Expression analysis and single-nucleotide polymorphisms of SYNDIG1L and UNC13C genes associated with thoracic vertebral numbers in sheep (Ovis aries)

Whole-Genome Resequencing of Ujimqin Sheep Identifies Genes Associated with Vertebral Number

The number of vertebrae is a crucial economic trait that can significantly impact the carcass length and meat production in animals. However, our understanding of the quantitative trait loci (QTLs) and candidate genes associated with the vertebral number in sheep (Ovis aries) remains limited. To identify these candidate genes and QTLs, we collected 73 Ujimqin sheep with increased numbers of vertebrae (T13L7, T14L6, and T14L7) and 23 sheep with normal numbers of vertebrae (T13L6). Through high-throughput genome resequencing, we obtained a total of 24,130,801 effective single-nucleotide polymorphisms (SNPs). By conducting a selective-sweep analysis, we discovered that the most significantly selective region was located on chromosome 7. Within this region, we identified several genes, including VRTN, SYNDIG1L, LTBP2, and ABCD4, known to regulate the spinal development and morphology. Further, a genome-wide association study (GWAS) performed on sheep with increased and normal vertebral numbers confirmed that ABCD4 is a candidate gene for determining the number of vertebrae in sheep. Additionally, the most significant SNP on chromosome 7 was identified as a candidate QTL. Moreover, we detected two missense mutations in the ABCD4 gene; one of these mutations (Chr7: 89393414, C > T) at position 22 leads to the conversion of arginine (Arg) to glutamine (Gln), which is expected to negatively affect the protein's function. Notably, a transcriptome expression profile in mouse embryonic development revealed that ABCD4 is highly expressed during the critical period of vertebral formation (4.5-7.5 days). Our study highlights ABCD4 as a potential major gene influencing the number of vertebrae in Ujimqin sheep, with promising prospects for future genome-assisted breeding improvements in sheep.

Advancements in Genetic Marker Exploration for Livestock Vertebral Traits with a Focus on China

In livestock breeding, the number of vertebrae has gained significant attention due to its impact on carcass quality and quantity. Variations in vertebral traits have been observed across different animal species and breeds, with a strong correlation to growth and meat production. Furthermore, vertebral traits are classified as quantitative characteristics. Molecular marker techniques, such as marker-assisted selection (MAS), have emerged as efficient tools to identify genetic markers associated with vertebral traits. In the current review, we highlight some key potential genes and their polymorphisms that play pivotal roles in controlling vertebral traits (development, length, and number) in various livestock species, including pigs, donkeys, and sheep. Specific genetic variants within these genes have been linked to vertebral development, number, and length, offering valuable insights into the genetic mechanisms governing vertebral traits. This knowledge has significant implications for selective breeding strategies to enhance structural characteristics and meat quantity and quality in livestock, ultimately improving the efficiency and quality of the animal husbandry industry.

Identification of circRNA-miRNA-mRNA networks to explore the molecular mechanism and immune regulation of postoperative neurocognitive disorder

Postoperative neurocognitive disorder (PND) is a common complication in older patients. However, its pathogenesis has still remained elusive. Recent studies have shown that circular RNA (circRNA) plays an important role in the development of neurodegenerative diseases, such as PND after surgery. CircRNA, as a competitive endogenous RNA (ceRNA), mainly acts as a molecular sponge for miRNA to "adsorb" microRNA (miRNA) and to reduce the inhibitory effects of miRNAs on target mRNA. The sequencing data of circRNA were obtained from the Gene Expression Omnibus (GEO) database. By bioinformatic methods, circAtlas, miRDB, miRTarBase and miRwalk databases were applied to construct circRNA-miRNA-mRNA networks and screen differentially expressed mRNAs. To improve the accuracy of the data, we randomly divided aging mice into control (non-PND group) and PND groups, and used high-throughput sequencing to analyze their brain hippocampal tissue for analysis. Three key genes were cross-detected in the data of both groups, which were Unc13c, Tbx20 and St8sia2 (as hub genes), providing new targets for PND treatment. According to the results of the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, immune cell infiltration analysis, gene set enrichment analysis (GSEA), Connectivity Map (CMap) analysis, quantitative real-time polymerase chain reaction (qRT-PCR), the genes that were not related to the central nervous system were removed, and finally, mmu_circ_0000331/miR-1224-3p/Unc13c and mmu_circ_0000406/miR-24-3p/St8sia2 ceRNA networks were identified. In addition, the CMap method was used to select the top 4 active compounds with the largest negative correlation absolute values, including cimaterol, Rucaparib, FG-7142, and Hydrocortisone.

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

Heat stress caused by climatic changes is one of the most significant stresses on livestock in hot and dry areas. It has particularly adverse effects on the ability of the breed to maintain homeothermy. Developing countries are advised to protect and prepare their animal resources in the face of potential threats such as climate change. The current study was conducted in Egypt’s three hot and dry agro-ecological zones. Three local sheep breeds (Saidi, Wahati, and Barki) were studied with a total of 206 ewes. The animals were exercised under natural heat stress. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on their response to meteorological and physiological parameters. Genomic variation in these breeds was assessed using 64,756 single nucleotide polymorphic markers (SNPs). From the perspective of comparative adaptability to harsh conditions, our objective was to investigate the genomic structure that might control the adaptability of local sheep breeds to environmental stress under hot and dry conditions. In addition, indices of population structure and diversity of local breeds were examined. Measures of genetic diversity showed a significant influence of breed and location on populations. The standardized index of association (rbarD) ranged from 0.0012 (Dakhla) to 0.026 (Assuit), while for the breed, they ranged from 0.004 (Wahati) to 0.0103 (Saidi). The index of association analysis (I^a) ranged from 1.42 (Dakhla) to 35.88 (Assuit) by location and from 6.58 (Wahati) to 15.36 (Saidi) by breed. The most significant SNPs associated with heat tolerance were found in the MYO5A, PRKG1, GSTCD, and RTN1 genes (p ≤ 0.0001). MYO5A produces a protein widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1_18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. Genome-wide association analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C, PEBP4, and GPAT2 genes.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

BACKGROUND

After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits.

REVIEW

Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation.

CONCLUSIONS

Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.

Genome-Wide Association Study of Parasite Resistance to Gastrointestinal Nematodes in Corriedale Sheep

Selection of genetically resistant animals is one alternative to reduce the negative impact of gastrointestinal nematodes (GIN) on sheep production. The aim of this study was to identify genomic regions associated with GIN resistance in Corriedale sheep by single-step genome-wide association studies (ssGWAS) using 170, 507 and 50K single nucleotide polymorphisms (SNPs). Analysis included 19,547 lambs with faecal egg counts (FEC) records, a pedigree file of 40,056 animals and 454, 711 and 383 genotypes from 170, 507 and 50K SNPs, respectively. Genomic estimated breeding values (GEBV) were obtained with single-step genomic BLUP methodology (ssGBLUP), using a univariate animal model, which included contemporary group, type of birth and age of dam as class fixed effects and age at FEC recording as covariate. The SNP effects as wells as p-values were estimated with POSTGSF90 program. Significance level was defined by a chromosome-wise False Discovery Rate of 5%. Significant genomic regions were identified in chromosomes 1, 3, 12 and 19 with the 170 SNP set, in chromosomes 7, 12 and 24 using the 507 SNP chip and only in chromosome 7 with the 50K SNP chip. Candidate genes located in these regions, using Oar_v4.0 as reference genome, were TIMP3, TLR5, LEPR and TLR9 (170 SNPs), SYNDIG1L and MGRN1 (507 SNP chip) and INO80, TLN2, TSHR and EIF2AK4 (50K SNP chip). These results validate genomic regions associated with FEC previously identified in Corriedale and other breeds and report new candidate regions for further investigation.