Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep

Genome-wide association study of health and production traits in meat sheep

Genotypes are currently widely used in animal breeding programmes to enhance the speed of genetic progress. With sufficient data, a Genome-Wide Association Study (GWAS) can be performed to identify informative markers. The aim of this study was to investigate the genetic background of health (footrot and mastitis) and production (birth weight, weaning weight, scan weight, and fat and muscle depth) traits using the available phenotypic and Single Nucleotide Polymorphism (SNP) data collected on the UK Texel sheep population. Initially, 10 193 genotypes were subject to quality control, leaving 9 505 genotypes for further analysis. Selected genotypes, recorded on four different Illumina chip types from low density (15 k SNPs) to high density (606 006 SNPs), were imputed to a subset of 45 686 markers from 50 k array, distributed on 27 chromosomes. Phenotypes collected on 32 farms across the UK for footrot and mastitis and extracted from the UK National database (iTexel) for the production traits were used along with pre-estimated variance components to obtain de-regressed breeding values and used to perform GWAS. Results showed three SNPs being significant on the genome-wise level ('OAR8_62240378.1' on chromosome 8 for birth weight, 's14444.1' on chromosome 19 for weaning weight and 's65197.1' on chromosome 23 for scan weight). Fourteen subsequent SNPs were found to be significant at the chromosome-wise level. These SNPs are located within or close to previously reported QTLs impacting on animal health (such as faecal egg count or somatic cell count) and production (such as body or carcass weight and fat amount). These results indicate that the studied traits are highly polygenic with complex genetic architecture.

Genome-Wide Signal Selection Analysis Revealing Genes Potentially Related to Sheep-Milk-Production Traits

Natural selection and domestication have shaped modern sheep populations into a vast range of phenotypically diverse breeds. Among these breeds, dairy sheep have a smaller population than meat sheep and wool sheep, and less research is performed on them, but the lactation mechanism in dairy sheep is critically important for improving animal-production methods. In this study, whole-genome sequences were generated from 10 sheep breeds, including 57 high-milk-yield sheep and 44 low-milk-yield sheep, to investigate the genetic signatures of milk production in dairy sheep, and 59,864,820 valid SNPs (Single Nucleotide Polymorphisms) were kept after quality control to perform population-genetic-structure analyses, gene-detection analyses, and gene-function-validation analyses. For the population-genetic-structure analyses, we carried out PCA (Principal Component Analysis), as well as neighbor-joining tree and structure analyses to classify different sheep populations. The sheep used in our study were well distributed in ten groups, with the high-milk-yield-group populations close to each other and the low-milk-yield-group populations showing similar classifications. To perform an exact signal-selection analysis, we used three different methods to find SNPs to perform gene-annotation analyses within the 995 common regions derived from the fixation index (F_ST), nucleotide diversity (Ɵπ), and heterozygosity rate (ZHp) results. In total, we found 553 genes that were located in these regions. These genes mainly participate in the protein-binding pathway and the nucleoplasm-interaction pathway, as revealed by the GO- and KEGG-function-enrichment analyses. After the gene selection and function analyses, we found that FCGR3A, CTSK, CTSS, ARNT, GHR, SLC29A4, ROR1, and TNRC18 were potentially related to sheep-milk-production traits. We chose the strongly selected genes, FCGR3A, CTSK, CTSS, and ARNT during the signal-selection analysis to perform a RT-qPCR (Reale time Quantitative Polymerase Chain Reaction) experiment to validate their expression-level relationship with milk production, and the results showed that FCGR3A has a significant negative relationship with sheep-milk production, while other three genes did not show any positive or negative relations. In this study, it was discovered and proven that the candidate gene FCGR3A potentially contributes to the milk production of dairy sheep and a basis was laid for the further study of the genetic mechanism underlying the strong milk-production traits of sheep.

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise F_ST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and F_ST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs

Growth rate plays a critical role in the pig industry and is related to quantitative traits controlled by many genes. Here, we aimed to identify causative mutations and candidate genes responsible for pig growth traits. In this study, 2360 Duroc pigs were used to detect significant additive, dominance, and epistatic effects associated with growth traits. As a result, a total number of 32 significant SNPs for additive or dominance effects were found to be associated with various factors, including adjusted age at a specified weight (AGE), average daily gain (ADG), backfat thickness (BF), and loin muscle depth (LMD). In addition, the detected additive significant SNPs explained 2.49%, 3.02%, 3.18%, and 1.96% of the deregressed estimated breeding value (DEBV) variance for AGE, ADG, BF, and LMD, respectively, while significant dominance SNPs could explain 2.24%, 13.26%, and 4.08% of AGE, BF, and LMD, respectively. Meanwhile, a total of 805 significant epistatic effects SNPs were associated with one of ADG, AGE, and LMD, from which 11 sub-networks were constructed. In total, 46 potential genes involved in muscle development, fat deposition, and regulation of cell growth were considered as candidates for growth traits, including CD55 and NRIP1 for AGE and ADG, TRIP11 and MIS2 for BF, and VRTN and ZEB2 for LMD, respectively. Generally, in this study, we detected both new and reported variants and potential candidate genes for growth traits of Duroc pigs, which might to be taken into account in future molecular breeding programs to improve the growth performance of pigs.

Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep

Simple Summary

Milk production is the most economically crucial dairy sheep trait and constitutes the major genetic enhancement purpose via selective breeding. Also, mastitis is one of the most frequently encountered diseases, having a significant impact on animal welfare, milk yield, and quality. The aim of this study was to identify genomic region(s) associated with the milk production traits and somatic cell score (SCS) in Valle del Belice sheep using single-step genome-wide association (ssGWA) and genotyping data from medium density SNP panels. We identified several genomic regions (OAR1, OAR2, OAR3, OAR4, OAR6, OAR9, and OAR25) and candidate genes implicated in milk production traits and SCS. Our findings offer new insights into the genetic basis of milk production traits and SCS in dairy sheep.

Abstract

The objective of this study was to uncover genomic regions explaining a substantial proportion of the genetic variance in milk production traits and somatic cell score in a Valle del Belice dairy sheep. Weighted single-step genome-wide association studies (WssGWAS) were conducted for milk yield (MY), fat yield (FY), fat percentage (FAT%), protein yield (PY), protein percentage (PROT%), and somatic cell score (SCS). In addition, our aim was also to identify candidate genes within genomic regions that explained the highest proportions of genetic variance. Overall, the full pedigree consists of 5534 animals, of which 1813 ewes had milk data (15,008 records), and 481 ewes were genotyped with a 50 K single nucleotide polymorphism (SNP) array. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. We considered the top 10 genomic regions in terms of their explained genomic variants as candidate window regions for each trait. The results showed that top ranked genomic windows (1 Mb windows) explained 3.49, 4.04, 5.37, 4.09, 3.80, and 5.24% of the genetic variances for MY, FY, FAT%, PY, PROT%, and total SCS, respectively. Among the candidate genes found, some known associations were confirmed, while several novel candidate genes were also revealed, including PPARGC1A, LYPLA1, LEP, and MYH9 for MY; CACNA1C, PTPN1, ROBO2, CHRM3, and ERCC6 for FY and FAT%; PCSK5 and ANGPT1 for PY and PROT%; and IL26, IFNG, PEX26, NEGR1, LAP3, and MED28 for SCS. These findings increase our understanding of the genetic architecture of six examined traits and provide guidance for subsequent genetic improvement through genome selection.

Breeding of African sheep reared under low-input/output smallholder production systems for trypanotolerance

Trypanosomiasis is a disease caused by unicellular protozoan parasites. Small ruminants succumb to trypanosomiasis in areas of high tsetse fly challenge, resulting in serious economic loss often to farmers in low-input smallholder systems. At present, trypanosomiasis is treated with trypanocidal drugs, but access to these can be limited, and increasing parasite resistance raises questions about their efficacy. The development of trypanotolerance in small ruminant flocks through targeted breeding strategies is considered a sustainable and economical option for controlling African trypanosomiasis. Recently, quantitative trait loci (QTLs) associated with trypanotolerance traits in sheep have been reported. The results of these studies form the basis for more studies to identify QTLs associated with trypanosomiasis resistance, particularly in African livestock species. For example, signatures of positive selection for trypanotolerance have been identified using genome-wide single-nucleotide polymorphism data. However, there are several challenges in performing genetic analyses using data from low-input smallholder systems, including a lack of recorded pedigree and production records and the need for large sample sizes when flock sizes are often fewer than 50 animals. Breeding strategies to improve trypanotolerance should also preserve existing genetic diversity as well as minimize excessive genetic introgression by trypanosusceptible breeds. This review discusses the possibilities of breeding for trypanosome tolerance/resistance in low-input/low-output small ruminant production systems. Potential challenges are outlined, and potential available genetic resources are described as a foundation for future work.

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.

Potential Novel Biomarkers for Mastitis Diagnosis in Sheep

Simple Summary

Inflammation of the mammary gland (mastitis) is an important disease of dairy sheep. Mastitis management depends mainly on the diagnosis. Conventional diagnostic methods including somatic cell count, California Mastitis Test, and microbial culture have limitations. Therefore researchers are looking for new diagnostic biomarkers of mastitis including specific proteins produced by the liver in case of disease (acute phase proteins), unique genetic sequences (miRNAs), or antimicrobial peptides produced by immune cells during inflammation (cathelicidines).

Abstract

This review aims to characterize promising novel markers of ovine mastitis. Mastitis is considered as one of the primary factors for premature culling in dairy sheep and has noticeable financial, productional, and animal welfare-related implications. Furthermore, clinical, and subclinical mammary infections negatively affect milk yield and alter the milk composition, thereby leading to lowered quality of dairy products. It is, therefore, crucial to control and prevent mastitis through proper diagnosis, treatment or culling, and appropriate udder health management particularly at the end of the lactation period. The clinical form of mastitis is characterized by abnormalities in milk and mammary gland tissue alteration or systemic symptoms consequently causing minor diagnostic difficulties. However, to identify ewes with subclinical mastitis, laboratory diagnostics is crucial. Mastitis control is primarily dependent on determining somatic cell count (SCC) and the California Mastitis Test (CMT), which aim to detect the quantity of cells in the milk sample. The other useful diagnostic tool is microbial culture, which complements SCC and CMT. However, all mentioned diagnostic methods have their limitations and therefore novel biomarkers of ovine subclinical mastitis are highly desired. These sensitive indicators include acute-phase proteins, miRNA, and cathelicidins measurements, which could be determined in ovine serum and/or milk and in the future may become useful in early mastitis diagnostics as well as a preventive tool. This may contribute to increased detection of ovine mammary gland inflammation in sheep, especially in subclinical form, and consequently improves milk quality and quantity.