Differentiation among Spanish sheep breeds using microsatellites

How have sheep breeds differentiated from each other in Morocco? Genetic structure and geographical distribution patterns

Background

Based on the relatively homogeneous origin of the sheep breeds in Morocco that originate mainly from Iberia, it is highly relevant to address the question of how these very diverse sheep populations differentiated from each other. The Mountains of the High Atlas and Middle Atlas are expected to constitute North–South and West–East geographical barriers, respectively, which could have shaped the history of the differentiation of sheep breeds. The aim of this study was to test this hypothesis by considering the genetic structure and the spatial distribution of five major breeds (Sardi, Timahdite, Beni Guil, Boujaad and D’man) and one minor breed (Blanche de Montagne), by analysing the mtDNA control region, using 30 individuals per breed.

Results

Phylogenetic and network analyses did not indicate any clear separation among the studied breeds and discriminant component principal analysis showed some overlap between them, which indicates a common genetic background. The calculated pairwise F_ST values and Nei’s genetic distances revealed that most breeds showed a moderate genetic differentiation. The lowest and highest degrees of differentiation were retrieved in the Beni Guil and Boujaad breeds, respectively. Analysis of molecular variance (AMOVA) indicated that more than 95% of the genetic diversity occurs within individuals, while between- and within-population variabilities represent only 1.332% and 2.881%, respectively. Isolation-by-distance, spatial Principal Component Analysis (sPCA), and spatial AMOVA analyses evidenced clear examples of geographical structuration among the breeds, both between and within breeds. However, several enigmatic relationships remain, which suggest the occurrence of complex events leading to breed differentiation.

Conclusions

The approaches used here resulted in a convergent view on the hypothetic events that could have led to the progressive differentiation between the Moroccan breeds. The major split seems to be linked to the West–East barrier of the Middle Atlas, whereas the influence of the High Atlas is less obvious and incompletely resolved. The study of additional breeds that have settled near the High Atlas should clarify the relationships between the breeds of the West part of the country, in spite of their small population size.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00679-2.

Genetic basis of thermotolerance in 2 local dairy sheep populations in the Iberian Peninsula

Sheep milk production in the Northern Mediterranean countries heavily relies on local breeds subject to selection schemes to improve milk production. Climate change may shift the range of thermal loads on the animals and challenge their adaptation to the new thermal gradient. The objective of this study was to characterize the genetic component of thermal tolerance of 2 local breeds from the Iberian Peninsula, Latxa and Manchega, belonging to different genetic types that have evolved under different climatic environments (Oceanic for Latxa and Continentalized Mediterranean for Manchega). A total of 79,243 and 2,388,853 test day monthly records of milk, fat and protein yields from 12,882 and 277,904 ewes of Latxa and Manchega breeds, respectively, along a 12-yr period, were matched with the value of the average temperature-humidity index (THI) on the day of milk recording of the closest weather station to the flocks. These data were used to fit individual reaction norms (Legendre polynomials) describing changes in yields along the THI gradient. Genetic values for thermal tolerance were obtained from the slopes of those reaction norms under cold or heat stress and variances and covariances between yield and thermal tolerance were derived from the (co)variance matrices of the polynomial random regression coefficients. Results showed differing patterns in the 2 breeds. The Latxa breed showed clearer signs of genotype by environment interaction than did Manchega. Estimated correlations between yields under extremes of cold and heat were always above 0.8 for Manchega and around 0.4 for Latxa for all traits. Estimates of correlations between comfort and thermal stress were again over 0.8 for Manchega and lower for the higher (hot end) values (down to 0.6) than for the lower (cold end) values (down to 0.84) of the THI gradient for Latxa, indicating greater thermal stress expected from high than from low temperatures in this breed. Substantial variability in thermal tolerance under the more extreme THI values was found in both breeds. Estimated genetic correlations between yield and thermal tolerance were close to 0 and 0.2 for Latxa and Manchega in the cold and down to -0.6 and -0.3 in the heat end, although small variation was observed for fat in Latxa. Estimated realized trends from the average estimated breeding value, by year of birth, showed a positive response for yields in both breeds [around 0.1 standard deviation (SD) unit], but a detrimental correlation for thermal tolerance (down to -0.03 SD units for heat tolerance in Latxa). These results can be used to design optimal selection strategies for sustainable improvement of productivity under a rising-temperature scenario associated with climate change.

Genetic diversity and phylogenetic relationship of nine sheep populations based on microsatellite markers

The objective of this study was to assess the genetic diversity and phylogenetic relationship of nine sheep populations, including two famous high prolific populations and seven popular mutton populations raised in China. Overall, these sheep populations in this study exhibited a rich genetic diversity. Both the expected heterozygosity and Nei's unbiased gene diversity ranged from 0.64 to 0.75, with the lowest value found in Dorset sheep (DST) and the highest in Hu sheep (HUS) and Ba Han sheep (BAS). The polymorphic information content (PIC) varied between 0.59 in DST and 0.71 in HUS and BAS. Specifically, for individual breeds, the small-tail Han sheep (STH) and the four introduced populations did not display the expected diversity; therefore more attention should be paid to the maintenance of diversity during management of these populations. The results of un-weighted pair-group method (UPGMA) phylogenetic tree and structure analysis indicated that the nine investigated populations can be divided into two groups. Suffolk (SUF) and DST were clustered in one group, and the other group can be further divided into three clusters: German Mutton Merino (GMM)–BAS–Bamei Mutton sheep (BAM), HUS–STH and Du Han (DOS)–Dorper (DOP). This clustering result is consistent with sheep breeding history. TreeMix analysis also hinted at the possible gene flow from GMM to SUF. Together, an in-depth view of genetic diversity and genetic relationship will have important implications for breed-specific management.

Genetic diversity and population structure of local and exotic sheep breeds in Jordan using microsatellites markers

Aim:

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.

Materials and 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.

Conclusion:

Results of this study offer insight toward the genetic conservation of the studied breeds and a base on which breeding plans can be made.

Short tandem repeat (STR) based genetic diversity and relationship of indigenous Niger cattle

Abstract. The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR) marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 %) was consistently higher than Zebu Arabe (59.3 to 70.4 %) and Kuri (80.0 to 83.3 %) cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu–taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites

Nuclear genetic diversity and differentiation of 341 sheep belonging to 12 sheep breeds from Croatia and Bosnia and Herzegovina were examined. The aim of the study was to provide the understanding of the genetic structure and variability of the analysed pramenka sheep populations, and to give indications for conservation strategies based on the population diversity and structure information. The genetic variation of the sheep populations, examined at the nuclear level using 27 microsatellite loci, revealed considerable levels of genetic diversity, similar to the diversity found in other European indigenous low-production sheep breeds. Population-specific alleles were detected at most loci and in breeds analysed. The observed heterozygosity ranged from 0.643 (in Lika pramenka) to 0.743 (in Vlasic pramenka), and the expected heterozygosity ranged from 0.646 (in Lika pramenka) to 0.756 (in Dalmatian pramenka). Significant inbreeding coefficients were found for half of the populations studied and ranged from 0.040 (Pag island sheep) to 0.091 (Kupres pramenka). Moderate genetic differentiation was found between the studied sheep populations. The total genetic variability observed between different populations was 5.29%, whereas 94.71% of the variation was found within populations. Cres island sheep, Lika pramenka and Istrian sheep were identified as the most distinct populations, which was confirmed by the factorial analysis of correspondence and supported through a bootstrapping adjustment to correct for the difference in the sample sizes. The population structure analysis distinguished 12 clusters for the 12 sheep breeds analysed. However, the cluster differentiation was low for Dalmatian, Vlasic, Stolac and Krk pramenka. This systematic study identified Lika pramenka and Rab island sheep as those with the lowest diversity, whereas Istrian sheep and Pag island sheep had the highest. Conservation actions are proposed for Istrian, Rab and Cres island sheep, Lika and Kupres pramenka because of high estimated coefficients of inbreeding.

Locus minimization in breed prediction using artificial neural network approach

Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.

Validation of a microsatellite panel for parentage testing of locally adapted and commercial goats in Brazil

Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.

Development of a model webserver for breed identification using microsatellite DNA marker

Background

Identification of true to breed type animal for conservation purpose is imperative. Breed dilution is one of the major problems in sustainability except cases of commercial crossbreeding under controlled condition. Breed descriptor has been developed to identify breed but such descriptors cover only “pure breed” or true to the breed type animals excluding undefined or admixture population. Moreover, in case of semen, ova, embryo and breed product, the breed cannot be identified due to lack of visible phenotypic descriptors. Advent of molecular markers like microsatellite and SNP have revolutionized breed identification from even small biological tissue or germplasm. Microsatellite DNA marker based breed assignments has been reported in various domestic animals. Such methods have limitations viz. non availability of allele data in public domain, thus each time all reference breed has to be genotyped which is neither logical nor economical. Even if such data is available but computational methods needs expertise of data analysis and interpretation.

Results

We found Bayesian Networks as best classifier with highest accuracy of 98.7% using 51850 reference allele data generated by 25 microsatellite loci on 22 goat breed population of India. The F_ST values in the study were seen to be low ranging from 0.051 to 0.297 and overall genetic differentiation of 13.8%, suggesting more number of loci needed for higher accuracy. We report here world’s first model webserver for breed identification using microsatellite DNA markers freely accessible at http://cabin.iasri.res.in/gomi/.

Conclusion

Higher number of loci is required due to less differentiable population and large number of breeds taken in this study. This server will reduce the cost with computational ease. This methodology can be a model for various other domestic animal species as a valuable tool for conservation and breed improvement programmes.

Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci

Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F(ST)). The exact test for Hardy-Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds.

Evaluation of the genetic diversity and population structure of Chinese indigenous horse breeds using 27 microsatellite markers

We determined the genetic diversity and evolutionary relationships among 26 Chinese indigenous horse breeds and two introduced horse breeds by genotyping these animals for 27 microsatellite loci. The 26 Chinese horse breeds come from 12 different provinces. Two introduced horse breeds were the Mongolia B Horse from Mongolia and the Thoroughbred Horse from the UK. A total of 330 alleles were detected, and the expected heterozygosity ranged from 0.719 (Elenchuns) to 0.780 (Dali). The mean number of alleles among the horse breeds ranged from 6.74 (Hequ) to 8.81 (Debao). Although there were abundant genetic variations found, the genetic differentiation was low between the Chinese horses, which displayed only 2.4% of the total genetic variance among the different breeds. However, genetic differentiation (pairwise FST) among Chinese horses, although moderate, was still apparent and varied from 0.001 for the Guizou-Luoping pair to 0.064 for the Jingjiang-Elenchuns pair. The genetic differentiation patterns and genetic relationships among Chinese horse breeds were also consistent with their geographical distribution. The Thoroughbred and Mongolia B breeds could be discerned as two distinct breeds, but the Mongolia B horse in particular suffered genetic admixture with Chinese horses. The Chinese breeds could be divided into five major groups, i.e. the south or along the Yangtze river group (Bose, Debao, Wenshan, Lichuan, Jianchang, Guizhou, Luoping, Jinjiang and Dali), the Qinghai-Tibet Plateau group (Chaidamu, Hequ, Datong, Yushu, Tibet Grassland and Tibet Valley), the Northeast of China group (Elenchuns, Jilin and Heihe), the Northwest of China group (Kazakh, Yili and Yanqi) and the Inner Mongolia group (Mongolia A, Sanhe, Xinihe,Wuzhumuqin and Sengeng). This grouping pattern was further supported by principal component analysis and structure analysis.

Microsatellite analysis to estimate genetic relationships among five bulgarian sheep breeds

Herein, genetic relationships among five breeds of Bulgarian sheep were estimated using microsatellite markers. The total number of alleles identified was 226 at the 16 loci examined. D_A distance values were used for phylogenetic tree construction with the UPGMA algorithm. The two Tsigai and two Maritza populations were found to be geneticallvery closely related to each other y (0.198, and 0.258 respectively). The Pleven Black Head population was distinct from the other four. These results could be useful for preserving genes in these breeds, thereby ensuring their preservation in Bulgaria.

Mitochondrial Sequence Reveals High Levels of Gene Flow Between Breeds of Domestic Sheep from Asia and Europe

Sequence variation present within the mitochondrial genome was used to investigate genetic diversity within sheep breeds from Asia and Europe. Comparison of 2027 bp of sequence from 121 animals revealed 44 phylogenetically informative nucleotide positions and a single insertion/deletion. A total of 57 haplotypes were observed which formed two distinct clades. Type A haplotypes were found in breeds from Asia (India, Indonesia, Mongolia, and Tibet), while type B haplotypes were observed at the highest frequency in breeds sourced from Europe (nine breeds from Austria, Aland, Finland, Spain, and northwestern Russia). The distribution of haplotypes indicates sheep appear to have the weakest population structure and the highest rate of intercontinental dispersal of any domestic animal reported to date. Only 2.7% of the sequence variation observed was partitioned between continents, which is lower than both goat (approximately 10%) and cattle (approximately 50%). Diagnostic restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) tests which distinguish type A and B haplotypes were used to test an additional 223 animals from 17 breeds of European and Asian origin. A mixture of the two lineages was found in every breed except Suffolk and the Indian Garole, indicating introgression has played a major part during breed development and subsequent selection.

Testing the usefulness of the molecular coancestry information to assess genetic relationships in livestock using a set of Spanish sheep breeds1

Recent studies have proposed the use of molecular coancestry coefficients as a measure of genetic variability and as a useful tool for conservation purposes. Using simulated data, molecular coancestry has been shown to become constant very quickly after separation of populations, leading to population diversity remaining constant. However, the use of molecular coancestry information to study the genetic relationships between breeds has not yet been widely explored. Here we analyze the polymorphism of 14 microsatellites in 222 unrelated individuals belonging to seven native Spanish breeds to ascertain the usefulness of molecular coancestry-based methodologies in providing information on their genetic relationships. Average kinship distance (D(k)) and average molecular coancestry coefficients (f(ij)) were compared with well-known genetic distances, such as between-breed Reynolds' distance (D(R)), Nei's standard distance (D(s)), and shared allele distance (D(AS)). Kinship distance and f(ij) have moderate to low correlations with the other genetic distances, showing that they provide different information: both D(k) and f(ij) account for the allele frequencies in the founder population, whereas D(R), D(s), and D(AS) characterize the short-term evolution of the populations. Furthermore, D(k) and f(ij) were only moderately correlated (-0.500). The present study used field data to confirm previous research pointing out the ability of molecular coancestry coefficients to assess genetic differentiation of an ancestral origin. In this respect, molecular coancestry-based parameters may be used with classical genetic parameters to obtain information on population dynamics in livestock breeds. This study additionally presents reliable evidence on the history of these sheep breeds.

Genetic relationships and admixture among sheep breeds from Northern Spain assessed using microsatellites

Although many research papers have studied diversity and differentiation within livestock species, genetic relationships among neighboring populations remain poorly understood. Here we apply recent methodologies to analyze the polymorphism of 14 microsatellites in 238 unrelated individuals belonging to six sheep breeds from Northern Spain to ascertain their historical relationships and the relative genetic contributions existing between populations. Individual genotypes were analyzed to assess the existence of an underlying genetic structure. Long-term and recent migration rates were estimated to identify patterns of relative genetic contribution among breeds. The complete data set showed a strong population structure derived from both different ancestral origins and some geographical patterns of recent gene flow. Two of the analyzed breeds (Black-faced Latxa and Churra) had a marked genetic background, supporting the hypothesis that, regardless of their phenotypical similarities, they have different ancestral origins. Some of the more presumably related breeds had negative long-term admixture coefficients, showing that they diverged only recently. In addition, we show how methodologies for estimation of long-term gene flow and recent patterns of migration are complementary, providing information about migration rates on different timescales.

Breed relationships and definition in British cattle: a genetic analysis

The genetic diversity of eight British cattle breeds was quantified in this study. In all, 30 microsatellites from the FAO panel of markers were used to characterise the DNA samples from nearly 400 individuals. A variety of methods were applied to analyse the data in order to look at diversity within and between breeds. The relationships between breeds were not highly resolved and breed clusters were not associated with geographical distribution. Analyses also defined the cohesiveness or definition of the various breeds, with Highland, Guernsey and Jersey as the best defined and most distinctive of the breeds.