Y. Bayón

Evidence of three maternal lineages in near eastern sheep supporting multiple domestication events

The variability of mtDNA was analysed in local sheep breeds reared throughout Turkey, for which a fragment of the D-loop region and the complete cytochrome b were sequenced. Phylogenetic analyses performed independently for the D-loop and the Cyt b gene revealed three clearly separated clusters indicating three major maternal lineages, two of which had been previously described as types B and A. The new type, C, was present in all the breeds analysed and showed considerable mtDNA variability. Divergence time was obtained on the basis of Cyt b gene and was estimated to be around 160 000–170 000 years ago for lineages B and A, whereas the divergence of lineage C proved to have occurred earlier (between 450 000 and 750 000 years ago). These times greatly predate domestication and suggest that the origin of modern sheep breeds was more complex than previously thought and that at least three independent sheep domestication events occurred. Our results, together with archaeological information and the current wild sheep populations in the Near East region support the high importance of this area in the sheep domestication process. Finally, the evidence of a third maternal lineage has important implications regarding the history of modern sheep.

Differentiation among Spanish sheep breeds using microsatellites

Genetic variability at 18 microsatellites was analysed on the basis of individual genotypes in five Spanish breeds of sheep – Churra, Latxa, Castellana, Rasa-Aragonesa and Merino -, with Awassi also being studied as a reference breed. The degree of population subdivision calculated between Spanish breeds from FST diversity indices was around 7% of total variability. A high degree of reliability was obtained for individual-breed assignment from the 18 loci by using different approaches among which the Bayesian method provided to be the most efficient, with an accuracy for nine microsatellites of over 99%. Analysis of the Bayesian assignment criterion illustrated the divergence between any one breed and the others, which was highest for Awassi sheep, while no great differences were evident among the Spanish breeds. Relationships between individuals were analysed from the proportion of shared alleles. The resulting dendrogram showed a remarkable breed structure, with the highest level of clustering among members of the Spanish breeds in Latxa and the lowest in Merino sheep, the latter breed exhibiting a peculiar pattern of clustering, with animals grouped into several closely set nodes. Analysis of individual genotypes provided valuable information for understanding intra- and inter-population genetic differences and allowed for a discussion with previously reported results using populations as taxonomic units.

Mitochondrial diversity and the origin of Iberian sheep.

Mitochondrial DNA diversity was analysed in 19 Iberian and six foreign sheep breeds. Three mtDNA lineages (B, A and C) were found in the Iberian sheep, with type B clearly predominating over the others. The results were analysed for each of the morphologically determined breed groups in Iberian sheep: Merino, Entrefino, Churro and Iberian trunks. MtDNA lineage C was found only in the Iberian trunk composed of Montesina and Ojalada. These two populations had high mtDNA variability, and in the Iberian sheep only Merino Branco had more variation. The other three Merino types studied showed moderate variability, including the most authentic Merino, the Spanish Merino. These three Merinos clustered closely in a multidimensional scaling representation of distances, while the fourth breed (Merino Branco) showed a clear separation. As for the other two trunks, breeds from the Churro group showed greater maternal uniformity while results for populations included in the so-called Entrefino trunk seemed to have a more heterogeneous maternal origin. The results obtained are discussed with available data from nuclear markers and with morphological classifications, and all this information is analysed in relation to the origin of the different Iberian sheep breeds.

Genetic variation at microsatellite loci in Spanish sheep.

Genetic variation at 18 microsatellite loci was analysed in six indigenous Spanish sheep: Churra; Latxa; Manchega; Rasa-Aragonesa; Castellana and Merino. Merinos had frequently the highest number of alleles per locus, whereas Latxas showed the lowest one at many loci. Markers ordered decreasingly according to the number of variants differentiated in the whole population were: MAF70; TGLA13; CSSM66; BM143, BM6444; MAF36; MAF64; CSSM6; TGLA53; OarFCB11; MAF33; BM4621; MAF48; MAF65; BM1258; ILSTS002; ADCYC and OarCP34. Parameters of variability such as effective number of alleles and gene diversities corroborated the high level of variation frequently displayed by microsatellite markers. Comparison of allele distributions among populations and loci did not reveal consistent shapes. Distributions were centralised in some cases, whereas in others some kind of skewness was evident. Breed-specific alleles were detected at most loci, being frequent in Merinos and rare in Churras.

GWA analysis for milk production traits in dairy sheep and genetic support for a QTN influencing milk protein percentage in the LALBA gene.

In this study, we used the Illumina OvineSNP50 BeadChip to conduct a genome-wide association (GWA) analysis for milk production traits in dairy sheep by analyzing a commercial population of Spanish Churra sheep. The studied population consisted of a total of 1,681 Churra ewes belonging to 16 half-sib families with available records for milk yield (MY), milk protein and fat yields (PY and FY) and milk protein and fat contents (PP and FP). The most significant association identified reached experiment-wise significance for PP and FP and was located on chromosome 3 (OAR3). These results confirm the population-level segregation of a previously reported QTL affecting PP and suggest that this QTL has a significant pleiotropic effect on FP. Further associations were detected at the chromosome-wise significance level on 14 other chromosomal regions. The marker on OAR3 showing the highest significant association was located at the third intron of the alpha-lactalbumin (LALBA) gene, which is a functional and positional candidate underlying this association. Sequencing this gene in the 16 Churra rams of the studied resource population identified additional polymorphisms. One out of the 31 polymorphisms identified was located within the coding gene sequence (LALBA_g.242T>C) and was predicted to cause an amino acid change in the protein (Val27Ala). Different approaches, including GWA analysis, a combined linkage and linkage disequilibrium study and a concordance test with the QTL segregating status of the sires, were utilized to assess the role of this mutation as a putative QTN for the genetic effects detected on OAR3. Our results strongly support the polymorphism LALBA_g.242T>C as the most likely causal mutation of the studied OAR3 QTL affecting PP and FP, although we cannot rule out the possibility that this SNP is in perfect linkage disequilibrium with the true causal polymorphism.

Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep

BackgroundFor ruminants reared on grazing systems, gastrointestinal nematode (GIN) parasite infections represent the class of diseases with the greatest impact on animal health and productivity. Among the many possible strategies for controlling GIN infection, the enhancement of host resistance through the selection of resistant animals has been suggested by many authors. Because of the difficulty of routinely collecting phenotypic indicators of parasite resistance, information derived from molecular markers may be used to improve the efficiency of classical genetic breeding.MethodsA total of 181 microsatellite markers evenly distributed along the 26 sheep autosomes were used in a genome scan analysis performed in a commercial population of Spanish Churra sheep to detect chromosomal regions associated with parasite resistance. Following a daughter design, we analysed 322 ewes distributed in eight half-sib families. The phenotypes studied included two faecal egg counts (LFEC0 and LFEC1), anti-Teladorsagia circumcincta LIV IgA levels (IgA) and serum pepsinogen levels (Peps).ResultsThe regression analysis revealed one QTL at the 5% genome-wise significance level on chromosome 6 for LFEC1 within the marker interval BM4621-CSN3. This QTL was found to be segregating in three out of the eight families analysed. Four other QTL were identified at the 5% chromosome-wise level on chromosomes 1, 10 and 14. Three of these QTL influenced faecal egg count, and the other one had an effect on IgA levels.ConclusionThis study has successfully identified segregating QTL for parasite resistance traits in a commercial population. For some of the QTL detected, we have identified interesting coincidences with QTL previously reported in sheep, although most of those studies have been focused on young animals. Some of these coincidences might indicate that some common underlying loci affect parasite resistance traits in different sheep breeds. The identification of new QTL may suggest the existence of complex host-parasite relationships that have unique features depending on the host-parasite combination, perhaps due to the different mechanisms underlying resistance in adult sheep (hypersensitivity reactions) and lambs (immunity). The most significant QTL identified on chromosome 6 for LFEC1 may be the target for future fine-mapping research efforts.

Quantitative trait loci underlying milk production traits in sheep

Improvement of milk production traits in dairy sheep is required to increase the competitiveness of the industry and to maintain the production of high quality cheese in regions of Mediterranean countries with less favourable conditions. Additional improvement over classical selection could be reached if genes with significant effects on the relevant traits were specifically targeted by selection. However, so far, few studies have been undertaken to detect quantitative trait loci (QTL) in dairy sheep. In this study, we present a complete genome scan performed in a commercial population of Spanish Churra sheep to identify chromosomal regions associated with phenotypic variation observed in milk production traits. Eleven half-sib families, including a total of 1213 ewes, were analysed following a daughter design. Genome-wise multi-marker regression analysis revealed a genome-wise significant QTL for milk protein percentage on chromosome 3. Eight other regions, localized on chromosomes 1, 2, 20, 23 and 25, showed suggestive significant linkage associations with some of the analysed traits. To our knowledge, this study represents the first complete genome scan for milk production traits reported in dairy sheep. The experiment described here shows that analysis of commercial dairy sheep populations has the potential to increase our understanding of the genetic determinants of complex production-related traits.

Mapping quantitative trait loci for milk production traits on ovine chromosome 6.

Spanish Churra sheep were studied in a daughter design for the presence on chromosome 6 of quantitative trait loci (QTL) influencing milk production traits. Eight half-sib families were genotyped for 11 microsatellites and marker-QTL effects analysed using yield deviations (YD) as quantitative measurements for the following traits: milk yield, protein yield, and protein percentage. QTL analysis was performed by interval mapping based on multimarker regression principles. Significance thresholds were estimated through a permutation test followed by a correction for multiple testing. The results suggest a region on ovine chromosome 6, close to the casein cluster, with an influence on milk traits and particularly on protein percentage. These results, the first ones reported for QTL affecting milk traits in sheep, are discussed in relation to data available for cattle, a closely related species.

Genetic relationships among Turkish sheep.

Genetic relationships among Turkish sheep breeds were analysed on the basis of 30 microsatellite markers. Phylogenetic analyses based on the estimation of genetic distances revealed the closest relationships for the Akkaraman, Morkaraman and Tuj breeds, which were clearly differentiated from the others in the dendrogram. Our pattern was completely confirmed by results from the Factorial Correspondence Analysis. All the results described analysing either population parameters or individuals revealed a clear separation between the fat-tailed group and the others. These results, based on nuclear DNA, are discussed along with those already reported for these breeds through the investigation of mitochondrial DNA, which had revealed the invaluable significance of the genetic background of these Turkish sheep.

Quantitative trait loci underlying udder morphology traits in dairy sheep.

A genome scan was conducted on the basis of the daughter design to detect quantitative trait loci (QTL) influencing udder morphology traits in Spanish Churra dairy sheep. A total of 739 ewes belonging to 11 half-sib families were genotyped for 182 microsatellite markers covering 3,248.2 cM (Kosambi) of the ovine autosomal genome. Phenotypic traits included scores for 5 linear udder traits: udder depth, udder attachment, teat placement, teat size, and udder shape. Quantitative measurements for the QTL analysis were calculated for each trait from evaluation scores using within-family yield deviations corrected for fixed environmental effects. Joint analysis of all families using Haley-Knott regression identified 5 regions that exceeded the 5% chromosome-wise significance threshold on chromosomes 7, 14, 15, 20, and 26. Based on the across-family results, a within-family analysis was carried out to identify families segregated according to the QTL and to estimate the QTL effect. The allelic substitution effect for individual families ranged from 0.47 to 1.7 phenotypic standard deviation units for udder shape on chromosome 15 and udder depth on chromosome 14, respectively. These QTL regions provide a starting point for further research aimed at the characterization of genetic variability involved in udder traits in Churra sheep. This paper presents the first report of a sheep genome scan for udder-related traits in a dairy sheep outbred population.