Search for genome-wide associations of single nucleotide polymorphisms with milk quality traits in sheep (Ovis aries L.) of lacon breed

Dairy sheep breeding has demonstrated dynamic development in Russia in recent years due to increasing consumer demand for premium dairy products. In dairy sheep breeding, marker-associated selection (MAS) and genome-wide association study (GWAS) are recognized as the most promising due to the sequencing of the sheep genome within the Sheep HapMap project and the development of DNA chips of different densities. For some dairy breeds of sheep, GWAS allowed to identify loci under selection pressure and affecting productivity traits and technological properties of sheep milk. At the same time, significantly fewer full genomic studies have been performed for dairy sheep than for dairy cattle and dairy goats, which determined the purpose of the present study. For the first time, a full genomic search for associations of single nucleotide substitutions with milk quality indicators in Lacon sheep breed was performed and genomic regions associated with their dairy productivity were determined. SNP profiles were generated using the Ovine HD BeadChip 600K high density chip (Illumina Inc., San Diego, USA) and the Rstudio 2023.03.0. Quality control, data filtering, association detection for each single nucleotide polymorphism with milk components determined on CombiFoss 7 DC automatic analyzer (FOSS, Denmark) were performed by multiple linear regression analysis in plink 1.90 software (http://zzz.bwh.harvard.edu/plink/), data visualisation was performed in qqman package using R programming language (https://github.com/stephenturner/qqman), gene identification by SNP positions set according to the sheep genome assembly OAR version 3.1, using the Ensembl Genes release 103 web resource, structural annotation of genomic regions covering a ±0.20 Mb window of identified SNPs in the DAVID v6.8 (https://david.ncifcrf.gov). 64 full genomic (p -6) and 270 prospective (p -5) SNPs were identified, with the largest number of full genomic SNPs (14, 6 and 13) identified on chromosomes 1, 3 and 13, respectively. Twenty-two and 19 full genome SNPs identified on five (OAR 1, 3, 12, 13 and 26) and four (OAR 1, 3, 13 and 26) chromosomes show associations with protein mass fraction and β-casein content, 6 SNPs on three chromosomes (OAR 1, 3, 26) are associated with fat mass fraction indicator, 7, 5 and 4 SNPs respectively on four (OAR 1, 3, 5 and 17) and three chromosomes (OAR 1, 24, 26 and OAR 1, 6, 17) are associated with polyunsaturated, saturated and monounsaturated fatty acids. Two SNPs of high significance, oar3_OAR1_24401030 and oar3_OAR2_241055039 are common to three traits, namely mass protein, β-casein and fat mass fraction. Structural annotation of genomic regions identified 61 genes with described biological functions, of which 11 genes show association with a number of phenotypic traits in sheep identified in other GWAS studies. The genes identified, according to gene ontology terms, were involved in immune formation and regulation system (GPX7, JAK1 , CD8B), cellular metabolism and transport of substances (UBE2U, ACO1, FABP1, ACBD5), formation and development of internal organs and skeletal cartilage system (BMPR1B, OXSM), oogenesis, fertilization and early embryo development (ZPBP, ZP2).