The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep

Abstract

In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.). This greatly complicates the use of GWAS results for breeding needs. Within the framework of human genetics, there are several technological solutions for researching the harmonized results of GWAS, including one of the largest, the GWAS-MAP platform. For other types of living organisms, including economically important agricultural animals, there are no similar solutions. To our knowledge, no similar solution has been proposed to date for any of the species of economically important animals. As part of this work, we focused on creating a platform similar to GWAS-MAP for working with the results of GWAS of sheep, since sheep breeding is one of the most important branches of agriculture. By analogy with the GWAS-MAP platform for storing, unifying and analyzing human GWAS, we have created the GWAS-MAP|ovis platform. The platform currently contains information on more than 34 million associations between genomic sequence variants and traits of meat production in sheep. The platform can also be used to conduct colocalization analysis, a method that allows one to determine whether the association of a particular locus with two different traits is the result of pleiotropy or whether these traits are associated with different variants that are in linkage disequilibrium. This platform will be useful for breeders to select promising markers for breeding, as well as to obtain information for the introduction of genomic breeding and for scientists to replicate the results obtained.

The Genetic Basis of Flocking Behavior in Sheep: Discoveries from Genome-Wide Association Studies

“…Genome-wide association studies (GWAS) are a powerful genetic research tool that can identify genetic markers associated with specific behavioral traits across the entire genome of sheep (Kirichenko et al, 2022). The application of GWAS has greatly advanced the study of the genetic basis of sheep flocking behavior, revealing many previously unknown genes and genomic regions related to social behavior.…”

DNA MARKERS AND MICROSATELLITE CODE (review)

“…К настоящему времени более 30000 быков голштинской породы генотипированы с использованием ДНК-микроматриц BovineSNP50 BeadChip («Illumina», США), позволяющих анализировать одновременно 54001 SNP (примерно один SNP на 50000 п.н.). С помощью таких микроматриц для разных видов построены карты распределения SNP по геномам (4) и созданы полногеномные карты ассоциаций сайтов локализации SNP с изменчивостью фенотипических характеристик (genome-wide association study, GWAS) (5,6).…”

ДНК МАРКЕРЫ И «МИКРОСАТЕЛЛИТНЫЙ КОД» (Обзор)

“…To date, more than 30,000 Holstein bulls have been genotyped using Bo-vineSNP50 BeadChip DNA microarrays (Illumina, USA), which allows simultaneous analysis of 54,001 SNPs (approximately one SNP per 50,000 bp). Using such microarrays, maps of SNP distribution across genomes have been constructed for different species [4] and genome-wide association maps of SNP localization sites with variability in phenotypic characteristics (genome-wide association study, GWAS) have been created [5,6].…”