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Additional file 6: Figure S3. Tessellated projection. Spatial geographic presentation of the estimated allele sharing distance matrix (DPS) among breeds using multi-allelic SNP-blocks.

Additional file 2. Detailed description of the indigenous Greek and Cypriot cattle. Compilation of information on Greek indigenous cattle breeds from diverse sources [16, 33, 71–87]. This includes also information from records in Greek, which were formerly not accessible to the international scientific community due to language barriers.

Additional file 7: Figure S4. Phylogenetic tree. Neighbor-joining tree based on Nei’s genetic distance DA using multi-allelic SNP blocks. Mongolian yak (YAK) was used as a root. Dotted lines indicate the reduced length of YAK and GIR to improve visibility. Special square marks represent the influence of East-Podolian (grey), Alpine (green) and North-West (olive green) group.

Additional file 4: Figure S2. Tessellated projection. Spatial geographic presentation of the estimated effective population number (Ne5, Ne50, Ne2000).

Additional file 3: Figure S1. Tessellated projection. Spatial geographic presentation of the herein estimated diversity parameters (mA, AR, HE, HE(SNP), npA, nspA).

Additional file 8: Figure S5. Admixture analysis. Population structure of the 114 studied breeds/populations presented for each of K inferred ancestral population value, using a genome‐wide set of bi-allelic SNPs. All the analyzed individuals are presented as colored vertical bars, divided at most K segments and with proportional heights, according to their genotype membership. In the depicted plots (K = 2 to K = 26), a different color is presented for each cluster. From left to right within each group the presented breeds are as follows: Minor Asia: ATER, ATBC, ATSR, ATSY, TRG; Greece and Cyprus: CYP, AGT, CRT, NSY, GRB, KAS, KEA, PRG, ROG, SYK, KTR; South East Europe: RHS, MKB, SRB, PRE, RMB, SHB, DGB, DBB, MAB, LKB, SKB, MNB, BHB, HRB; East Podolian: HRI, HRP, UKP; Tyrrhenian: PODO, CINI, MOSI, RSIC, MOSA, SARD, SBRU, CORS, AGER, MARE, CHI, MPIS, CALV, MCH, RMG, GARF, PONT, MODE, CABA, REGG, PMT, BURL; Alpine: PRDO, OVAR, REND, BPUS, PUST, SIC, PIN, TGV, MWF, OBV, BBV, DFV, FGV, VOG, ABO, MON, TAR; France: RDBI, SAL, AUB, LIM, CHR, PAR, BAQ, GAS; Iberian: MNRQ, MALL, NGAN, CANA, MARI, ALEN, BAR, MARO, SYG; North West Europe: BPN, NOR, MAN, BBB, LKF, HF, GNS, JSY, HER, SHR, KRY, DXT, GLW, AAN, HGL, NRC, SERC, FJL, FIAY, FINE, FINW, FINN, YARO.

Additional file 1: Table S1. Sample description, group allocation, RGB (color) code assigned to the pre-defined groups within this paper, breed names, breed code, number of sampled and genotyped individuals (N), number of genotyped and unrelated individuals used to estimate the diversity parameters (Nd), current breeding purposes as well as sporadic or recent past breeding purposes in parenthesis, breed origin, and source of the samples or genotypes used in this study or from previous studies [17, 25, 28, 30, 34, 35, 67–70]. Table S2. Phenotypic, productive and reproductive traits. Description of phenotype, productive and reproductive traits of the 11 Greek and Cypriot analyzed breeds. Table S3. Evolution of bovine population sizes on the islands during the last 60 years. Statistical information regarding the evolution of cattle population on the Greek island based on [62].

The Ovar-DRB1 gene locus is one of the most polymorphic genes of the Major Histocompatibility Complex (Ovar-MHC) and holds a functional role to antigen presentation. The aim of this study was: a) to describe the Ovar-DRB1 locus variability in two dairy Greek sheep breeds and b) to investigate associations between this variability with resistance to gastrointestinal parasitosis. Blood and faecal samples were collected from 231 and 201 animals of Arta and Kallarytiko breeds, respectively. The identification of alleles was performed using the sequence–base method. Faecal egg counting (FEC) of the gastrointestinal parasites and measures of blood plasma pepsinogen levels were performed in order to evaluate parasitological parameters. From this study in the overall examined animals, thirty-nine Ovar-DRB1 alleles were identified, among them, ten new alleles, reported for the first time in the literature. In Arta breed a total of twenty-four alleles were found. Among the detected alleles, ten were breed specific and five were new. Regarding the Kalarrytiko breed, twenty-nine alleles were found, fifteen of them were unique and nine were new. The studied breeds differed in their allelic profile, with only 12 common from the total of 134 different recorded genotypes. A higher number of animals with high parasitic load and high plasma pepsinogen values were found in Kalarrytiko. Associations between Ovar-DRB1 alleles with FEC values were found with certain heterozygous genotypes to present significantly reduced FEC values. The large number of detected alleles with low frequencies and the fact that the majority of animals were heterozygous, make hard to find strong associations., International Journal of Health, Animal Science and Food Safety, Vol 3, No 1 (2016)