Whole-genome association studies of distribution of developmental abnormalities and other breeding-valuable qualitative traits in offspring of the Russian large-white boars

Identifying genome regions that are directly or indirectly associated with developmental defects and malformations in domesticated pigs can help identify genomic traits used as biomarkers of the structural and functional composition of the body, their metabolic status and genetic diseases as well. Such studies are directly related to the improvement of the economic efficiency, as they allow identification and exclusion of defect animals, who may carry target genes not appearing phenotypically, from the breeding process. In the current work, we have searched for these kind of target genes and genome regions with conducting the genome-wide association studies using PorcineSNP60K BeadChips (Illumina, San Diego, USA). A total of 48 boars of a large white breed of the nucleus farm “Znamenskoe” were analyzed for 21 traits of indicated shortcomings of the exterior and defects of development in 39,153 their offspring.  Calculations were made using a mixed type linear model in package GEMMA. In this study, we selected only 36,704 polymorphic SNPs from an initial 61,000-strong SNP set. After GWAS, we obtained 24 alleles in 11 corresponding genes  (P < 0.1) in the genome of pigs, which are significantly correlated with traits of developmental abnormalities such as anal atresia (ARMC7,FANCC,RND3,ENSSSCG00000017216), limb problems (PAWR,NTM,OPCML,ENSSSCG00000040250, ENSSSCG00000017018) and tremor of piglets (RIC3,ENSSSCG00000032665). Also, co-expression of the NTM,OPCMLand  RND3genes was revealed. This study confirms the relevance of using the single SNP detection according to the single trait approach in associative studies, even for small sample numbers

Study of genetic diversity and differentiation of regional populations of Romanov sheep using micro satellite markers

The Romanov breed is the most interesting local Russian sheep breed with unique biological traits (out-ofseason breeding ability, prolificacy). Conservation of genetic resources of the breed requires constant careful monitoring using DNA markers. In this regard, the aim of our work was to compare the parameters of the allele pool and genetic diversity, as well as to assess genetic similarity of regional populations of the Romanov breed in comparison with archetypal animals. Tissue samples were selected in different regions of Russia (Yaroslavl, Ryazan and Tula regions, Republics of Khakassia and Komi). Polymorphism of 11 microsatellites was studied with the genetic analyzer АВІЗ 130x1. We estimated an average number of alleles (Na), effective number of alleles (Ne), number of informative alleles (Na>5%), observed (Ho) and expected heterozygosity (He), fixation index (FIS), constructed Neighbour-Net and carried out PCoA and cluster analyzes. The Khakass population was characterized by the greatest allelic diversity: Na = 11.30; Ne = 5.99 and Na>5% = 5.50 alleles, while minimal Ne (3.95) and Na>5% (4.30) were detected for the first and second Yaroslavl populations, respectively. Deficiency of heterozygotes from 6 to 19.5% was observed in all groups, except for the Tula population. Based on the results of Neighbour-Net, PCoA and cluster analysis, genetic isolation of three Yaroslavl populations was found. Also, a certain genetic detachment of the Ryazan population (Fst from 0.038 to 0.059) was revealed. Thus, we demonstrated that the parameters of allele pool and the indices of genetic diversity can vary greatly within the breed. In addition, it has been established that the Yaroslavl populations of the Romanov breed still represent a separate group