis of GVHD by Whole-Genome Association Studies in a Large Series from the Japan Marrow Donation Program (JMDP).

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3232-3232
Author(s):  
Yasuhito Nannya ◽  
Makoto Onizuka ◽  
Koichi Kashiwase ◽  
Masashi Sanada ◽  
Yoshiki Akatsuka ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Basis ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Whole Genome ◽  
Minor Histocompatibility Antigens ◽  
Therapeutic Benefits ◽  
Gvhd Prophylaxis ◽  
Genome Association ◽  
Whole Genome Association

Abstract Allogeneic stem cell transplantation (allo-HSCT) has been established as one of the most effective therapeutic options for hematopoietic malignancies. Its major therapeutic benefits are obtained from allo-immunity directed against patients’ tumor cells (graft-versus-tumor effects, GVT). However, the same kind of allo-immune reactions can also be directed to normal host tissues resulting in graft-versus-host disease (GVHD) and subsequently offset the potential benefit from GVT. Because both reactions are initiated by donor T-cells that recognize minor histocompatibility antigens (mHA) that are incompatible between donor and recipient, the knowledge of these mHA is of particular importance to develop a new measure to prevent GVHD while harnessing the antitumor potential of allo-HSCT. On the other hand, the incompatibility of mHAs, as well as other predispositions to development of GVHD, is basically determined genetically, and thus, are plausible targets of genetic association studies, which have recently been enabled with the advent of large-scale genotyping technology. In the current study, we explored genetic basis of GVHD by whole genome association studies, in which relevant SNPs to GVHD development were explored by genotyping a large cohort of GVHD-positive and negative transplantations performed through the Japan Marrow Donor Program (JMDP). Among 7,800 transplants genotyped for HLA types, we selected 1856 transplants (3712 donors/recipients) for large scale genotyping of more than 500,000 SNPs using Affymetrix® GeneChip® 500K arrays, according to the following criteria: HLA A, B, C, DR, DQ loci were completely matched at the DNA level Short term MTX (stMTX) + CyA or stMTX + FK506 was employed as GVHD prophylaxis, and Genome DNA from both donor and recipient and record of clinical course was available. Based on the genotyping data, possible association was tested for each SNP in donors and recipients with regard to the development of GVHD. Association of genotype incompatibilities was also investigated for major HLA subtypes to identify the mHA loci that are relevant to GVHD pathogenesis. In the intermediate analysis, a number of candidate polymorphisms in donors and recipients have been identified together with possible mHA loci.

Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 967-972 ◽  
Author(s):  
Robbie Waugh ◽  
David Marshall ◽  
Bill Thomas ◽  
Jordi Comadran ◽  
Joanne Russell ◽  
...  
Keyword(s):  
Gene Pool ◽  
Physical Map ◽  
Association Studies ◽  
Population Substructure ◽  
Whole Genome ◽  
Data Set ◽  
Genome Wide ◽  
Marker Loci ◽  
Genome Association ◽  
Whole Genome Association

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare ) gene pool extends, on average, for <1–5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.

scholarly journals A Randomization Test for Controlling Population Stratification in Whole-Genome Association Studies

2007 ◽  
Vol 81 (5) ◽  
pp. 895-905 ◽  
Author(s):  
Gad Kimmel ◽  
Michael I. Jordan ◽  
Eran Halperin ◽  
Ron Shamir ◽  
Richard M. Karp
Keyword(s):  
Population Stratification ◽  
Association Studies ◽  
Randomization Test ◽  
Whole Genome ◽  
Genome Association ◽  
Whole Genome Association

Weighting sequence variants based on their annotation increases power of whole-genome association studies

2016 ◽  
Vol 48 (3) ◽  
pp. 314-317 ◽  
Author(s):  
Gardar Sveinbjornsson ◽  
Anders Albrechtsen ◽  
Florian Zink ◽  
Sigurjón A Gudjonsson ◽  
Asmundur Oddson ◽  
...  
Keyword(s):  
Association Studies ◽  
Sequence Variants ◽  
Whole Genome ◽  
Genome Association ◽  
Whole Genome Association
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