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Feed cost accounts for a high proportion of sheep production, and improving sheep's utilization of feed will reduce production costs and improve economic benefits. The purpose of this study was to investigate the expression characteristics of PLIN1 and MOGAT1 genes and the relationship between their polymorphisms and feed efficiency traits in Hu sheep, and to find molecular Genetic marker that can be used in breeding. The expression levels of PLIN1 and MOGAT1 genes in various tissues were determined using quantitative real-time PCR (qRT-PCR). The results showed that PLIN1 and MOGAT1 genes were widely expressed in heart, liver, spleen, lungs, kidneys, rumen, duodenum, muscle, lymph, and tail fat. The PLIN1 gene had the highest expression level in in the tail fat compared to the other nine tissues. The expression levels of MOGAT1 gene in liver, tail fat, lung and heart was significantly higher than in kidney, muscle and lymph. The expression level of MOGAT1 was lowest in muscle compared to the other tissues (heart, liver, spleen, lung, rumen and tail fat). We recorded the body weight (BW80 and BW180) and feed intake (FI) information of 985 male Hu sheep at 80 and 180 days of age, and calculated the daily average feed intake (ADFI), average daily gain (ADG), and feed conversion rate (FCR) from 80 to 180 days of age. Two intronic mutations, g.18517910 A > G and g.224856118 G > C, were identified in PLIN1 and MOGAT1 genes by PCR amplification and Sanger sequencing. MassARRAY ® SNP detection technology was used to genotype the DNA of 985 Hu sheep and analyze its association with feed efficiency traits. The results showed that the SNP g.18517910 A > G was significantly associated with BW80, BW180, FI, ADFI and FCR (P < 0.05), while SNP g.2248561118 G > C was significantly associated with FCR (P < 0.05). Meanwhile, significant differences were also observed in different combinations of genotypes (P < 0.05). Therefore, these two polymorphic loci can serve as candidate molecular markers for improving feed utilization efficiency in Hu sheep., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Growth traits are the economically important traits of sheep, and screening for genes related to growth and development is helpful for the genetic improvement of ovine growth traits. The fatty acid desaturase 3 ( FADS3 ) is one of the important genes affecting the synthesis and accumulation of polyunsaturated fatty acids in animals. In this study, the expression levels of the FADS3 gene and polymorphism of the FADS3 gene associated with growth traits in Hu sheep were detected using quantitative real-time PCR (qRT-PCR), Sanger sequencing, and KAspar assay. The result showed that the expression levels of the FADS3 gene were widely expressed in all tissues, and the expression level of FADS3 in the lung was significantly higher than in other tissues ( p  < .05). Then, the polymorphism locus g. 2918 A > C was detected in intron 2 of the FADS3 gene, and associated analysis showed that the mutation in the FADS3 gene was associated significantly with growth traits (including body weight, body height, body length, and chest circumference, p  < .05). Therefore, individuals with AA genotype showed significantly better growth traits than those with CC genotype, and FADS3 gene could be a candidate gene for improving growth traits in Hu sheep.

Growth traits is a critical economic trait for animal husbandry. In this study, the SNPs of CTNNA3 and CAP2 genes were investigated to check whether they are associated with growth traits (body weight, body height, body length and chest circumference) in Hu sheep. The result of the association analysis indicated that the mutation in CTNNA3 (g.2018018 A > G) were associated significantly with body weight, body height, body length and chest circumference (P < 0.05), the mutation in CAP2 (g.8588 T > C) were associated significantly with body height at 140, 160, 180 days (P < 0.05), AA and CC of CTNNA3 and CAP2 were the dominant genotypes associated with growth traits in Hu sheep. Moreover, combined effect analyses indicated that the growth traits with combined genotypes AA CTNNA3 -CC CAP2 and AA CTNNA3 -CT CAP2 were higher than those with genotype GG CTNNA3 -CT CAP2 . RT-qPCR indicated that CTNNA3 expression levels were significantly higher in liver and lung than in other nine tissues (P < 0.05), CAP2 expression levels were significantly higher in bone, heart, liver, lung and duodenum than in other six tissues (P < 0.05). In conclusion, CTNNA3 and CAP2 polymorphisms could be used as genetic markers for improving growth traits in Hu sheep husbandry., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Herein we detected single nucleotide polymorphisms in MEF2B and UCP3 by DNA sequencing and the KASPar technology and analyzed their association with sheep growth traits. Two synonymous mutations, g.1826 C > T and g.10266 G > C, were detected, respectively, and they were found to be significantly associated with sheep growth traits ( p  < 0.05). In case of MEF2B g.1826 C > T, the average body weight and chest and cannon circumference of sheep with the CC genotype were significantly higher than those of sheep with the CT and TT genotypes ( p  < 0.05). Moreover, in case of UCP3 g.10266 G > C, the average body weight and chest and cannon circumference of sheep with the GG genotype were significantly higher than those of sheep with the GC and CC genotypes ( p  < 0.05). Moreover, the average body weight of sheep with the CC/GG genotype was higher compared with those of other genotype combinations. We also assessed MEF2B and UCP3 expression in different sheep tissues, confirming their expression in all examined tissues. To summarize, we believe that the polymorphisms identified in MEF2B and UCP3 can serve as molecular markers for sheep growth traits.

Improving feed efficiency would increase profitability for producers. The objective of this study was to detect the expression levels of ME1 and CA1 and the polymorphisms of ME1 and CA1 associated with the feed conversion ratio (FCR) and residual feed intake (RFI) of Hu sheep by using qRT-PCR, pooled DNA sequencing and KASPar assay. The qRT-PCR results indicated that the expression levels of ME1 and CA1 were significantly higher in the liver tissues of low-RFI sheep than in those of the high-RFI sheep (p <.01). Association analysis demonstrated that the polymorphism ME1 g.453 C > T was significantly associated with FCR and RFI (p <.05). The polymorphism CA1 g.199 C > T had a significantly associated with FCR (p <.05) and no association with RFI (p >.05). Significant differences were observed between the combined genotypes and FCR and RFI at different measurement periods (p <.05). Thus, we propose the use of these two polymorphisms as new candidate molecular markers for improving feed efficiency in sheep populations., (© 2021 John Wiley & Sons Ltd.)

G-protein coupled receptor143 (GPR143) plays an important role in melanogenesis. In this study, we investigated the expression pattern and localization of GPR143 in skin of sheep with different coat colors and explored the correlation between GPR143 gene and coat color. The mRNA level and protein level of GPR143 in skin of sheep with different coat colors were detected by qRT-PCR and immunoblotting separately while the localization of GPR143 in sheep skin was detected by immunofluorescence assay following optical density analysis. The qRT-PCR results showed that the relative expression level of GPR143 mRNA in black sheep skin was 7.84 times of that in white sheep skin (P<0.01). Immunoblotting results demonstrated that the expression level of GPR143 protein in black sheep skin was 1.30 times of that in white sheep skin (P<0.05). Immunofluorescence assay revealed that GPR143 was primarily expressed in the outer root sheath of hair follicles and epidermal skin tissue. Optical density analysis showed that expression levels of GPR143 in the outer root sheath and epidermis of black sheep skin were significantly higher than that of white sheep skin. Our studies demonstrated that GPR143 is expressed in skin of sheep with different coat colors. However, the mRNA and protein levels of GPR143 in black sheep skin are significantly higher than that in white sheep skin, indicating that GPR143 mRNA and protein levels are upregulated in skin of black sheep while downregulated in skin of white sheep. GPR143 may participate in the formation of coat color by regulating the level of MITF and the number, size, motility and maturation of the melanosome.

In this study, a single nucleotide polymorphism of HTR4 (hydroxytryptamine receptor 4) was detected using DNA sequencing and KASPar (Kompetitive Allele-Specific PCR) technique with the aim of analyzing its effect on growth traits in 1102 sheep. A synonymous mutation g.101220 C > T located on the fifth intron of the ovis HTR4 gene was detected, and association analysis showed that this mutation was significantly associated with growth traits in sheep (p ＜.05), with TT genotypes having significantly lower body weight, height, length and chest circumference than TC and CC genotypes. It showed that the polymorphism of this locus was significantly associated with growth traits in sheep. In addition, qRT-PCR results showed that HTR4 was expressed in different tissues of sheep. It is highly expressed in the liver, spleen and duodenum. As important metabolic, immune and digestive absorption organs in animals, the above tissues can regulate the excitability of intestinal smooth muscle by participating in the body metabolism and nutrient metabolism of sheep, so that sheep can show better growth characteristics. In conclusion, the polymorphic locus identified in HTR4 gene can be used as candidate molecular marker in sheep breeding. [ABSTRACT FROM AUTHOR]

Feed efficiency makes up a large part of sheep production, which also has a crucial impact on the economic benefits of producers. This study explores the polymorphism of Adenylyl cyclase 8 gene associated with feed efficiency and detects the expression characteristics of ADCY8 in ten tissues of Hu sheep. The polymorphism of ADCY8 was recognized by using PCR amplification and Sanger sequencing, KASPar technology was used for genotyping subsequently, and the relationship between SNP and RFI is also studied. The results indicated that an intronic mutation g.24799148 C > T (rs 423395741) was identified in ADCY8, and association analysis showed that the SNP g.24799148 C > T (rs 423395741) was significantly associated with RFI at 100–120, 100–140, 100–160, and 100–180 days (p < 0.05). The quantitative real-time PCR (qRT-PCR) result showed that ADCY8 was expressed in ten tissues, and the expression of ADCY8 gene in rumen tissue was significantly higher than in the other tested tissues. Therefore, these results indicated that the ADCY8 mutation locus may be used as a candidate molecular marker for evaluating the feed efficiency of Hu sheep. [ABSTRACT FROM AUTHOR]

Growth traits are important economic characteristics of livestock and poultry. In the present study, the expression features of KLF15 and the relationship between KLF15 gene polymorphisms and growth traits in Hu sheep were investigated by using real-time quantitative PCR technology (qPCR), Sanger sequencing, and Kaspar genotyping technology. The qPCR results showed that the KLF15 gene is expressed widely in the tested tissues of Hu sheep, and the expression level of the KLF15 gene in the heart and the muscle was significantly higher than in other tissues (p < 0.05). Missense mutation c.62565119 A > G was found in KLF15, and an association analysis showed that it was correlated with the growth traits (body weight, body height, and body length) of Hu sheep (p < 0.05). The body weight, body height, and body length of the sheep carrying the AA genotype were remarkably higher than those of the GG and AG genotypes (p < 0.05). These results showed that novel polymorphisms at the KLF15 gene can be used as a genetic marker of growth traits of Hu sheep. [ABSTRACT FROM AUTHOR]

Increased body growth and feed efficiency are important for breeding due to expensive feed costs. This study estimated the genetic parameters for two feed efficiency traits [the feed conversion ratio (FCR) and the residual feed intake (RFI)] and other important economic traits in male Hu sheep using 1642 male Hu lambs. The heritability of the RFI was estimated at 0.31 (±0.10)–0.54 (±0.1) and the heritability of the FCR was 0.05 (±0.07)–0.77 (±0.12). There was a negative genetic correlation between rib-eye muscle area traits and RFI. A positive genetic correlation was found between fat deposition traits and feed efficiency traits. The digestive tract weight decreased with the direction of RFI: however, the FCR showed the opposite: A low FCR was accompanied by a high digestive tract weight. The genetic correlation between feed efficiency (RFI and FCR) and rumen weight was negative. Heritability estimates for feed efficiency generate fluctuations with different experimental intervals. The weight of other traits should be reasonably allocated to avoid losses in production and feed efficiency in the selection of feed efficiency traits. The present study added to our understanding of the genetic parameters of sheep under the condition of house feeding. [ABSTRACT FROM AUTHOR]

The aim of this study was to analyze the effect of OSMR and GHR genes polymorphisms on growth traits in sheep. The single nucleotide polymorphisms of sheep OSMR and GHR genes were identified by DNA sequencing technology. A total of two intronic mutations g.2443 T > C and g.170196 A > G were identified in OSMR and GHR, respectively. Correlation analysis was carried out between the obtained genotypes and the growth traits of sheep. The results showed that at the OSMR g.2443 T > C locus, the body weight, chest circumference and cannon circumference of the TT genotype sheep were significantly higher than those of the CC genotype sheep (p <.05). At the GHR g.170196 A > G locus, the body weight, body length, chest circumference and cannon circumference of the AA genotype sheep were significantly higher than those of the AG genotype and GG genotype sheep (p <.05). Moreover, the body weight of sheep of combination TTOSMR/AAGHR genotype was significantly higher than that of other combination genotypes (p <.05). Therefore, we believe that the polymorphic sites identified in the OSMR and GHR genes can be used as candidate molecular markers for breeding good traits in sheep. [ABSTRACT FROM AUTHOR]

Small ruminants farming plays an important role in the livelihood of a large part of the population. Herein we aimed to analyze the effects of single nucleotide polymorphisms in PRKAA2 gene on the growth-related traits of Hu sheep and Dorper sheep. The body weight and body type of 1254 sheep were measured at 80, 100, 120, 140, 160 and 180d, and 37620 phenotypic data were collected. RT-qPCR analysis was performed to test PRKAA2 gene expressed in different tissues of sheep, with the highest expression level in spleen, followed by kidney. In the present study, the PRKAA2 gene sequencing revealed one polymorphism located on Chr1 (Oar_rambouillet_v1.0), termed as chr1:32832382 G > A, and were significantly associated with growth traits of sheep (p < 0.05). The body weight, body length, chest circumference, and cannon circumference of individuals with AA genotype were significantly higher than those with the GG and GA genotypes (p < 0.05). Our findings reveal that PRKAA2 gene could be used as a marker-assisted selection to improve the growth-related traits of sheep. [ABSTRACT FROM AUTHOR]

The growth traits are economically important traits in sheep. Improving growth rates will increase the profitability of producers. The aim of this study was to identify alleles of CD8B (encoding T-cell surface glycoprotein CD8 beta chain) that are aberrantly expressed in different tissues and to assess the effects and associations of its different genotypes on weight and size traits in sheep. Using quantitative real-time reverse transcription PCR arrays, expression profiling of CD8B was performed in various organs and tissues. CD8B was ubiquitously expressed, with very high expression in the lung, spleen, lymph, duodenum, and liver. One intronic mutation (chr3:62,718,030 (Oar_rambouillet_v1.0, same below) G > A) was identified using pooled DNA sequencing. Subsequently, the variants (AA, AG, and GG) were genotyped using the KASPar® PCR single nucleotide polymorphism (SNP) genotyping system. The results of association analysis with body weight and body size traits in 1304 sheep showed that increases in multiple phenotypic traits correlated with the AA genotype (body weight, p < 0.05; body length, p < 0.05). Thus, SNP chr3:62,718,030 G > A is a promising molecular marker for marker-assisted selection in sheep breeding. [ABSTRACT FROM AUTHOR]

This study aimed to analyze the effects of polymorphisms in GP5 on blood physiological indices of 1065 sheep. The coefficients of variation of the red blood cell count (RBC), hemoglobin concentration (HGB), mean platelet volume (MPV), mean erythrocyte hemoglobin content (MCH), and red blood cell distribution-coefficient of variation (RDW-CV) were greater than 10%, and there was a very significant correlation between the main indices such as RBC, white blood cell, and platelet count (PLT) and most other indices (p < 0.01). qRT-PCR showed that GP5 was expressed in the heart, liver, spleen, lung, kidney, rumen, duodenum, muscle, tail fat, and lymph tissue, with significantly higher expression in the lymph. Subsequently, we detected single nucleotide polymorphisms (SNPs) in GP5 from group, which identified synonymous mutation g.657 T > C in the first exon of GP5. Association analysis showed significant correlations between the SNP and the physiological traits (p < 0.05), in which the RBC, neutrophilic granulocyte (NEUT) and RDW-CV values in sheep with the TC genotype and TT genotype were markedly lower than those in the CC genotype (p < 0.05). Thus, GP5 polymorphisms could be candidate biomarkers to screen blood physiological indices. [ABSTRACT FROM AUTHOR]

Hu sheep is an excellent short fat-tailed breed in China. Fat deposition in Hu sheep tail affects carcass quality and consumes a lot of energy, leading to an increase in feed cost. The objective of this study was to analyze the effects of HMGA1 polymorphism on tail fat weight in Hu sheep. Partial coding and non-coding sequences of HMGA1 were amplified with PCR and single nucleotide polymorphisms (SNP) of HMGA1 in 1163 Hu sheep were detected using DNA sequencing and KASPar technology. RT-qPCR analysis was performed to test HMGA1 expression in different tissues. The results showed that the expression of HMGA1 was higher in the duodenum, liver, spleen, kidney, and lung than in the heart, muscle, rumen, tail fat, and lymph. A mutation, g.5312 C > T, was detected in HMGA1; g.5312 C > T was significantly associated with tail fat weight, relative weight of tail fat (body weight), and relative weight of tail fat (carcass) (p < 0.05). The tail fat weight of the TT genotype was remarkably higher than that of the CC and TC genotypes. Therefore, HMGA1 can be used as a genetic marker for marker-assisted selection of tail fat weight in Hu sheep. [ABSTRACT FROM AUTHOR]

The present study aimed to investigate the relationship between growth performance, body composition, and fat deposition factors, and feed efficiency in growing lambs. We measured average daily feed intake (ADFI) and body weight (BW) from 653 Hu sheep that were fed a pellet diet. The residual feed intake (RFI) not significantly genetic and phenotypic correlated with the metabolic body weight (MBW) and average daily gain (ADG), but it was significantly genetic and phenotypic correlated with ADFI and the feed conversion ratio (FCR) (p < 0.01). However, the FCR was significantly associated with growth traits (p < 0.01). With the same ADG, body fat deposition was greater in animals with low feed efficiency compared with high feed efficiency. Therefore, excessive fat deposition can affect the feed efficiency of the body, and organ weight and gut-weight have a greater impact on the feed efficiency of lambs. The reticulum stomach and jejunum of lambs with a low RFI were smaller compared with that in the high RFI, indicating that lambs with a low RFI have less intake and a higher absorption rate. Small organs, such as the liver, of lambs with high FE might be associated with low energy expenditure and slow metabolism. This study provides a new perspective to study the biological processes responsible for feed efficiency variation in lambs. [ABSTRACT FROM AUTHOR]

As an excellent local sheep breed in China, Hu sheep have the characteristics of producing more lambs and good motherhood. The purpose of this study was to identify the polymorphism of the mitogen-activated protein kinase 5 (MAP3K5) gene and determine whether it was associated with the body size traits (body height, body length, chest circumference, and cannon circumference) in Hu sheep. The polymorphism of MAP3K5 was identified by using PCR amplification, followed by Sanger sequencing, and KASPar (Kompetitive Allele Specific PCR) technology was used for genotyping subsequently. The results of the association analysis showed that MAP3K5 (g.205261 A > G) was significantly associated with body height at 80, 100, 140, 160, and 180 d; body length at 80 and 160 d; chest circumference at 100, 140, 160, and 180 d; and cannon circumference at 100 and 120 d, respectively. The results of qRT-PCR showed that the expression level of MAP3K5 in the heart was significantly higher (P < 0.05) than in the other 10 tissues. In summary, the MAP3K5 mutation loci may be used as a candidate molecular marker for the body size traits of Hu sheep. [ABSTRACT FROM AUTHOR]

Rumen microbes play an important role in the growth and development of ruminants. Differences in variety will affect the rumen community structure. The three excellent sheep breeds were selected for this study (Hu sheep, Tan sheep, and Dorper sheep) have different uses and origins. The sheep were raised on the same diet to 180 d of age in a consistent environment. 16S rDNA V3 to V4 region sequencing was used to assess the rumen microbes of 180 individuals (60 per breed). There were differences in microbial diversity among different sheep breeds (P < 0.05). Principal coordinate analysis showed that the three varieties were separated, but also partially overlapped. Linear discriminant analysis effect size identified a total of 19 biomarkers in three breeds. Of these biomarkers, five in Hu sheep were significantly negatively correlated with average feed conversion rate (P < 0.05). Six biomarkers were identified in the rumen of Dorper sheep, among which Ruminococcus was significantly positively correlated with body weight at 80 d (P < 0.05). In Tan sheep, Rikenellaceae_RC9_gut_group was significantly positively correlated with meat fat, and significantly positively correlated with volatile fatty acids (VFAs), such as butyric acid and isobutyric acid (P < 0.05). The Rikenellaceae_RC9_gut_group may regulate Tan mutton fat deposition by affecting the concentration of VFAs. Functional prediction revealed enrichment differences of functional pathways among different sheep breeds were small. All were enriched in functions, such as fermentation and chemoheterotrophy. The results show that there are differences in the rumen microorganisms of the different sheep breeds, and that the microorganisms influence the host. [ABSTRACT FROM AUTHOR]

In sheep meat production, the rib eye area is an important index to evaluate carcass traits. However, conventional breeding programs have led to slow genetic progression in rib eye muscle area. Operationalizing molecular marker assisted breeding is an optimized breeding method that might improve this situation. Therefore, the present study used whole genome sequencing data to excavate candidate genes associated with the rib eye muscle. Male Hu lambs (n = 776) with pedigrees and 274 lambs with no pedigree were included. The genetic parameters of the rib eye area were estimated using a mixed linear mixed model. The rib eye area showed medium heritability (0.32 ± 0.13). Whole-genome sequencing of 40 large rib eye sheep [17.97 ± 1.14, (cm2)] and 40 small rib eye sheep [7.89 ± 0.79, (cm2)] was performed. Case-control genome-wide association studies and the fixation index identified candidate rib eye-associated genes. Seven single nucleotide polymorphisms (SNPs) in six genes (ALS2 , ST6GAL2 , LOC105611989 , PLXNA4 , DPP6 , and COL12A1) were identified as candidates. The study population was expanded to 1050 lambs to perform KASPar genotyping on five SNPs, which demonstrated that SNPs in LOC105611989 , DPP6 , and COL12A1 correlated significantly with the rib eye area, which could be used as genetic markers for molecular breeding of the rib eye area. The results provided genetic parameters estimated on the rib eye area and information for breeding based on carcass traits in Hu sheep. [ABSTRACT FROM AUTHOR]

The aims of this study were to analyze the effects of PPARGC1B and ZEB2 polymorphisms on the body weight of Hu sheep. DNA sequencing and KASPar technologies were used to detect single nucleotide polymorphisms (SNPs) within the PPARGC1B and ZEB2 genes of Hu sheep (n = 207). Two synonymous mutations, g.300 G > A and g.645 C > T, were detected in PPARGC1B and ZEB2, respectively. The body weights of sheep were recorded at 80, 100, 120, 140, 160 and 180-days, and associations between these polymorphisms and body weight changes were analyzed. Association analysis demonstrated that the polymorphisms in PPARGC1B and ZEB2 significantly associated with body weight (p < 0.05). At the g.300 G > A locus, individuals with the GG genotype had significantly higher body weight than those with the AA genotype, and at the g.645 C > T locus, individuals with the TT genotype had significantly higher body weight than those with the TC genotype. Individuals with both polymorphisms exhibited significantly different growth (p < 0.05). These data suggest that polymorphisms in the PPARGC1B and ZEB2 genes can be used as candidate molecular markers for the breeding of desirable growth traits in Hu sheep. [ABSTRACT FROM AUTHOR]

Brucellosis is a zoonotic disease and a major public health problem. However, the genetic mechanism of brucellosis in sheep remains unclear. In this study, serum samples were collected from 6,358 sheep from the F2 population (Dorper sheep ♂ × Hu sheep ♀), and antibody levels were continuously measured at 14 days and 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 months after administration of brucellosis vaccine. Finally, 19 brucellosis-resistant group (BRG) sheep and 22 brucellosis-susceptible group sheep (BSG) were screened for whole-genome sequencing. Using the fixation index, Fisher's exact test, and chi-square test, a total of 205 candidate SNP sites were identified. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis suggested that 138 candidate genes were significantly enriched in adherens junction (CTNNA3 , PARD3 , and PTPRM), cell adhesion molecules (NLGN1 , CNTNAP2 , NCAM1 , and PTPRM), salivary secretion (LOC101102109 , PRKG1 , and ADCY2), and hippo signaling pathway (CTNNA3 , YAP1 , and PARD3). These findings provide valuable molecular markers for brucellosis resistance breeding in sheep and novel insights into the genetic mechanism of brucellosis resistance. [ABSTRACT FROM AUTHOR]

In the genetic improvement of livestock and poultry, residual feed intake (RFI) is an important economic trait. However, in sheep, the genetic regulatory mechanisms of RFI are unclear. In the present study, we measured the feed efficiency (FE)-related phenotypes of 137 male Hu lambs, and selected six lambs with very high (n = 3) and very low (n = 3) RFI values and analyzed their liver transcriptomes. A total of 101 differentially expressed genes were identified, of which 40 were upregulated and 61 were downregulated in the low-RFI group compared with that in the high-RFI group. The downregulated genes were mainly concentrated in immune function pathways, while the upregulated genes were mainly involved in energy metabolism pathways. Two differentially expressed genes, ADRA2A (encoding adrenoceptor alpha 2A) and RYR2 (ryanodine receptor 2), were selected as candidate genes for FE and subjected to single nucleotide polymorphism scanning and association analysis. Two synonymous mutations, ADRA2A g.1429 C > A and RYR 2 g.1117 A > C, were detected, which were both significantly associated with the feed conversion rate. These findings provide a deeper understanding of the molecular mechanisms regulating FE, and reveal key genes and genetic variants that could be used to genetically improve FE in sheep. [ABSTRACT FROM AUTHOR]

• FTO gene was associated with the traits of tail fat deposition. • FTO gene has the highest expression at 3 month of age. • The expression of FTO in small-tail group was highest. Fat mass and obesity associated (FTO) gene is a famous dominant predictor of obesity, and plays pivotal roles in the regulating fatty acid transport and fat metabolism. In the current study, the quantitative real-time PCR (qRT-PCR), DNA-pooled sequencing and KAspar assay were performed to detect the expression features of FTO and the polymorphisms of FTO associated with the tail fat weight related-traits of Hu sheep. The results indicated that the expression of FTO gene is widely expressed in the tissues tested, and the expression level of FTO in tail fat tissue was evidently higher compared with that in the other tissues. In addition, FTO showed the highest expression level in tail fat tissue at three months. The expression of FTO mRNA was lower in the large-tail fat group compared with that in the small-tail fat group in 6 months old. Subsequently, the polymorphism loci g. 23704451C > A detected in the FTO gene was confirmed to be significantly related to the tail length and the weight of tail fat. These results suggested that the polymorphism might be regarded as novel molecular marker for the breeding of small tail sheep. [ABSTRACT FROM AUTHOR]

Simple Summary: In modern sheep production systems, less energy is required to gain lean tissue than to deposit fat; therefore, producers are attempting to decrease fat deposition costs by altering nutrient use to benefit the production of leaner carcasses. Microbes in the rumen have vital functions in feed digestion; however, limited research has been performed on the rumen microbiome's effect on fat deposition. This study revealed variations in microbial populations in rumen carrying different fat deposition phenotypes in a characteristic way, and these findings could aid in developing strategies for manipulating rumen microbiota to alter the production performance of sheep. Microbial communities of the sheep rumen have been studied extensively; however, their involvement in the regulation of fat deposition is unknown. Herein, we aimed to identify the correlations among fat deposition-related phenotypes and the effect of microbiota on changes in body fat accumulation. The rumen microbiota of 141 lambs was profiled by 16S ribosomal RNA sequencing, and the volatile fatty acids' (VFAs') concentrations were quantified by gas chromatography. Subsequently, the animals were grouped according to body mass index (BMI) to compare the microbiota of the rumen among the sheep with different fat deposition levels. Results further revealed differences in terms of the species abundance, diversity, and microbial composition between sheep with different fat deposition levels. Linear discriminant analysis (LDA) Effect Size (LEfSe) analysis and Random Forest (RF) regression analysis identified changes in 29 ruminal bacteria, which may be the main driver for different fat deposition. [ABSTRACT FROM AUTHOR]

Abstract Background Investigating the molecular biology underpinning the early-stage of traumatic temporomandibular joint (TMJ) ankylosis is crucial for discovering new ways to prevent the disease. This study aimed to explore the dynamic changes of transcriptome from the intra-articular hematoma or the newly generated ankylosed callus during the onset and early progression of TMJ ankylosis. Methods Based on a well-established sheep model of TMJ bony ankylosis, the genome-wide microarray data were obtained from samples at postoperative Days 1, 4, 7, 9, 11, 14 and 28, with intra-articular hematoma at Day 1 serving as controls. Fold changes in gene expression values were measured, and genes were identified via clustering based on time series analysis and further categorised into three major temporal classes: increased, variable and decreased expression groups. The genes in these three temporal groups were further analysed to reveal pathways and establish their biological significance. Results Osteoblastic and angiogenetic genes were found to be significantly expressed in the increased expression group. Genes linked to inflammation and osteoclasts were found in the decreased expression group. The various biological processes and pathways related to each temporal expression group were identified, and the increased expression group comprised genes exclusively involved in the following pathways: Hippo signaling pathway, Wnt signaling pathway and Rap 1 signaling pathway. The decreased expression group comprised genes exclusively involved in immune-related pathways and osteoclast differentiation. The variable expression group consisted of genes associated with DNA replication, DNA repair and DNA recombination. Significant biological pathways and transcription factors expressed at each time point postoperatively were also identified. Conclusions These data, for the first time, presented the temporal gene expression profiling and reveal the important process of molecular biology in the early-stage of traumatic TMJ bony ankylosis. The findings might contributed to identifying potential targets for the treatment of TMJ ankylosis.

The number of ribs is an important economic trait in the sheep industry when the sheep are raised for mutton. However, in sheep, the genetic mechanisms regulating rib number are poorly understood. In the present study, we aimed to identify important candidate genes that affect the increase in rib number in sheep. Whole-genome resequencing of 36 Hu sheep with an increased number of ribs (R14) and 36 sheep with normal (R13) rib numbers was carried out. Analysis using three methods (fixation index (F ST), Fisher's exact test, and Chi-squared test) showed that 219 single nucleotide polymorphism sites overlapped among the results of the three methods, which represented 206 genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the genes were mainly associated with regulation of developmental process, inorganic anion transport, cellular biosynthetic process, tight junction, the oxytocin signaling pathway, and arrhythmogenic right ventricular cardiomyopathy. Four mutations were selected according to the significantly selected genomic regions and important pathways for genotyping and association analysis. The result demonstrated that three synonymous mutations correlated significantly with the rib number. Importantly, we revealed that the CPOX (encoding coproporphyrinogen oxidase), KCNH1 (encoding potassium voltage-gated channel subfamily H member 1), and CPQ (encoding carboxypeptidase Q) genes have a combined effect on rib number in Hu sheep. Our results identified candidate molecular markers for rib number in sheep breeding. • The major candidate genes associated with the rib number were identified using whole-genome resequencing in Hu sheep. • A total of 219 single nucleotide polymorphism sites were found using three methods. • Four single nucleotide polymorphism sites were selected for subsequent genetic effect analysis in a large population. [ABSTRACT FROM AUTHOR]

CD274 and PLEKHH2 genes have been identified as immune- and multiple diseases-related genes, and have recently garnered significant interest. However, their role in regulating immune functions in sheep remains largely unexplored. In this study, we aimed to investigate the effects of polymorphisms in CD274 and PLEKHH2 on hematologic parameters in 915 sheep. Our results showed that the CD274 and PLEKHH2 genes were most highly expressed in the spleen and tail fat, respectively, as determined by qRT-PCR. We also identified a G to A mutation (g 0.11858 G > A) in the exon 4 region of CD274, and a C to G mutation (g 0.38384 C > G) in the intron 8 region of PLEKH2. Association analysis revealed that CD274 g 0.11858 G > A was significantly associated with RBC, HCT, MCHC, and MCV (P < 0.05), while PLEKHH2 g 0.38384 C > G was significantly associated with HCT, MPV, MCHC, and MCV (P < 0.05). These results suggest that CD274 and PLEKHH2 genes may play a role in regulating blood physiological indicators and could be potential functional candidates for influencing immune traits in sheep breeding programs. • The SNPs of CD274 and PLEKHH2 genes were associated with hematologic parameters in sheep. • Combined genotypes of CD274 and PLEKHH2 genes were associated with hematologic parameters in sheep. • The ovine CD274 and PLEKHH2 genes had the highest mRNA expression in the spleen and tail fat, respectively. [ABSTRACT FROM AUTHOR]

• The SNP of ALB was significantly associated with ADG. • The SNP of AHSG was significantly associated with ADG and FCR. • The SNP of GC was significantly associated with BW, BH and BL. • ALB , AHSG , and GC expression levels were significantly higher in H_BW group. Growth traits are economically important traits in sheep breeding. This study was conducted to evaluate the polymorphisms of ALB , AHSG and GC genes and their association with growth traits in Hu sheep. We measured and recorded the body weight (BW), body height (BH), body length (BL) and feed conversion ratio (FCR) of 1418 male Hu sheep raised in the same environment from 80 to 180 days of age. The total of four SNPs in the ALB , AHSG and GC genes were identified by direct sequencing technology. The results of association analysis showed that two loci (g.8699 A>T and g.13458 T>C) of ALB gene significantly affect average daily gain (ADG; P < 0.05). The genotypes of SNP g.2454 T>C in AHSG gene were significantly associated with ADG and FCR (P < 0.05). There were significant associations between GC g.19484 A>C and BW, BH and BL (P < 0.05). The results of qRT-PCR showed that ALB , AHSG , and GC genes were extremely significantly higher in H_BW sheep compared with those in the L_BW sheep (P < 0.01). These results revealed that ALB-1 g.8699 A>T, ALB-2 g.13458 T>C, AHSG g.2454 T>C and GC g.19484 A>C loci are potential molecular markers for Hu sheep breeding. [ABSTRACT FROM AUTHOR]

Meat quality is becoming more important for sheep breeding programs. Meat quality is a complex trait affected by genetic and environmental factors. In the present study, an integrative analysis of the longissimus thoracis tissue transcriptome and proteome was conducted to identify genes, proteins, and pathways related to meat quality in sheep. The sheep breeds Hu and Dorper were considered. These breeds were compared for the differences in muscle fiber structure, chemical composition, and amino acid composition. In the Hu sheep vs. Dorper sheep comparison, 22 DEGs/DEPs showed the same mRNA and protein expression trends. These genes are associated with lipid transport, lipid metabolism, and muscular system development. Moreover, some pathways such as "lipid transport", "lipoprotein metabolic process", "Alanine, aspartate and glutamate metabolism", and "Arginine biosynthesis" were significantly enriched in this study. The reliability of the RNA-Seq results was verified by qRT-PCR. These findings provide new insights into the molecular mechanisms of meat quality in sheep. • The chemical composition and amino acid content of muscle were investigated. • Measuring the morphological characteristics of the longissimus thoracis muscle fibers. • RNA-Seq and Label-free were used to explore meat quality related mechanisms in sheep. • qRT-PCR was performed to verify the RNA-Seq results. [ABSTRACT FROM AUTHOR]

Body weight (BW) is a critical economic trait for meat production in sheep, and it is a complex trait affected by numerous elements. The aim of this study was to investigate the genetic mechanisms of sheep BW by a label-free proteomics approach. The result showed, a total of 27, 14, 61, and 65 differentially abundant proteins (DAPs) were identified in the Hu_HBW vs. Hu_LBW, DP_HBW vs. DP_LBW, Hu_HBW vs. DP_HBW, and Hu_LBW vs. DP_LBW comparisons, respectively. Five proteins (including ILK, AHCYL2, MLIP, CYB5A, and SMTNL1) related to fat synthesis and muscle development were detected in the Hu sheep group. In the Dorper sheep group, the screened DAPs strictly related to muscle development and fat synthesis were significantly enriched in MAP kinase activity (MAPK12), Arachidonic acid metabolism, and Steroid hormone biosynthesis (PGFS, LOC101107119) pathways. Several DAPs related to immune responses (SERPINA1, FGG, SERPINC1, and LOC101108131), fat deposition (APOH, GC, AHSG, SKP1, ACSL1, ACAT1, and ACADS), and muscle development (LMOD3 and LRRC39) were detected in the Hu vs. Dorper sheep comparison. These analyses indicated that the BW of sheep is regulated via a variety of pathways, and these DAPs can be further investigated as candidate markers for predicting the BW of sheep. Body weight is one of the key traits in sheep and involves multiple coordinated regulatory mechanisms, but the genetic mechanism of BW is still unclear in sheep. In the current study, the label-free method was used to identify the proteins and pathways related to BW using LT muscle of Hu sheep and Dorper sheep with different BW. These findings will provide new candidate proteins and vital pathways into the molecular mechanisms involved growth traits in sheep. [Display omitted] • Label-free proteomics were used to explored BW related mechanisms of sheep. • Muscle development and fat synthesis play a key role in body weight of sheep. • The body weight of sheep is regulated via a variety of pathways. • Western blot was performed to verify the proteomic results. [ABSTRACT FROM AUTHOR]

• 460 bp and 1708 bp of RPS23 and HPSE genes were cloned, and bioinformatics analysis were performed. • The mutation RPS23 g.720 A > G and HPSE g.1077 G > A were found and associated with hematologic parameters by SNP identification. In addition combined genotypes were also associated with hematologic parameters, such as GG HPSE /GG RPS23 , AG HPSE /GG RPS23. • RPS23 and HPSE were widely expressed in sheep, and the expression levels of RPS23 and HPSE were highest at 3 months by RT-qPCR. Ribosomal protein S23 (RPS23) and Heparanase (HPSE) were located on chromosome 5 and chromosome 6, respectively, which play vital roles in protein synthesis and immunity. The objective of this study was to clone RPS23 and HPSE and to detect the expression levels of RPS23 and HPSE and the polymorphisms of RPS23 and HPSE associated with the hematologic parameters by using qRT-PCR, DNA sequencing and KASPar assay. The quantitative real-time PCR (RT-qPCR) showed that the two genes were expressed widely in the ten tissues of sheep. The expression levels of RPS23 and HPSE were the highest in lung and liver, respectively. The expression levels of RPS23 and HPSE in lung and liver increased from 0 to 3 months, decreased from 3 to 6 months, respectively. Furthermore, two mutations g.720 A > G and g.1077 G > A were detected in the RPS23 and HPSE, respectively, which were confirmed to be significantly associated with hematologic parameters. These results supported RPS23 g.720 A > G and HPSE g.1077 G > A as genetic markers of sheep. [ABSTRACT FROM AUTHOR]

• Both ELOVL5 and FASN genes was associated with the traits of tail fat deposition. • ELOVL5 and FASN expression levels were highest in tail fat. • ELOVL5 expression levels in the big-tail group were highest. • The expression of FASN in small-tail group were highest. • ELOVL5 and FASN have the highest expression at 6 months and 3 months of age. Reducing tail fat deposition can increase the economic value of a carcass and improve feed efficiency. This study aimed to explore ELOVL5 and FASN polymorphisms associated with tail fat deposition and their expression levels of sheep. Association analysis showed that ELOVL5 synonymous mutation g.62534 C > T was associated with tail width, tail fat weight, and relative tail fat weight (P < 0.05). FASN synonymous mutation g.12694 A > G was associated with tail length and width (P < 0.05). Combined effect analyses indicated significant differences between the combined genotypes and tail fat deposition. Quantitative real-time reverse transcription PCR indicated that the ELOVL5 and FASN expression levels were significantly higher in tail fat than in other tissues (P < 0.05). ELOVL5 expression levels in tail-fat tissue of big-tail sheep was significantly higher than that in small-tail sheep (P < 0.01). FASN expression levels were significantly higher in tail-fat tissue of small-tail sheep than in that of big-tail sheep (P < 0.05). During development, ELOVL5 tail fat expression increased significantly from 0 to 6 months old (P < 0.05), and FASN expression at 3 months old was significantly higher than that at 0 (minimum) and 6 months old (P < 0.05). Therefore, ELOVL5 and FASN polymorphisms could represent new candidate molecular markers and targets to reduce tail fat deposition in sheep. [ABSTRACT FROM AUTHOR]