Indigenous Sheep Research Articles

Phenotypic characterization of indigenous sheep breeds in the Jimma Zone, Oromia, Ethiopia

ABSTRACT The objective of the study was to undertake phenotypic characterization of sheep, in their production environment. A total of 570 sheep were used in this study for body measurements. After the data were collected, using the Proc GLM model, quantitative data were analysed by SAS version 9.3 (2014) and qualitative data were analysed by SPSS. The dominant coat colour pattern observed was 81.1% plain, 16.4% patchy and sheep with spotted pattern (2.5%), respectively. Brown (43.5%), fawn (17.5%) and red (13.0%) were the most frequently observed coat colour types. The majority (91.1%) of sheep were polled whereas (8.9%) of the sheep were horned. The effect of the district on body weight and most of the linear body measurements were significant (p < 0.05) except head length, canon bone length, ear length and tail length. Chest girth explains more variation than any other linear body measurements in both ewes (94%) and rams (93%). The prediction of body weight based on regression equation y = −21.82 + 0.68x for female sheep and y = −49.90 + 1.08x for male sheep, where y and x are body weight and chest girth, respectively. In general, it could help as an input for efficient utilization, conservation and improvement in the future.

Adaptive dynamics of indigenous sheep in Canary Islands, Spain: A machine learning approach.

The objective of the study was to characterize the adaptive profile of Ibero-American sheep of the Canaria breed, evaluating the possible changes in thermoregulatory responses and coat characteristics to which the animals are exposed in the different seasons of the year. Data collected over a period of 12 months were analyzed, with information being observed in the interval of 15 days of each month, in 23 adult ewes kept in an intensive breeding system. The rectal temperature (RT) of Canaria ewes was higher (P < 0.001) in the summer and spring seasons. In contrast, the respiratory rate (RR) of the animals was higher in autumn. The surface temperature (ST) of the herd was lower during the spring. It was observed that the hair length (HL) and the hair density (NH) did not vary during the seasons. However, the hair diameter (HD) and the coat thickness (CT) varied, being in the spring, the season in which the animals had the highest HD and autumn, the season in which they had the lowest. The performance was similar throughout the seasons (P > 0.05). The morphological variables of the coat presented 63.8% of original cases grouped, which may characterize the morphological responses of the coat of these animals as an important trait of the adaptive profile of the breed, whereas the opposite occurred for thermoregulatory responses. The variables most used by the herd and that were most important were autumn (CT, NH, HD, HR, RT, and HL), summer (ST and RR), spring (RR, ST, and RT), and winter (RT, HD, HR, and RR). Sheep of the Canaria breed have an adaptive profile that dynamically uses thermoregulatory and morphological responses, molding themselves according to climate changes resulting from seasonal periods on the Island of Tenerife, Spain. The Canaria sheep stood out for the modification of the morphological characteristics of the coat, especially during autumn and spring, and can be considered an excellent genetic resource with excellent adaptive characteristics for arid environments such as those found in the Canary Islands.

Comparative genomic characterization of indigenous fat‐tailed Akkaraman sheep with local and transboundary sheep breeds

AbstractThe domestic sheep with over 1200 breeds descended from those early domesticated animals that are bred for a variety of resources such as meat, milk and wool. Akkaraman, a fat‐tailed indigenous sheep breed of Türkiye, is widespread throughout Central Anatolia, with the largest indigenous sheep population. Assessing the genetic diversity and genomic structure of animal breeds is among the key contributors to deciphering adaptation to environmental extremes and constructing efficient genetic improvement strategies. Therefore, this study aimed to characterize the genome of Akkaraman breed against various world‐renowned transboundary sheep and indigenous sheep with fat and thin tails. Genetic similarities and differences between those breeds have been displayed by estimating and comparing various genetic diversity indices, linkage disequilibrium (LD) estimates and fixation index (FST), runs of homozygosity (ROH) as well as PCA and neighbour‐joining tree analysis. Akkaraman sheep were observed to form a cluster alongside Moghani, Karakas, Tibetan and Cyprus Fat Tail sheep, which are primarily the sole representatives of fat‐tailed sheep in the study. This clustering was evident in both the PCA and neighbour‐joining tree analysis. The Akkaraman sheep was also observed to have the lowest genomic inbreeding and one of the lowest numbers of ROHs, which might also indicate that the breed has not been exposed to historical intensive selection pressure, inbred mating or a massive population bottleneck that might leave strong marks of genomic homozygosity. The results improve our understanding of the genetic diversity in Akkaraman sheep in comparison with certain mainstream sheep breeds as well as those indigenous breeds from around the world. Additionally, findings will also provide valuable insights to perform further GWAS effectively by considering population structure, diversity and LD patterns observed among the breeds while providing practical knowledge that will contribute to designing efficient and successful genome‐based selection programmes for worldwide sheep production systems.

Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection

BackgroundCopy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding.ResultsCNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, VST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences.ConclusionsCollectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.

Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China

Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.

Association of MTNR1A and GDF9 gene allelles with the reproductive performance, response to oestrus induction treatments and prolificacy, in improved and non-improved local indigenous sheep breeds.

Sheep farming plays a crucial role for Mediterranean countries, wherefrom a plethora of dairy products is produced. Yet, numerous indigenous sheep breeds in temperate latitudes such as the Mediterranean present a serious drawback that milk production is impaired by the seasonality of reproduction. Towards the efforts for reduction of this phenomenon, the purpose of this study was to evaluate and compare different oestrus synchronization treatments, as well as to associate two genes alleles', namely the MTNR1A and the GDF9, with the response to those treatments. Three indigenous breeds were investigated (Florina, Chios and Karagouniko sheep) and inside each breed three different oestrus synchronization treatments were applied (A: intravaginal sponges, B: GNRH use and C: male effect). In group A, Florina ewes expressed oestrus at 90% in July and fecundity was 85%. Karagouniko and Chios ewes exhibited an oestrus expression of 100% with fecundity rates at 95% and 99%, respectively. In group B, Florina ewes expressed oestrus at 60% with fecundity at 57%, Karagouniko ewes expressed oestrus at 65% with fecundity at 54%, whereas Chios breed animals expressed oestrus at 87% with fecundity rate at 85%. In group C, 68% of the Florina breed expressed oestrus 20-25 days post ram induction, whereas this proportion was 84% and 94%, for Karagouniko and Chios breed, respectively. For the molecular analysis, partial segments of the two genes were sequenced and analysed, whereas alleles were scored based on the detected SNPs. All frequencies of the four detected SNPs in MTNR1A gene were statistically and significantly different in ewes that expressed oestrus in comparison with ewes that did not express oestrus in Florina and Karagouniko breeds concerning all treatments. Two SNP's were detected in GDF9 gene, G1 and FecG , from which, only the FecG mutation exhibited statistically significant difference in twins and triplets than in singles in Florina and Karagouniko breeds.

Characterization and discrimination of the flavor profiles of Chinese indigenous sheep breeds via electronic sensory, smart instruments and chemometrics

This study was conducted to analyze the flavor profile of six commercially available Chinese indigenous breeds of sheep meat and to distinguish them based on their flavor characteristics. Various techniques such as gas chromatography-mass spectrometry (GC-MS), electronic nose (E-nose), high performance liquid chromatography (HPLC) and electronic tongue (E-tongue) were employed to analyze both volatile and non-volatile compounds in the meat samples. The results showed that, a total of 28 volatile compounds in sheep meat were detected, with 1-octen-3-ol, 1-pentanol, hexanal, octanal, and nonanal identified as the major contributors to its aroma. Tan Sheep and Oula Sheep had significantly higher concentrations of 1-pentanol, nonanal, 1-octen-3-ol, 1-octanol, and hexanoic acid than other breeds. Sweet amino acids were the most abundant free amino acids, comprising 72–85% of the total FAAs, and inosinic acid was the most abundant ATP-related compound. Small-Tailed Han sheep had significantly higher levels of SFAAs, total FAAs, and AMP, while Tan sheep had significantly higher levels of UFAAs, and Oula Sheep had significantly higher levels of GMP. The response values of differential electronic sensors W5S, W1W, NMS, PKS, and SCS were found to be useful in discriminating between breeds of sheep meat. The fusion electronic sensory signals were used to train support vector machine and random forest models, both achieving 100% accuracy in discriminating between sheep breeds.

Comparative proteomics of ovaries elucidated the potential targets related to ovine prolificacy.

Small Tail Han (STH) sheep, a unique Chinese breed, is recognized for its early maturity, year-round estrus, and prolificacy. However, the molecular mechanism of its high prolificacy has not been fully elucidated. The Proteomics approach is feasible and effective to reveal the proteins involved in the complex physiological processes of any organism. Given this, we performed the protein expression profiling of ovarian tissues during the luteal phase using polytocous STH sheep (litter size ≥2, three consecutive lambings) and monotocous STH sheep (litter size =1, three consecutive lambings) (PL vs. ML), and the follicular phase using polytocous STH sheep (litter size ≥2, three consecutive lambings) and monotocous STH sheep (litter size =1, three consecutive lambings) (PF vs. MF), respectively. Parallel Reaction Monitoring (PRM) was conducted to validate the differentially abundant proteins (DAPs). The tandem mass tag (TMT) quantitative proteomic results showed that a total of 5,237 proteins were identified, of which 49 and 44 showed differential abundance in the PL vs. ML and PF vs. MF groups, respectively. Enrichments analyses indicated that the DAPs including TIA1 cytotoxic granule-associated RNA-binding protein-like 1 (TIAL1), nicotinamide phosphoribosyltransferase (NAMPT), and cellular retinoic acid-binding protein 1 (CRABP1) were enriched at the luteal phase, while TIAL1, inhibin beta-a-subunit (A2ICA4), and W5PG55 were enriched at the follicular phase, potentially mediating reproductive processes in polytocous ewes. Furthermore, six DAPs were verified using PRM, confirming the accuracy of the TMT data acquired in this study. Together, our work expanded the database of indigenous sheep breeds and provided new ovarian candidate molecular targets, which will help in the study of the genetic mechanisms of ovine prolificacy.

Impact of Haemonchus contortus infection on feed intake, digestion, liveweight gain, and enteric methane emission from Red Maasai and Dorper sheep

A study was conducted with Red Maasai and Dorper lambs to evaluate the effects of infection with the gastrointestinal nematode (GIN) Haemonchus contortus on feed intake, liveweight gain (LWG), feed energy and nitrogen partitioning, and enteric methane (CH4) emissions. Six- to seven-month-old Red Maasai (n=12) and Dorper (n=12) lambs were randomly allocated to three treatments (n=8, four lambs per breed) in a 2×3 factorial cross-over study over two periods (P1 and P2) of 36 days each. The treatments consisted of three combinations of GIN infection and feeding level: Infected + ad libitum feeding (I-adlib), uninfected + ad libitum feeding (Un-adlib), and uninfected + restricted feeding (Un-restd), across the two breeds. Lambs in the I-adlib group were trickle-infected daily with 1,000 L3 stage larvae of H. contortus for four consecutive days (Days 1–4), whereas lambs in the other experimental treatments were kept GIN free. The feed intake was measured daily. Liveweight (LW), faecal egg counts (FEC), and packed cell volume (PCV) were measured on Day 1 and weekly thereafter. On Days 29–33 total faecal and urine outputs were determined in metabolic crates. The lambs were then housed in respiration chambers for three consecutive days (Days 34–36). There was a washout period of 21 days before P2 started. Uninfected lambs (Un-adlib and Un-restd) had undetectable FEC throughout the study. On Day 36, FEC did not differ between the breeds (P&amp;gt;0.05). Infected lambs (I-adlib) had lower PCV than uninfected (Un-adlib and Un-restd) lambs on day 36. Neither breed nor infection influenced feed and nutrient intake, but as expected, restricted-fed lambs had a lower intake (P&amp;lt;0.05). The LWG of Un-adlib lambs was significantly higher than that of I-adlib and Un-restd lambs (P&amp;lt;0.05), whereas there was no breed difference (P&amp;gt;0.05). Neither breed nor infection affected feed digestibility, nitrogen retention or energy metabolisability (P&amp;gt;0.05). However, feed restriction decreased feed intake, LWG and N retention, whereas feed digestibility and energy metabolisability were unaffected. Neither daily CH4 emissions nor yield (per unit of feed intake) were affected by experimental infection, but Un-restd lambs had lower CH4 emissions per day. Red Maasai lambs had consistently lower daily CH4 emissions and yields than Dorper (P&amp;lt;0.01). This study confirmed the relative resistance of indigenous sheep (Red Maasai) to H. contortus infection, but the increased CH4 emission and yield due to GIN observed in other studies was not confirmed. Further investigations are needed to test whether in environments with multiple stress factors, local or indigenous breeds or their crossbreeds with exotic breeds may be better equipped to sustain production and simultaneously have a reduced carbon footprint than purebred exotic breeds.

Comparison of Nonlinear Growth Models to Estimate Growth Curves in Kivircik Sheep under a Semi-Intensive Production System.

The Kivircik is an indigenous sheep breed from Turkey, and it has superior meat quality compared to other indigenous breeds. Therefore, farmers prioritize Kivircik lamb fattening instead of milk production. Here, we aimed to determine the best nonlinear growth model, i.e., Gompertz, Logistic, Von Bertalanffy, and Brody, to describe the growth curve of Kivircik lambs. The body weight data from birth until 150 days of age belonging to 612 lambs were used as the material of this study. The best fitting model was selected by considering the adjusted coefficient of determination (R2adj), residual mean square, and Akaike's (AIC) and Bayesian information criteria (BIC). Even though the Brody model had a better statistical fit, considering its biological interpretation, the Gompertz model was identified as an appropriate model for describing Kivircik lamb growth. Male lambs, twin lambs, and lambs born in winter had higher mature live weights (44.2 kg, 71.2 kg, and 38.5 kg, respectively) and rate of weight gain (2.1, 2.6, and 2.0, respectively). However, our subgroups revealed a similar rate of maturity (0.01). Growth models are important tools for deciding the optimal slaughter age and they provide valuable information on the management practices of both sexes, birth types, and birth seasons. These results can be applied to breeding programs for early selection, enabling intervention strategies when needed.

Phenotypic Characterization of Indigenous Sheep Breeds in Saudi Arabia

Saudi&amp;rsquo;s farm animal genetic resources have a particular role to play in managing the rural environment and assisting in maintaining wild biological diversity. Our indigenous livestock breeds are of great economic, social and cultural importance. The presence of livestock is a very positive feature for many who live in, work in or visit the countryside and livestock farming is frequently a core activity on which whole communities depend. The Kingdom has a rich and diverse population of livestock breeds sheep, goats, poultry, horses &amp;amp; Camel most of it are at risk. The conservation and sustainable use of genetic resources for food and agriculture is a widely supported international objective contributing to efforts to eliminate global poverty and achieve world food security.&#x0D; &#x0D; The data of the present study were collected form Noemi, Najdi and Hari breeds raised in Najd (96, 108, and 90 animals, respectively) Qassim region. Eight body measurements were studied, Wither heights (WH), Rum heights (RH), Body length (BL), Head length (HL), Heart girth (HG), Muzzle diameter (MD), Cannon circumference (CC) and Cannon length (CL). Noemi is taking the second size breed of the sheep breeds in Saudi Arabia. Hari is the smallest breed of sheep breeds in Saudi Arabia and it is the main breed in Hejaz and Asir regions which belong to the sheep with coarse hair and thick tail strain. The results of the present study on these breeds showed that Najdi breed has the biggest sizes in all body measurements 10.9% and 11.4% bigger than Noemi and Hari, Approximate respectively. By the other way in comparing Noemi&amp;rsquo;s breed with Hari breed, Noemi having the biggest sizes (10.5% Approximate) in all body measurements than Hari. Three categories of ages were presents in this study, eight, eighteen and forty-eight months. The first category eight months showed the smallest size in all body measurements by 11.2% in compare with eighteen months. No big differences were showed among eighteen and forty-eight months the different around 2% in favor of forty-eight category. &#x0D; &#x0D; In addition, the effect of sex was significant, male always have biggest body measurements in compare with female. The results showed that male have around 10.9% more in all studied measurements more than female. All the fixed effect (effect of: Age, Breed and Sex) are significant on all body measurements traits expect Cannon circumference (CC) trait. The correlations coefficients among all studied traits were moderate to high and highly significant. The highest correlation coefficient was found between RH and WH traits (0.872), and the lowest one was found between CC and HG traits (0.214).

Morphometric traits and stepwise regression of indigenous sheep in southwestern region, Ethiopia

This research was carried out to characterize differences in morphometric features and assess the effectiveness of various linear body measures in forecasting the live weight of local sheep grown in Bench Sheko zone, southwestern Ethiopia. Purposive followed by random sampling procedures were used, to choose the potential samples. Qualitative trait, body weight, and linear body measurements were taken from 660 sheep. Plain (69.8%) and patchy (16.7%) coat color patterns were predominant in both districts. The bulk of the sheep in the research locations had narrow tails, short hair, horned males, dark red coat colors, Cylindrical and turned up at the tip tail shape, straight head and back profile, and sloping rump profile. Live weight and linear body measurements are significantly influenced by age, sex, sex-age interaction, and location. The mean body weight, heart girth, wither height, body length, ear length, tail length, rump height, rump length, rump width, and scrotal circumference were, 28.4 ± 0.15 cm, 75.5 ± 0.18 cm, 64.0 ± 0.12 cm, 62.8 ± 0.14 cm, 11.1 ± 0.06 cm, 28.2 ± 0.20 cm, 64.8 ± 0.12 cm, 20.8 ± 0.05 cm, 16.6 ± 0.06 cm and 26.1 ± 0.16 cm respectively. Heart girth was the best correlated with the sheep of different age class in both the districts. The greatest predictor of body weight (BW) was heart girth (HG) along with other linear body measurements. Therefore, HG was found to be the most significant factor influencing the bulk of the changes in BW, indicating that it could be utilized as a valid estimator for the sheep breed investigated. Genetic improvement must be prioritized since indigenous sheep in the study area have a large body frame.

Unraveling candidate genes related to heat tolerance and immune response traits in some native sheep using whole genome sequencing data

BackgroundIn the sheep breeding industry, heat stress caused by the general increase in global temperature has become a significant issue, having both direct and indirect effects on animal health and productivity. The identification of effective pathways for responding to heat stress and immune responses, as well as the discovery of related genes, can improve the production and sustainability of genetic diversity in this area. In this study, we used nucleotide diversity (θπ) and FST statistical measurements to analyze the genomic data of the native Iranian sheep in order to find potential genes related to heat adaptation and immune response. We also compared the whole genome sequencing data of 29 indigenous Iranian sheep (the Afshari, Ghezel, Makuei, Moghani, Shal, Zel, Karakul, Grey-Shiraz, Baluchi, and Kermani breeds) with a number of other sheep breeds from Asia (n = 28), Europe (n = 28), and Africa (n = 25) to evaluate the genetic structure of the Iranian sheep population. The resultsThe results from the sheep population genetic analysis showed a clear separation between different populations that corresponds well with their geographic origins. Iranian sheep were further divided into a southern and a northern group, which coincided with the most prominent climatic division in Iran. Our search to identify potential genomic regions under selection showed several candidate genes involved in (1) response to heat stress (SIK2, FER, ATP1A1, CDK5RAP3, and TLR4), (2) immune response in hot and dry environments (CD109, CR2, EOMES, and MARCHF1), (3) response to drought stress and adaptation to desert areas (ZFP1, PLCB1, and PDGFD), and also (4) response to heat stress by controlling digestive metabolism (HTR4, TRHDE, and ALDH1A3). ConclusionsThe findings of this study may aid in our understanding of the molecular processes by which tiny ruminants adapt to hot, dry environments. In addition to the results of earlier studies, our findings also revealed a number of novel candidate genes related to heat adaptation. These genes will be valuable for future studies to choose livestock breeds that live in desert regions.

Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds.

Knowledge of linkage disequilibrium (LD), genetic structure and genetic diversity are some key parameters to study the breeding history of indigenous small ruminants. In this study, the OvineSNP50 Bead Chip array was used to estimate and compare LD, genetic diversity, effective population size (Ne) and genomic inbreeding in 186 individuals, from three Iranian indigenous sheep breeds consisting of Baluchi (n = 96), Lori-Bakhtiari (n = 47) and Zel (n = 47). The results of principal component analysis (PCA) revealed that all animals were allocated to the groups that they sampled and the admixture analysis revealed that the structure within the populations is best explained when separated into three groups (K = 3). The average r2 values estimated between adjacent single nucleotide polymorphisms (SNPs) at distances up to 10Kb, were 0.388±0.324, 0.353±0.311, and 0.333±0.309 for Baluchi, Lori-Bakhtiari and Zel, respectively. Estimation of genetic diversity and effective population size (Ne) showed that the Zel breed had the highest heterozygosity and Ne, whereas the lowest value was found in Baluchi breed. Estimation of genomic inbreeding using FROH (based on the long stretches of consecutive homozygous genotypes) showed the highest inbreeding coefficient in Baluchi and the lowest in Zel breed that could be due to higher pressure of artificial selection on Baluchi breed. The results of genomic inbreeding and Ne showed an increase in sharing haplotypes in Baluchi, leading to the enlargement of LD and the consequences of linkage disequilibrium and haplotype blocks confirmed this point. Also, the persistence of the LD phase between Zel and Lori-Bakhtiari was highest indicating that these two breeds would be combined in a multi-breed training population in genomic selection studies.

Genomic Diversity Analyses of Some Indigenous Montenegrin Sheep Populations

Montenegro has a great diversity of indigenous and locally developed sheep breeds, adapted to different regions and climates. However, the current trend of the steady decline in sheep populations means that some of them are threatened with extinction. The aim of this study was the investigation of the genetic diversity and population structure of five Montenegrin sheep populations, using the OvineSNP50K BeadChip. Data from the studied sheep were supplemented with publicly available genotypes of worldwide breeds to determine admixture contributions and genetic relationships. Higher genetic diversity and low inbreeding were observed in Pivska Pramenka and Sjenicka sheep, with Ho = 0.411, He = 0.423, and FROH&gt;2Mb = 0.056 and Ho = 0.421, He = 0.421, and FROH&gt;2Mb = 0.041, respectively. Zetska Zuja had much lower FIS (0.001) and high FROH inbreeding (0.090), indicating a small population size and genetic drift. An analysis of the genetic population structure showed that Montenegrin sheep populations are genetically distinct populations. This analysis revealed the presence of admixture in most sheep populations (high heterogeneity), while genetic purity was observed in Zetska Zuja. The obtained results will help in the conservation management of endangered Montenegrin sheep populations.

Genome-wide DNA methylation analysis reveals different methylation patterns in Chinese indigenous sheep with different type of tail.

The study was aimed to analyze the difference of genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which the typical breeds with different type tails, as to screen the differentially methylated genes (DMGs) that affect the type of tails. In this study, three Lanzhou Large-tailed sheep, three Altay sheep and three Tibetan sheep were detected by whole genome bisulfite sequencing (WGBS). The degree of genome-wide DNA methylation, differentially methylated regions (DMRs) and DMGs were analyzed. The candidate genes affecting the tail type of sheep were identified by GO and KEGG pathway enrichment analysis of DMGs. we identified 68,603 different methylated regions (DMCs) and 75 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in biological process, cellular component and molecular function, Some of the genes in these pathways are involved in fat metabolism: NFATC4, LPIN2, MGAT2 and MAT2B. Our results may help to further understand the epigenetic regulation mechanisms of deposition of fat in the tail of sheep and provide new basic data for the study of local sheep.

Genetic diversity and selection of Tibetan sheep breeds revealed by whole-genome resequencing.

This study aimed to elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and the discovery of important genes encoding valuable traits. We used whole-genome resequencing to explore the genetic relationships, phylogenetic tree, and population genetic structure analysis. In addition, we identified 28 representative Tibetan sheep single-nucleotide polymorphisms (SNPs) and genomic selective sweep regions with different traits in Tibetan sheep by fixation index (Fst) and the nucleotide diversity (θπ) ratio. The genetic relationships analysis showed that each breed partitioned into its own clades and had close genetic relationships. We also identified many potential breed-specific selective sweep regions, including genes associated with hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9, TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool traits (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), and horn phenotypes (RXFP2). In particular, a horn-related gene, RXFP2, showed the four most significantly associated SNP loci (g. 29481646 A>G, g. 29469024 T>C, g. 29462010 C>T, g. 29461968 C>T) and haplotypes. This finding demonstrates the potential for genetic markers in future molecular breeding programs to improve selection for horn phenotypes. The results will facilitate the understanding of the genetic basis of production and adaptive unique traits in Chinese indigenous Tibetan sheep taxa and offer a reference for the molecular breeding of Tibetan sheep.

Single-Nucleotide Polymorphisms Identified within Exon 2 of Fertility-Associated Bone Morphogenetic Protein (BMP15) Gene in Three Romanian Sheep Breeds

The improvement of the reproductive traits of animals is of great interest for livestock production. Due to its positive impact on the sheep industry’s profitability, prolificacy is one of the most economically significant biological traits, showing variation between and within breeds of domestic sheep (Ovis aries). Different mutations in BMPR-1B, BMP15 and GDF9 genes coding for the transforming growth factor-β (TGFβ) superfamily have been shown to influence the ovulation rate and litter size. Numerous single-nucleotide polymorphisms (SNPs) in the bone morphogenetic protein 15 (BMP15) gene have been linked to ewe fecundity. Using targeted PCR amplification and Sanger sequencing, we were able to identify heterozygous SNPs in exon 2 of BMP15 in three sheep breeds reared in Romania: Tsigai, Cluj Merino and Tsurcana. The sequence analysis revealed three previously documented mutations, namely the missense mutation c.755T&gt;C (L252P), which is predicted to change the tertiary structure of the BMP15 protein, and two silent mutations, c.747T&gt;C (P249P) and c.1047G&gt;A (V349V). In addition, we also identified one novel silent mutation, c.825G&gt;A (S275S). Based on our findings and publicly available data, we indicate four putative mutational hotspots within exon 2 of BMP15 that could be considered for improving the indigenous sheep breeds through targeted gene editing and SNP genotyping strategies.

Insertion/Deletion (InDel) Variants within the Sheep Fat-Deposition-Related PDGFD Gene Strongly Affect Morphological Traits.

Platelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations in PDGFD and body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 of PDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation of PDGFD was found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates that PDGFD InDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.

Genetic diversity and within-breed variation in three indigenous Ethiopian sheep based on whole-genome analysis

The objective of this work was to study genetic diversity by comparing whole genome sequence data of Rutana, Gumuz and Washera sheep found in Amhara and Benishanguel gumuz regional states of Ethiopia. We employed variant calling format tools version 0.1.15 to calculate some genetic diversity indices such as observed heterozygosity, expected heterozygosity, inbreeding coefficient, and nucleotide diversity. The results revealed that, observed heterozygosity ranged from 0.33 in Gumuz to 0.34 in Rutana and Washera sheep. Expected heterozygosity ranged from 0.37 in Rutana to 0.38 in Gumuz and Washera sheep. Expected heterozygosity was found to be higher than observed heterozygosity. Higher inbreeding coefficient (0.12) was recorded for Gumuz sheep compared to 0.09 of Rutana and Washera sheep. Mean nucleotide diversity values were 0.0029, 0.0030 and 0.0028 for Gumuz, Rutana and Washera sheep, respectively. Higher values of nucleotide diversity were recorded. Population structure analysis using principal component analysis revealed no clear separation between Gumuz, Rutana and Washera sheep populations with possibility of gene flow attributed to geographical location proximity. The smaller population size, closed breeding system, genetic drift and uncontrolled (non-random) mating might lead to higher rate of inbreeding in Gumuz, Rutana and Washera sheep, requiring timely intervention. This intervention helps to prevent inbreeding depression and extinction of these valuable breeds of sheep, which helps in sustaining the livelihood of sheep keepers in lowlands and highlands. Nevertheless, the whole-genome analysis revealed high within-breed variation. Uncovered areas of studies like mapping quantitative trait loci, identifying genes underpinning productivity traits such as carcass quantity and meat quality could be carried out on diversified sheep resources identified by the current study. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. Designing conservation-based within-breed sheep selective breeding programs are recommended considering economically important traits into account.