Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

BACKGROUND

Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs).

RESULTS

Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms.

CONCLUSIONS

In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)

Identifying genetic markers of economically valuable traits has practical benefits for the meat goat industry. To better understand the genomic variations influencing body conformation traits, a genome-wide association study was performed on Tashi goats, an indigenous Chinese goat breed. A total of 155 Tashi goats were phenotyped for eight body conformation traits: body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Then, 100 Tashi goats were randomly selected for whole-genome sequencing and genotyped. We obtained 1676.4 Gb of raw data with an average sequencing depth of 6.2X. Clean reads were aligned to the ARS1.2 reference genome, and 11,257,923 single nucleotide polymorphisms (SNPs) were identified. The structure analysis showed that these Tashi goats were almost not genetically related. The 109, 20, 52, 14, 62, 51, 70, and 7 SNPs were significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Within the ±500 kb region of significant SNPs, 183 genes were annotated. The most significantly enriched KEGG pathway was "olfactory transduction", and the most significantly enriched gene ontology (GO) terms were "cellular process", "cellular anatomical entity", and "molecular transducer activity". Interestingly, we found several SNPs on chromosomes 10 and 11 that have been identified multiple times for all eight body conformation traits located in two fragments (114 kb and 1.03 Mb). In chr.10:25988403-26102739, the six SNPs were tightly linked, the TACTAG genotype was the highest at 91.8%, and the FNTB (Farnesyltransferase, CAAX Box Beta) and CHURC1 (Churchill Domain Containing 1) genes were located. In chr.11:88216493-89250659, ten SNPs were identified with several dependent linkage disequilibrium (LD) blocks, and seven related genes were annotated, but no significant SNP was located in them. Our results provide valuable biological information for improving growth performance with practical applications for genomic selection in goats.

A Combined Approach for the Characterization of Small Ruminant Lentivirus Strains Circulating in the Islands and Mainland of Greece

Small ruminant lentiviruses are a group of viruses infecting goat and sheep worldwide. These viruses exhibit an extraordinary degree of genetic and antigenic variability that severely influence in vivo and in vitro features, as well as diagnostic test results. Small ruminant farming is the most important animal farming business in Greece, with a high impact on the Greek primary economy. Although SRLV infection and its impact on animal production are well established in the country, little is known about the circulating SRLV strains and their prevalence. The aim of this study was to characterize SRLVs circulating in Greece with a combined serological and molecular approach, using the bulk milk matrix collected from 60 farms in different municipalities. This study allowed us to estimate a seroprevalence of around 52% at the herd level. The B1, B2 and A3 subtypes and a novel A viral cluster were identified. Moreover, the amplicon sequencing method allowed us to identify more than one viral subtype in a sample. These results again confirm the high variability of these viruses and highlight the importance of the constant monitoring of viral evolution, in particular in antigens of diagnostic interest.

Genomics of founders for conservation breeding: the Jasper caribou case

Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10592-023-01540-3.

Assessing Genetic Diversity and Searching for Selection Signatures by Comparison between the Indigenous Livni and Duroc Breeds in Local Livestock of the Central Region of Russia

Indigenous pig breeds are mainly associated with the adaptive capacity that is necessary to respond adequately to climate change, food security, and livelihood needs, and natural resources conservation. Livni pigs are an indigenous fat-type breed farmed in a single farm in the Orel region and located in the Central European part of the Russian Federation. To determine the genomic regions and genes that are affected by artificial selection, we conducted the comparative study of two pig breeds with different breeding histories and breeding objectives, i.e., the native fat-type Livni and meat-type Duroc breeds using the Porcine GGP HD BeadChip, which contains ~80,000 SNPs. To check the Livni pigs for possible admixture, the Landrace and the Large White breeds were included into the study of genetic diversity as these breeds participated in the formation of the Livni pigs. We observed the highest level of genetic diversity in Livni pigs compared to commercial breeds (UHE = 0.409 vs. 0.319–0.359, p < 0.001; AR = 1.995 vs. 1.894–1.964, p < 0.001). A slight excess of heterozygotes was found in all of the breeds. We identified 291 candidate genes, which were localized within the regions under putative selection, including 22 and 228 genes, which were specific for Livni and Duroc breeds, respectively, and 41 genes common for both breeds. A detailed analysis of the molecular functions identified the genes, which were related to the formation of meat and fat traits, and adaptation to environmental stress, including extreme temperatures, which were different between breeds. Our research results are useful for conservation and sustainable breeding of Livni breed, which shows a high level of genetic diversity. This makes Livni one of the valuable national pig genetic resources.

Trajectory of livestock genomics in South Asia: A comprehensive review

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Grazing Land Productivity, Floral Diversity, and Management in a Semi-Arid Mediterranean Landscape

Most grazing lands in Mediterranean ecosystems that support extensive sheep farming systems are characterized by unfavorable edapho-climatic conditions, especially in semi-arid areas. Often, though, their use is far from sustainable, causing erosion and ecosystem degradation impacts. In this paper, we explore the use, productivity, and flora diversity of typical Mediterranean grazing lands in four farms at the Agra locality in the western part of Lesvos Island, Greece. For a period of two consecutive growing seasons (September to June), we recorded herbage biomass on 16 plots of grazing lands with three measurements per season of land cover and plant productivity (biomass) inside small exclosures (cages) protected from grazing. We recorded the species richness of herbaceous plant communities within and outside the cages at the end of every growing season, the period of maximum growth of herbaceous species. We also chemically analyzed the biomass for crude protein at the end of each season. Results show sizable productivity differences among pasture plots as well as seasons and an overall medium to high degree of productivity and species richness considering the relatively intensive grazing, with little differences over the different cages and the degree of grazing intensity. These results suggest that the “history” of the fields is important, as grazing lands that had been used for arable crops in the past, as well as those leveled and in favorable locations, were the most productive and diverse ones, while shallower soils and inclined grazing lands showed signs of overuse and degradation. Overall, though, these ecosystems showed a high degree of resilience despite their intensive use.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.