Capturing Genetic Diversity and Selection Signatures of the Endangered Kosovar Balusha Sheep Breed

Adeniyi, Olusegun O; Simon, Rebecca; Bytyqi, Hysen; Kugler, W. F.; Mehmeti, H.; Berisha, Kaltrina; Simčić, Mojca; Magdy, Mohamed; Lühken, Gesine

doi:10.3390/genes13050866

Cited by 4 publications

(1 citation statement)

References 80 publications

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“…Four methods developed to identify selection signatures in livestock populations, all based on within-population approaches: i) extremely high SNP incidence in ROH ("extreme ROH islands" or "eROHi"), ii) integrated haplotype score (iHS), iii) number of segregating sites by length (nSL), and iv) composite likelihood ratio test (CLR), are widely used to identify hard and soft selection signals [ 12 – 18 ]. For example, many previous studies on Mediterranean sheep used statistical methods with medium density genomic data and found candidate genes for coat color, morphology, milk, and wool [ 19 – 24 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Lukic,

Curik,

Drzaic

et al. 2023

J Animal Sci Biotechnol

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Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. Results We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

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Section: Introductionmentioning

confidence: 99%

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Lukic,

Curik,

Drzaic

et al. 2023

J Animal Sci Biotechnol

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Comparative genomic studies of Tomtom and Nuaimi sheep breeds of Bahrain, and Asian and European sheep breeds revealed selection signatures

Tibbo,

Jawasreh,

Stella

et al. 2024

Preprint

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The segments of the genome harboring genes subject to past selection because of their biological relevance can be identified due to their lower genetic divergence and distinctive regional linkage disequilibrium (LD) patterns. The origins of the sheep breeds known as Tomtom and Nuaimi in Bahrain are unknown, as are the special genetic variants that they carried throughout their evolution and presumably differ from ancient breeds native to Europe and Asian. We pinpointed signals of selection in sheep breeds by comparing the regional genomic (50k SNp chip) differences in LD variation between the Tomtom and Nuaimi sheep breeds with the Afshari, European Mouflon, Asian Mouflon, and Zel breeds. The autosomal genome's LD variation among breeds was compared using the VarLD approach. The NCBI assembly was used to assess the genomic regions bearing the top 0.01 and 0.1 percentiles of signals, determine the genes in those regions, and compare those regions with previously published selection signatures. The wild Mouflon (Asian and European) and Tomtom breeds were divided into three separate components by the PCA, whereas Nuaimi, Zel, and Afshari were grouped inside a single quartile and given special distinction because their individuals looked to be close to one another (genetically related). A total of 59 genes were found to be close to the selection signatures (94 selection signatures) detected on various ovine chromosomes, and many were crucial for reproductive and productive attributes that were influenced by selection as the Tomtom and Nuaimi sheep breeds evolved. According to the genome scan, the Tomtom sheep breed is genetically distant as it was isolated in a separate quartile, far from the Nuaimi, Zel, and Al-Afshari on the one hand, and Asian and European Mouflon on the other. The differences found between the studied breeds combinations may have resulted from special genomic selection signals (94) detected on different chromosomes. The results obtained for the Bahraini local sheep breeds are critical for the future genetic selection plan, as they will serve as a foundation for comparison with any future evolution.

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Population structure and selective signature of sheep around Tarim Basin

et al. 2023

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Extreme climate change may lead to a decline in biodiversity and species extinction. And it also results in different population structure and genetic diversity of sheep. Therefore, studying the effects of extreme climate change on the distribution pattern of sheep is of great value. We used Illumina Ovine SNP 50K BeadChip to study the sheep around in southern Xinjiang of China, living around the Taklimakan Desert. Among them, 6 sheep breeds were from Xinjiang, China, and 3 sheep breeds were from other countries (Indian, Iran and Bangladeshi). We examined their genetic diversity and population structure and Genes related to year-round estrous in sheep were obtained by selective sweep. The principal component analysis, Admixture and Neighbor-Joining tree showed that a distinct pattern of population structure was observed in 9 sheep breeds. The candidate genes related to year-round estrous were ZO2, IGF1, TSHB and DLG1, and the candidate genes related to sheep reproductive performance were BMP4, LRP8, NF1, and INSL3. This study contributes to a better understanding of the genetic structure and population history of sheep populations in the Taklimakan Desert environment, as well as the regulatory mechanisms of year-round estrous in sheep in the desert environment, which has important implications for the global livestock industry to cope with the challenges of rapidly changing climate and to explore important economic traits.

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Capturing Genetic Diversity and Selection Signatures of the Endangered Kosovar Balusha Sheep Breed

Cited by 4 publications

References 80 publications

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Comparative genomic studies of Tomtom and Nuaimi sheep breeds of Bahrain, and Asian and European sheep breeds revealed selection signatures

Population structure and selective signature of sheep around Tarim Basin

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