Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep

Genome-wide study for signatures of selection identifies genomic regions and candidate genes associated with milk traits in sheep

Milk production traits in sheep are influenced by complex genetic factors, and understanding these traits requires the identification of candidate genes under selection. This study employed two methods, FST and XP-EHH, to identify selection signatures and candidate genes associated with milk production traits in sheep. For this purpose, 9 different breeds from the Sheep HapMap dataset generated by the International Sheep Genomics Consortium (ISGC) based on analysis of the Ovine SNP50 BeadChip were used. The dairy breeds included Brown East Friesian (n = 39), Milk Lacaune (n = 103), Chios (n = 23), Churra (n = 120), and Comisana (n = 24), while the non-dairy breeds included Afshari (n = 37), Moghani (n = 34), Galway (n = 49), and Australian Suffolk (n = 109). Genomic regions in the top 0.1 percentile of FST values revealed 71 genes, while regions with the highest positive XP-EHH values identified 69 genes. Five overlapping genes-DHRS3, TNFRSF1B, AADACL4, ARHGEF11, and LRRC71-were detected by both methods, highlighting their relevance to milk production. Several candidate genes in regions identified from FST, such as PER2, SH3PXD2A, TMEM117, DDX6, PDCD11, CALHM2, and CALHM3, have been previously associated with milk production traits. Notably, CRABP2, PEAR1, PGM1, ALG6, COX15, and OAT were identified in regions with high XP-EHH values in the dairy group. Gene ontology analysis indicated that the identified genes are enriched in pathways related to chemokine receptor activity, gap junction channel activity, and gap junction-mediated intercellular transport, as well as cellular components like the connexin complex. Further studies on these genes may improve understanding of the genetic architecture of milk production traits in sheep.

The investigation of SNP in SOCS2 gene and its effect on milk yield, fat, protein, and somatic cell count in Awassi ewes

BACKGROUND

Livestock farmers face financial losses every year because milk yield and components are severely affected by udder diseases. These udder infections attract the immune response from the host and lead to the influx of neutrophils into milk to fight infection and thus the number of somatic cell count (SCC) is increased. The SCC value of milk could be used as an important indicator in detecting clinical mastitis in dairy animals. Also, the milk yield and milk quality (e.g. fat) are negatively affected by the increased SCC. The SCC is used to estimate the somatic cell score (SCS)of the milk, which is used as an indirect measure to detect subclinical mastitis. Therefore, the purpose of this study was to investigate the presence of a significant SNP rs868996547, on the suppressor of cytokine signaling 2 gene (SOCS2) which is related to milk yield and milk quality in Awassi sheep.

METHODS

In this study, milk production data was obtained from 210 healthy Awassi ewes with different parties and ages. The general linear model (GLM) process analysis of variance (ANOVA) was used to determine fixed effects on milk traits. The DNA extraction was done using a blood DNA extraction kit from Qiagen. To validate the presence of SNP a customized SNP detection developed by Thermofisher Scientific was used. The presence of the SNP in the SOCS2 gene was detected with genotypes (C/T, T/T, and C/C) and T being the mutated allele and it had a significant (p < 0.015) effect on the milk yield (p < 0,015;0.091), fat (p < 0,001;0,003), fat/protein ratio (p < 0.001;0,037) and log10SCC value (p < 0,006;0,015) of Awassi ewes. However, the protein, total solid, and lactose percentages in the wild type and the mutated ewes found having no significant difference (P > 0.05).

CONCLUSION

Our result showed the increase in SCC or SCS of the milk significantly affected the milk yield and composition. Parity and age had significant effects on ewes' milk yield (p < 0.001). In conclusion, we investigated the presence of SOCS2 gene of Awassi ewes in the study flock and its effect on milk yield, fat, and somatic cell count, and the change in milk composition and milk yield because of SCC.

Study on Single Nucleotide Polymorphism of LAP3 Gene and Its Correlation with Dairy Quality Traits of Gannan Yak

This study explored the polymorphism of the leucine aminopeptidase (LAP3) gene and its relationship with milk quality characteristics in Gannan yak. A cohort of 162 Gannan yak was genotyped utilizing the Illumina Yak cGPS 7K BeadChip, and the identified single nucleotide polymorphisms (SNPs) were evaluated for their association with milk protein, casein, lactose, and fat concentrations. The results showed that four SNPs (g.4494G > A, g.5919A > G, g.8033G > C, and g.15,615A > G) in the LAP3 gene exhibited polymorphism with information content values of 0.267, 0.267, 0.293, and 0.114, respectively. All four SNPs were in Hardy-Weinberg equilibrium (p > 0.05). The g.4494G > A and g.5919A > G SNPs were significantly associated with protein content (p < 0.05), with homozygous genotypes showing significantly higher protein content than heterozygous genotypes (p < 0.05). The g.8033G > C SNP was significantly associated with casein content, protein content, non-fat solids, and acidity (p < 0.05), with the CC genotype having significantly higher casein, protein, and non-fat solids content than the GG and GC genotypes (p < 0.05). The g.15,615A > G SNP was significantly associated with average fat globule diameter (p < 0.05). In general, the mutations within the LAP3 gene demonstrated a positive impact on milk quality traits in Gannan yak, with mutated genotypes correlating with enhanced milk quality. These results indicate that the LAP3 gene could be a significant or candidate gene affecting milk quality traits in Gannan yak and offer potential genetic markers for molecular breeding programs in this species.

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data

Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.

Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries)

Sheep (Ovis aries) is one of the important livestock with diverse phenotypic traits. However, little is known about the molecular mechanism of diverse phenotypic traits in domestic sheep. Using the genome-wide high-density SNP data (600K) in 253 samples from 13 populations, we conducted the tests of selective sweeps (i.e., pairwise F_ST and XP-CLR) associated with several important phenotypic traits (e.g., tail types, horn morphology, prolificacy, coat pigmentation, ear size, milk production, meat production, body size and wool fineness). We identified strong selective signatures in previously reported (e.g., T, RXFP2, BMPR1B, TYRP1, MSRB3, TF, CEBPA, GPR21 and HOXC8) and novel genes associated with the traits, such as CERS6, BTG1, RYR3, SLC6A4, NNAT and OGT for fat deposition in the tails, FOXO4 for fertility, PTCH1 and EMX2 for ear size, and RMI1 and SCD5 for body size. Further gene annotation analysis showed that these genes were identified to be the most probable genes accounting for the diverse phenotypic traits. Our results provide novel insights into the genetic mechanisms underlying the traits and also new genetic markers for genetic improvement in sheep and other livestock.