OBJECTIVE: Qianhua Mutton Merino sheep is a new breed of meat wool sheep cultivated independently in China. In 2018, it was approved by the state and brought into the national list of livestock and poultry genetic resources. Qianhua Mutton Merino sheep have the common characteristics of typical meat livestock varieties with rapid growth and development in the early stage and high meat production performance. The objective of this research is to investigate the Genome-wide association of the reproductive traits of Qianhua Mutton Merino sheep.
METHODS: Qianhua Mutton Merino sheep from the breeding core group were selected as the research object, genome-wide association analysis was conducted on genes associated with the reproductive traits (singleton or twins, birth weight, age [in days] for sexual maturity, weaning weight, and daily gain from birth to weaning) of Qianhua mutton merino.
RESULTS: Our study findings showed that 151 loci of single-nucleotide polymorphisms (SNPs) were detected, among which 3 SNPs related to birth weight and weaning weight occupied a significant portion of the wide genome. The candidate genes preliminarily obtained were SYNE1, SLC12A4, BMP2K, CAMK2D, IMMP2L, DMD, and BCL2.
CONCLUSIONS: We found 151 SNP loci for five traits related to reproduction (including singleton or twins, birth weight, age [in days] at sexual maturity, weaning weight, and daily weight gain from birth to weaning). The functions of these candidate genes were mainly enriched in nucleotide metabolism, metal ion binding, oxytocin signaling pathway, and neurotrophin signaling pathway.

This study analysed the genetic diversity and population structure of eight sheep breeds in Turkey and nearby countries. Moderate genetic diversity was observed, with the Sakiz (SKZ) exhibiting the highest diversity based on heterozygosity and allelic richness (AR) values. Genetic distances revealed differentiation between the populations, with the most significant divergence between the Cyprus Fat Tail (CFT) and SKZ breeds. PCA demonstrated SKZ and Chios (CHI) clustering together, indicating genetic similarity. Karakas (KRS), Norduz (NDZ), Afshari (AFS), Moghani (MOG) and others showed overlap, reflecting genetic relationships. Ancestry analysis found that KRS was predominantly inherited from the second ancestral population, while SKZ and NDZ were primarily derived from the first and second ancestral lineages. This illustrated the populations\' diverse origins. Most genetic variation (96.84%) was within, not between, populations. The phi-statistic (PhiPT) indicated moderate differentiation overall. Phylogenetic analysis further demonstrated the genetic distinctiveness of the SKZ breed. ROH and FROH analyses showed that SKZ exhibited the highest homozygosity and inbreeding, while KRS displayed the lowest. This study elucidates these breeds\' genetic diversity, structure and relationships. Key findings include moderate diversity, evidence of differentiation between breeds, diverse ancestral origins and distinct ROH patterns. This provides insights into the population\'s genetic characteristics and conservation requirements.

This study provides estimates on genetic parameters, inbreeding depression and purging for meat performance measures from 25 German sheep breeds. All German meat, merino sheep breeds and breeds of other breeding directions with a sufficient number of pedigree and performance data were included in this study. Phenotypic traits retrieved from the national database OviCap were evaluated: daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness. We employed animal models to estimate heritability, variance and covariance components for these meat performance traits as well as inbreeding depression and purging. The heritabilities, on average, reached estimates of 0.55, 0.34, 0.53 and 0.61 for daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness, respectively. We estimated the linear regression slopes for the individual rate of inbreeding, new and ancestral inbreeding, as well as the inbreeding coefficient and its interaction with the inbreeding coefficient of Ballou, employing animal models with non-genetic effects and the additive genetic effect of the animal. Across all breeds, inbreeding was only significant for daily weight gain, whereas for all other traits, estimates were not significant. Within sheep breeds, we found significant inbreeding depression for daily weight gain in German Mutton Merino and German Blackheaded Mutton as well as for the meatiness score in German Whiteheaded Mutton. Significant effects for purging, based on ancestral inbreeding and the interaction effect of the classical inbreeding coefficient with the inbreeding coefficient of Ballou, were not obvious either across or within any sheep breed. A 1% increase in inbreeding significantly decreased the phenotypic trait median of daily weight gain across all sheep breeds by 0.50% and 0.70% of phenotypic and genetic standard deviation, respectively. Purging effects due to ancestral inbreeding were not significant in any breed or across breeds. The results of this study may indicate that inbreeding depression may be more harmful in traits under stronger selection than in traits that exert low selection pressure. The results of this study demonstrate the different effects that result in meat performance traits due to inbreeding. With increasing rates of inbreeding and critical effective population sizes, selection intensity for breeding objectives has to be critically reviewed for each sheep breed. Inbreeding depression and purging should be evaluated in order to prevent a decrease in trait means due to inbreeding and to determine whether detrimental alleles are eliminated.

In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of Ovar-DRB diversity across sheep breeds of India. Here, Ovar-DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN > dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.

Three sampling strategies with a 16s rRNA high-throughput sequencing and gene expression assay (by RT-PCR) were designed, to better understand the host and probiotics effect on gut microbiota in sheep. Sampling: (1) colon contents and back-fat tissues from small-tailed Han sheep (SHS), big-tailed Hulun Buir sheep (BHBS), and short-tailed Steppe sheep (SHBS) (n = 12, 14, 12); (2) jejunum, cecum and colon contents, and feces from Tan sheep (TS, n = 6); (3) feces from TS at 4 time points (nonfeeding, 30 and 60 feeding days, and stop feeding 30 days) with probiotics supplementation (n = 7). The results indicated SHS had the highest Firmicutes abundance, the thinnest back-fat, and the lowest expression of C/EBPβ, C/EBPδ, ATGL, CFD, and SREBP1. Some bacteria orders and families could be potential biomarkers for sheep breeds with a distinct distribution of bacterial abundance, implying the host genotype is predominant in shaping unique microbiota under a shared environment. The microbiota diversity and Bifidobacterial populations significantly changed after 60 days of feeding but restored to its initial state, with mostly colonies, after 30 days ceased. The microbiota composition was greatly different between the small and large intestines, but somewhat different between the large intestine and feces; feces may be reliable for studying large intestinal microbiota in ruminants.

The aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds using the hierarchical clustering method. In total, 240 individual data records were used as experimental material. Placental characteristics such as total cotyledon surface area, small and large cotyledon length, small cotyledon depth, etc. were used as explanatory variables to classify the breeds\' characteristics. Hierarchical clustering was used with the nearest neighbour method with Euclidean distance in order to classify the sheep breeds\' variations. As a result, six breeds were separated into three clusters: the first cluster consisted of Bafra, Karayaka, and Awassi breeds; the second consisted of Akkaraman and Malya breeds; and the third cluster included only the Morkaraman breed. Bafra and Karayaka were pointed as the nearest breeds, with a similarity of 98.7% in terms of placental characteristics. The similarity rate of the Akkaraman and Malya breeds was at a level of 97.5%, whereas it was 96.8% for Bafra, Karayaka, and Awassi breeds. The similarity of Akkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds was estimated as 95.7%. The overall similarity was found to be at a level of 93.2% among sheep breeds. The outcomes of the study might be useful as a selection tool for reproductivity and can be used to select the breed to be reared.

The present study established multiple linear regression models using two ultrasound in vivo measurements (at lumbar and sternal regions, with different real-time ultrasonography machines and probes) and live weight, to predict simultaneously carcass composition and body fat depots of different breeds of sheep and goat. This study is important for the small ruminant industry, considering the feasibility of using the ultrasound methodology in field conditions, as well as an online system of the carcass evaluation. The multiple linear regression models were obtained by selecting the best subset of variables between using the in vivo measurements (raw variables), their second degree and interactions, evaluated in terms of prediction performance using cross-validation \"K-folds\" and validated by a test group. Overall, high accuracy (adj R2) was obtained from the linear relationship between predicted and experimental values of the group test for each of the nine dependent variables, with values varying between adj R2 0.88 and 0.98.

In sheep, the coiled-coil-helix-coiled-coil-helix domain containing 7 (CHCHD7) gene and the pleiomorphic adenoma gene 1 (PLAG1) are on the same growth-related major quantitative trait locus, positioned head-to-head approximately 420 bp apart on chromosome 9. PLAG1 affects sheep growth, but the effects of CHCHD7 have not been determined. In this study, an 8-bp deletion downstream of CHCHD7 was analyzed in 2350 sheep from seven breeds. The associations between the deletion and growth traits of Tan sheep were also determined. Both genotypes (homozygous wild-type and heterozygous) for the 8-bp deletion were found in Tan (TS), Luxi Blackhead (LXBH), Small-Tail Han (STHS), and Lanzhou Fat-Tail (LFTS) sheep. However, there were no polymorphic sites for the mutation in Hu (HS), Sartuul (SS), and Australian White (AUW) sheep. In TS, LXBH, STHS, and LFTS sheep, the deletion genotype was less frequent than the wild-type genotype, and the allele frequencies of the deletion variant were 0.007 (TS), 0.011 (LBXH), 0.008 (STHS), and 0.010 (LFTS). The 8-bp deletion was significantly associated with body length (p = 0.032), chest depth (p = 0.015), and chest width (p = 0.047) in Tan sheep. Thus, the 8-bp deletion downstream of the CHCHD7 gene might be associated with growth and development traits of sheep.

OBJECTIVE: Sheep farming is an important source of livelihood in the southern Khyber Pakhtun Khwa province of Pakistan where they are reared under extensive system (ES). This system has limitations of improper feeding, rearing, and management which negatively affect their productivity. The present study compares different rearing systems and their stresses on fertility, behavior, and growth rate potential of two sheep breeds of Pakistan.
METHODS: Eighty ewes were selected; forty each from Damani and Balkhi breeds reared in semi-intensive system (SIS) and ES at Paharpur district, Dera Ismail Khan. Blood samples were collected in triplicate on days 0, 14, and 28 of May, and the molecular and behavioral stress, growth, and fertility rates were recorded.
RESULTS: The highest growth and fertility rate were observed in both the breeds in SIS than in ES (p < 0.01). The values of stress indicators (cortisol, heat shock protein (HSP-70)) and behavioral stress parameters were found lower in Damani breed as compared to Balkhi breed in both rearing systems (p < 0.01). All the molecular stress and behavioral stress parameters were negatively associated with metabolic hormones (T3 and T4) (p < 0.01). A positive correlation was observed among all the molecular stress and behavioral stress parameters (p < 0.01). Similarly, T3 and T4 were positively interlinked to one another (p < 0.01).
CONCLUSIONS: It was concluded that both Damani and Balkhi sheep showed lower stress levels and better fertility and growth parameter in SIS than ES system of rearing. Local Damani breed exhibited well tolerant ability and genetic adaptation to the local environment as compared to Balkhi breed.

OBJECTIVE: This study was conducted to study the genetic and population structure of local (Awassi) and exotic (Romanov, Charollais, Assaf, Awassi, and Suffolk) sheep breeds in Jordan using eight microsatellite markers.
METHODS: A total of 125 sheep were used (25 from each breed) in the study. The number of alleles (A), the mean values of observed (Ho) and expected (He) heterozygosity, polymorphism information content (PIC), fixation index as a measure of heterozygote deficiency or excess, and Hardy-Weinberg equilibrium (HWE) were analyzed using PopGen and CERVUS softwares. Nei\'s standard genetic distances among breeds and dendrogram of unweighted pair group method with arithmetic mean (UPGMA) were calculated and constructed using PopGen software.
RESULTS: A total of 40 alleles were detected with an average number of alleles of 5. The mean Ho value was higher than the mean He value for all breeds. Awassi breed showed the highest average PIC value while Romanov had the lowest. There was a significant (p<0.05) deviation from HWE at each locus within and between breeds. Deviations from HWE were found to be highly significant for all markers except OARFCP304 locus. The genetic distance estimates revealed a close relationship between Romanov and Charollais and between Awassi and Charollais. In the UPGMA dendrogram, Charollais, Romanov, and Awassi breeds were placed together in one main cluster while Assaf was in a different subcluster. Awassi was placed alone in a second main cluster.
CONCLUSIONS: Results of this study offer insight toward the genetic conservation of the studied breeds and a base on which breeding plans can be made.