Limits...
Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds.

Mastrangelo S, Di Gerlando R, Tolone M, Tortorici L, Sardina MT, Portolano B, International Sheep Genomics Consorti - BMC Genet. (2014)

Bottom Line: Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed.Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population.The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy. salvatore.mastrangelo@unipa.it.

ABSTRACT

Background: The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array.

Results: Average r (2) between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r (2) estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r (2) was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed.

Conclusions: This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

Show MeSH

Related in: MedlinePlus

Relationship between breeds based on Neighbor network obtained using pair-wise estimates ofFST..
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4197223&req=5

Fig5: Relationship between breeds based on Neighbor network obtained using pair-wise estimates ofFST..

Mentions: Results from within population substructure through Admixture analysis, considering a range of 2 through 20 potential clusters (K), pointed out that the best fitting number of populations present in the total sample was K = 12. A graphic representation of the estimated membership coefficients to the 12 clusters is shown in Figure 4, where model-based clustering partitioned the genome of each sample into a predefined number of components [25]. The first breeds to be differentiated from the others were Lacaune and Valle del Belice (K = 2). Other breed-specific clusters were Chios and Merinos (K = 6); at K = 8 some genomic components appeared to be shared by several breeds, as for example between Comisana and Pinzirita, whereas at K = 10, each breed tends to have its own distinct cluster but with some differences; in fact, Sicilian breeds showed less distinct clusters than other breeds as Lacaune, Chios and Sarda black. For some breeds, as the two from Sardinia island, the admixture analysis revealed a shared ancestry; in fact these breeds clustered together at high K value (K = 10). These results reflect geographic proximity and confirmed the findings based on the PCA, where, for example, Chios and Lacaune formed separated and differentiated clusters. For the Sicilian breeds, results were in agreement with a previous study conducted on the genetic structure and relationship using microsatellite markers [22] that showed low genetic differentiation and high level of admixture among Valle del Belice, Comisana, and Pinzirita breeds. Moreover, at K = 10 the results evidenced again that Comisana is split in two mixed groups. The degree of genetic differentiation between pairs of breeds was showed in Table 2. Considering pairwise FST among all populations, Chios was the most divergent breed. The highest values were observed between Chios and both Sarda breeds (FST = 0.139 and 0.120 for Sarda black and Sarda white, respectively), while the lowest one was observed between Comisana and Pinzirita breeds (FST = 0.025). These results may be explained considering the geographic origin of the breeds: Chios and the two Sarda breeds belonging to different countries, whereas Comisana and Pinzirita were two breeds reared in the same island. The FST value between pairs of breeds was also used to reconstruct the NeighborNet graph (Figure 5), showing some clear clusters and relationships between breeds that originated from the same regions: Sicilian, Sardinian, and European breeds. The shortest branch was observed for Pinzirita breed, while the longest one was found for Chios breed that was the most differentiated and isolated population among the analyzed breeds. Considering only the Sicilian breeds, Valle del Belice showed the longest branch, while Pinzirita the shortest one, according to the results of genetic diversity for these breeds (Table 3). In fact, Kijas et al. [26] in a study on genome-wide analysis of the world’s sheep breeds showed short branches for breeds with high heterozygosity, while long branches for breeds with low heterozygosity. The topology of the NeighborNet constructed with FST distances between breeds perfectly coincides with PCA (Figure 2). NeighborNet graph was also depicted considering the substructure present in Comisana breed (Additional file 5: Figure S2). The figure showed that the two sub-populations originated from the same branch and displayed a very close relationship, which was expected considering that belonging to the same breed. The reticulations towards the extremity of the graphs indicated increasing genetic relatedness between breeds. In fact, NeighborNet provide a robust framework for inferring and investigating phylogenetic networks.Figure 4


Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds.

Mastrangelo S, Di Gerlando R, Tolone M, Tortorici L, Sardina MT, Portolano B, International Sheep Genomics Consorti - BMC Genet. (2014)

Relationship between breeds based on Neighbor network obtained using pair-wise estimates ofFST..
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4197223&req=5

Fig5: Relationship between breeds based on Neighbor network obtained using pair-wise estimates ofFST..
Mentions: Results from within population substructure through Admixture analysis, considering a range of 2 through 20 potential clusters (K), pointed out that the best fitting number of populations present in the total sample was K = 12. A graphic representation of the estimated membership coefficients to the 12 clusters is shown in Figure 4, where model-based clustering partitioned the genome of each sample into a predefined number of components [25]. The first breeds to be differentiated from the others were Lacaune and Valle del Belice (K = 2). Other breed-specific clusters were Chios and Merinos (K = 6); at K = 8 some genomic components appeared to be shared by several breeds, as for example between Comisana and Pinzirita, whereas at K = 10, each breed tends to have its own distinct cluster but with some differences; in fact, Sicilian breeds showed less distinct clusters than other breeds as Lacaune, Chios and Sarda black. For some breeds, as the two from Sardinia island, the admixture analysis revealed a shared ancestry; in fact these breeds clustered together at high K value (K = 10). These results reflect geographic proximity and confirmed the findings based on the PCA, where, for example, Chios and Lacaune formed separated and differentiated clusters. For the Sicilian breeds, results were in agreement with a previous study conducted on the genetic structure and relationship using microsatellite markers [22] that showed low genetic differentiation and high level of admixture among Valle del Belice, Comisana, and Pinzirita breeds. Moreover, at K = 10 the results evidenced again that Comisana is split in two mixed groups. The degree of genetic differentiation between pairs of breeds was showed in Table 2. Considering pairwise FST among all populations, Chios was the most divergent breed. The highest values were observed between Chios and both Sarda breeds (FST = 0.139 and 0.120 for Sarda black and Sarda white, respectively), while the lowest one was observed between Comisana and Pinzirita breeds (FST = 0.025). These results may be explained considering the geographic origin of the breeds: Chios and the two Sarda breeds belonging to different countries, whereas Comisana and Pinzirita were two breeds reared in the same island. The FST value between pairs of breeds was also used to reconstruct the NeighborNet graph (Figure 5), showing some clear clusters and relationships between breeds that originated from the same regions: Sicilian, Sardinian, and European breeds. The shortest branch was observed for Pinzirita breed, while the longest one was found for Chios breed that was the most differentiated and isolated population among the analyzed breeds. Considering only the Sicilian breeds, Valle del Belice showed the longest branch, while Pinzirita the shortest one, according to the results of genetic diversity for these breeds (Table 3). In fact, Kijas et al. [26] in a study on genome-wide analysis of the world’s sheep breeds showed short branches for breeds with high heterozygosity, while long branches for breeds with low heterozygosity. The topology of the NeighborNet constructed with FST distances between breeds perfectly coincides with PCA (Figure 2). NeighborNet graph was also depicted considering the substructure present in Comisana breed (Additional file 5: Figure S2). The figure showed that the two sub-populations originated from the same branch and displayed a very close relationship, which was expected considering that belonging to the same breed. The reticulations towards the extremity of the graphs indicated increasing genetic relatedness between breeds. In fact, NeighborNet provide a robust framework for inferring and investigating phylogenetic networks.Figure 4

Bottom Line: Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed.Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population.The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy. salvatore.mastrangelo@unipa.it.

ABSTRACT

Background: The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array.

Results: Average r (2) between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r (2) estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r (2) was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed.

Conclusions: This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

Show MeSH
Related in: MedlinePlus