Less than 2% of mammalian genomes code for proteins, but ‘the majority of its bases can be found in primary transcripts’ – a phenomenon termed the pervasive transcription, which was first reported in 2007. Even though most of the transcripts do not code for proteins, they play a variety of biological functions, with regulation of gene expression appearing as the most common one. Those transcripts are divided into two groups based on their length: small non-coding RNAs, which are maximally 200 bp long, and long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides. The advances in next-generation sequencing methods provided a new possibility of investigating the full set of RNA molecules in the cell. In this review, we summarized the current state of knowledge on lncRNAs in three major livestock species – Sus scrofa, Bos taurus and Gallus gallus, based on the literature and the content of biological databases. In the NONCODE database, the largest number of identified lncRNA transcripts is available for pigs, but cattle have the largest number of lncRNA genes. Poultry is represented by less than a half of records. Genomic annotation of lncRNAs showed that the majority of them are assigned to introns (pig, poultry) or intergenic (cattle). The comparison with well-annotated human and mouse genomes indicates that such annotation is a result of lack of proper lncRNA annotation data. Since lncRNAs play an important role in genomic studies, their characterization in farm animals’ genomes is critical in bridging the gap between genotype and phenotype.

Although Slavic populations account for over 4.5% of world inhabitants, no centralised, open-source reference database of genetic variation of any Slavic population exists to date. Such data are crucial for clinical genetics, biomedical research, as well as archeological and historical studies. The Polish population, which is homogenous and sedentary in its nature but influenced by many migrations of the past, is unique and could serve as a genetic reference for the Slavic nations. In this study, we analysed whole genomes of 1222 Poles to identify and genotype a wide spectrum of genomic variation, such as small and structural variants, runs of homozygosity, mitochondrial haplogroups, and de novo variants. Common variant analyses showed that the Polish cohort is highly homogenous and shares ancestry with other European populations. In rare variant analyses, we identified 32 autosomal-recessive genes with significantly different frequencies of pathogenic alleles in the Polish population as compared to the non-Finish Europeans, including C2, TGM5, NUP93, C19orf12, and PROP1. The allele frequencies for small and structural variants, calculated for 1076 unrelated individuals, are released publicly as The Thousand Polish Genomes database, and will contribute to the worldwide genomic resources available to researchers and clinicians.

One major problem in dairy cattle husbandry is the prevalence of udder infections. In today’s breeding programmes, top priority is being given to making animal evaluation more cost-effective and reliable and less time-consuming. We proposed tumor necrosis factor α (TNF-α), lactoferrin (LTF) and macrophage-expressed lysozyme (mLYZ) genes as potential DNA markers in the improvement of immunity to mastitis.

Longevity expressed as the number of days between birth and death is a trait of great importance for both human and animal populations. In our analysis we use dairy cattle to demonstrate how the association of Single Nucleotide Polymorphisms (SNPs) located within selected genes with longevity can be modeled. Such an approach can be extended to any genotyped population with time to endpoint information available. Our study is focused on selected genes in order to answer the question whether genes, known to be involved into the physiological determination of milk production, also influence individual's survival.

Mastitis is an inflammatory disease of the mammary gland, which has a significant economic impact and is an animal welfare concern. This work examined the association between single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) with the incidence of clinical mastitis (CM). Using information from 16 half-sib pairs of Holstein-Friesian cows (32 animals in total) we searched for genomic regions that differed between a healthy (no incidence of CM) and a mastitis-prone (multiple incidences of CM) half-sib. Three cows with average sequence depth of coverage below 10 were excluded, which left 13 half-sib pairs available for comparisons. In total, 191 CNV regions were identified, which were deleted in a mastitis-prone cow, but present in its healthy half-sib and overlapped in at least nine half-sib pairs. These regions overlapped with exons of 46 genes, among which APP (BTA1), FOXL2 (BTA1), SSFA2 (BTA2), OTUD3 (BTA2), ADORA2A (BTA17), TXNRD2 (BTA17) and NDUFS6 (BTA20) have been reported to influence CM. Moreover, two duplicated CNV regions present in nine healthy individuals and absent in their mastitis-affected half-sibs overlapped with exons of a cholinergic receptor nicotinic α 10 subunit on BTA15 and a novel gene (ENSBTAG00000008519) on BTA27. One CNV region deleted in nine mastitis-affected sibs overlapped with two neighbouring long non-coding RNA sequences located on BTA12. Single nucleotide polymorphisms with differential genotypes between a healthy and a mastitis-affected sib included 17 polymorphisms with alternate alleles in eight affected and healthy half-sib families. Three of these SNPs were located introns of genes: MET (BTA04), RNF122 (BTA27) and WRN (BTA27). In summary, structural polymorphisms in form of CNVs, putatively play a role in susceptibility to CM. Specifically, sequence deletions have a greater effect on reducing resistance against mastitis, than sequence duplications have on increasing resistance against the disease.

The number of studies of Copy Number Variation in cattle has increased in recent years. This has been prompted by the increased availability of data on polymorphisms and their relationship with phenotypes. In addition, livestock species are good models for some human phenotypes. In the present study, we described the landscape of CNV driven genetic variation in a large population of 146 individuals representing 13 cattle breeds, using whole genome DNA sequence. A highly significant variation among all individuals and within each breed was observed in the number of duplications (P < 10−15) and in the number of deletions (P < 10−15). We also observed significant differences between breeds for duplication (P = 0.01932) and deletion (P = 0.01006) counts. The same variation CNV length - inter-individual and inter-breed differences were significant for duplications (P < 10−15) and deletions (P < 10−15). Moreover, breed-specific variants were identified, with the largest proportion of breed-specific duplications (9.57%) found for Fleckvieh and breed-specific deletions found for Brown Swiss (5.00%). Such breed-specific CNVs were predominantly located in intragenic regions, however in Simmental, one deletion present in five individuals was found in the coding sequence of a novel gene ENSBTAG00000000688 on chromosome 18. In Brown Swiss, Norwegian Red and Simmental breed-specific deletions were located within KIT and MC1R genes, which are responsible for a coat colour. The functional annotation of coding regions underlying the breed-specific CNVs showed that in Norwegian Red, Guernsey, and Simmental significantly under- and overrepresented GO terms were related to chemical stimulus involved in sensory perception of smell and the KEGG pathways for olfactory transduction. In addition, specifically for the Norwegian Red breed, the dopaminergic synapse KEGG pathway was significantly enriched within deleted parts of the genome. The CNV landscape in Bos taurus genome revealed by this study was highly complex, with inter-breed differences, but also a significant variation within breeds. The former, may explain some of the phenotypic differences among analysed breeds, and the latter contributes to within-breed variation available for selection.