Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis

A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds

BACKGROUND

To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones.

RESULTS

The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses.

CONCLUSIONS

To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.

A genogeographic study of the Kyrgyz mountain merino via microsatellite markers

The aim was to ascertain the genetic and geographical structure of the Kyrgyz mountain merino (KMM). We analyzed DNA samples of 109 Kyrgyz mountain merino specimens, bred in three state breeding factories (STB), including "Orgochor" in the Issykul Province, "Katta-Taldyk" in the Osh Province and STb named after Luschikhin in the Talas Province. We identified 126 alleles in 12 microsatellite markers (McM042, INRA006, McM527, ETH152, CSRD247, OarFCB20, INRA172, INRA063, MAF065, MAF214, INRA005, INRA023). There were 6 to 16 alleles in each locus (mean 10.500 ± 0.957 alleles per locus). We identified 67 rare alleles (prevalence less than 5.0 %), which made up 53.2 % of all alleles found. The greatest number of rare alleles was found in STR-markers of CSRD247, INRA023, INRA005, INRA006, MAF214 and OarFCB20. For each group, there were individual differences in the distribution of allele frequencies across all the STR loci studied. The most significant of them were as follows: with regard to the McM042 locus, allele 87 was major in the TALAS and OSH groups (35.6 and 45.7 %, respectively), whereas allele 95 was major in the ISSYK- KUL group (36.2 %); allele 154 was major in all groups with regard to the INRA172 locus, but it was 1.25 times less prevalent in the ISSYK-KUL and 1.66 times less prevalent in the OSH groups compared to TALAS (55.2 and 41.4 %, respectively), whereas alleles 156 and 158 were found only in the ISSYK-KUL group. Considering the ETH152 locus, 186 allele prevalence in the TALAS group was 51.1 %, but allele 190 was also markedly prevalent in the ISSYK-KUL and OSH groups, 34.5 and 34.3 %, respectively. The genetic division of the studied groups of KMM (with K from 3 to 10) was homogeneous - the contribution of each subcluster was equivalent. The AMOVA analysis revealed that the groups are located equidistantly. To conclude, the genetic diversity of the Kyrgyz mountain merino in three state breeding factories of the Kyrgyz Republic was high and comparable with each other.

Genetic Diversity of Montenegrin Local Sheep Breeds Based on Microsatellite Markers

The Montenegrin sheep population mostly consists of local breeds and their crossbreeds that are very valuable from their genome preservation point of view. The aim of this study was the investigation of the genetic diversity of seven Montenegrin sheep breeds (Jezeropivska-JP, Sora-SOR, Zetska zuja-ZZ, Bardoka-BAR, Sjenička-SJ, Ljaba-Lj, and Piperska zuja-PIP) using 18 microsatellite sets of markers. The genotyping was done for 291 samples from seven populations using the multiplex amplification of sequences with polymerase chain reaction (PCR). The parameters of genetic diversity were estimated using several software tools. In total, 243 alleles were found, with a range of 6 to 25 by locus. The mean observed heterozygosity (Ho), polymorphism information content (PIC), and Fis values (fixation index) per marker were 0.728, 0.781, and -0.007, respectively. The mean number of alleles per breed varied from 4.889 in ZZ to 10.056 in JP. The highest Ho was estimated for JP (0.763) and the lowest for ZZ (0.640). The genetic structure showed close relations between SOR and JP, and both of them with SJ, while ZZ, LJ, and PIP were more distanced. This study provides useful indicators for the development of further in-depth studies and the creation of appropriate conservation programs.

SNP Genotyping Characterizes the Genome Composition of the New Baisary Fat-Tailed Sheep Breed

Lamb meat has become increasingly popular in several nations during the last few decades, especially in Kazakhstan. Due to the rising demand for lamb meat, our sheep breeders developed a new fat-tailed sheep and named the breed Baisary. Animals of the Baisary breed are characterized by a large physique, strong constitution, stretched body, deep and wide chest, medium or large-sized fat tail, long legs (height at the withers of adult rams 85–100 cm, sheep 75–90 cm), long lanceolate ears and strong hooves. Lambs of the Baisary breed surpass their peers of the original parent breeds by 15–20% in live weight at the weaning period. To characterize the genetic structure of Baisary sheep and compare it with the ancestral breeds, we genotyped 247 individuals from five sheep breeds with Ovine SNP50K. The estimated private allelic richness ranged from 0.0030 to 0.0047, with the minimum and maximum provided by the Gissar (Giss1) and Kazakh meat-wool breeds, respectively. The highest and lowest FIS values, meanwhile, were observed in the Afghan fat-tailed population and Baisary sheep, respectively. The calculated inbreeding coefficient showed that Edilbay and Baisary sheep have excess heterozygosity. According to principal components analysis, Baisary are close to Gissar populations, the Afghan fat-tailed breed and Edilbay sheep. These results were consistent with the Admixture and phylogenetic analysis. Overall, our results indicated that Baisary sheep differ genetically from their progenitors.

Genetic Differentiation among Livestock Breeds-Values for Fst

(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.

Identifications of immune-responsive genes for adaptative traits by comparative transcriptome analysis of spleen tissue from Kazakh and Suffolk sheep

Aridity and heat are significant environmental stressors that affect sheep adaptation and adaptability, thus influencing immunity, growth, reproduction, production performance, and profitability. The aim of this study was to profile mRNA expression levels in the spleen of indigenous Kazakh sheep breed for comparative analysis with the exotic Suffolk breed. Spleen histomorphology was observed in indigenous Kazakh sheep and exotic Suffolk sheep raised in Xinjiang China. Transcriptome sequencing of spleen tissue from the two breeds were performed via Illumina high-throughput sequencing technology and validated by RT-qPCR. Blood cytokine and IgG levels differed between the two breeds and IgG and IL-1β were significantly higher in Kazakh sheep than in Suffolk sheep (p < 0.05), though spleen tissue morphology was the same. A total of 52.04 Gb clean reads were obtained and the clean reads were assembled into 67,271 unigenes using bioinformatics analysis. Profiling analysis of differential gene expression showed that 1158 differentially expressed genes were found when comparing Suffolk with Kazakh sheep, including 246 up-regulated genes and 912 down-regulated genes. Utilizing gene ontology annotation and pathway analysis, 21 immune- responsive genes were identified as spleen-specific genes associated with adaptive traits and were significantly enriched in hematopoietic cell lineage, natural killer cell-mediated cytotoxicity, complement and coagulation cascades, and in the intestinal immune network for IgA production. Four pathways and up-regulated genes associated with immune responses in indigenous sheep played indispensable and promoting roles in arid and hot environments. Overall, this study provides valuable transcriptome data on the immunological mechanisms related to adaptive traits in indigenous and exotic sheep and offers a foundation for research into adaptive evolution.

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 relationship among indigenous Turkish Karayaka sheep subpopulations

The Karayaka is the most populous sheep breed in the Black Sea region of Turkey. In the present study, we investigated the intra- and inter-population genetic relationships among indigenous Karayaka sheep subpopulations. Nine microsatellites were genotyped for 64 individuals from Samsun, Ordu, Giresun and Tokat provinces. The average number of alleles (Na), allelic richness (Ar), observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information content (PIC) and inbreeding coefficient (FIS) for all subpopulations were estimated as Na=16.44, Ar=9.887, Ho=0.303, He=0.886, PIC=0.866 and FIS=0.630, respectively. The observed and expected heterozygosity ranged from 0.171 (Giresun) to 0.376 (Ordu) and 0.757 (Samsun) to 0.845 (Ordu), respectively. It was determined that a 10.5 % of total genetic variation (FIT=66.9 %) in Karayaka sheep corresponded to genetic differences among subpopulations (FST), whereas 63.0 % was explained by genetic difference among individuals (FIS). This study gives the first evidence about genetic relationships of Karayaka subpopulations. The results show that Karayaka sheep subpopulations are genetically different from each other. These findings revealed that the Karayaka breed has discrete subpopulations and should be taken into consideration when preparing conservation programs and future breeding strategies.