90 research outputs found
British sheep breeds as a part of world sheep gene pool landscape: looking into genomic applications
Sheep farming has been an important sector of the UK’s economy and rural life for many centuries. It is the favored source of wool, meat and milk products. In the era of exponential progress in genomic technologies, we can now address the questions of what is special about UK sheep breed genotypes and how they differ genetically form one another and from other countries. We can reflect how their natural history has been determined at the level of their genetic code and what traces have been left in their genomes because of selection for phenotypic traits. These include adaptability to certain environmental conditions and management, as well as resistance to disease. Application of these advancements in genetics and genomics to study sheep breeds of British domestic selection has begun and will continue in order to facilitate conservation solutions and production improvement
Editorial: Traditional and up-to-date genomic insights into domestic animal diversity
Domesticated animals play a significant role in local, national, and international agricultural output as well as in daily human life and culture. Additionally, they make up a sizeable portion of the biodiversity of the planet, which is essential for producing food and other animal products for human consumption. The present Frontiers in Genetics Research Topic (Figure 1) is devoted to various issues pertinent diversity of farm animals. The latter is at serious risk today, which could result in a reduction in the resources available to produce breed-specific food products and other necessities of everyday living. Importantly, genetic diversity is necessary for future animal breeding to be flexible enough to adapt livestock populations to changing customer demands and climatic conditions. Continued efforts are required to protect biodiversity, stop the loss of animal breeds, and maintain genetic diversity and develop strategies to use resource population in regional (niche) production systems
Investigation of gene pool and genealogical links between sheep breeds of southern Russia by blood groups and DNA microsatellites
To study the gene pool and the establishment of genealogical relationships between breeds of sheep of different directions productivity bred in Russia, were used two classes of genetic markers - blood and DNA microsatellites. The included sample sheep are fine-wool Merino breeds: Grozny (GR), Caucasian (CA), Manychskij merino (MM), the Soviet Merino (SM), Stavropol (ST) and coarse wool breeds: Edilbaevskaya (ED), Karakul (CR) and Romanov (RO). For the study of erythrocyte, were selected antigens (blood group) in 1159 samples from 11 breeding farms. For microsatellite DNA study - 598 from 10 breeding farms. Microsatellite analysis revealed that the most polymorphic were Stavropol breed sheep that have identified an average of 18.27 alleles per locus were relatively conservative Romanov breed sheep - 9.7 alleles per locus. The minimum genetic distances established between Grozny and Soviet Merino - 0.0569 (for microsatellites) and 0.0741 (blood groups - later in the same sequence). The rocks of the Stavropol - Grozny were 0.0861 and 0, 0810. Whereas Stavropol and Soviet Merino 0.0861 and 0.1094. Also relatively close between Grozny - Edilbaevskoy, Grozny Karakul, Edilbaevskoy - Karakul: 0.1364 and 0.0851, respectively; 0.1620 and 0.1208; 0.1875 and 0.1192. The highest genetic distances were between Stavropol and Karakul 0.2664 and 0.1804, as well as between the Romanov and all studied species - 0.2491 ... 0.3211 and 0.1734 ... 0.2235
Eggology and mathematics of a quail egg: an innovative non-destructive technology for evaluating egg parameters in Japanese quail
Quail eggs, the smallest ones among poultry species, require special methodological aspects for their non-destructive examination and quality analysis. Using eggs from a cross between the Japanese and Texas breeds, we devised a methodology for defining the main geometric parameters of quail eggs. Calculation formulae were proposed to estimate indirectly egg volume and surface area. Our findings on the weights of structural egg components enabled to obtain mathematical equations for computing the weights of shell, yolk and albumen, depending on the complex of measured parameters including the egg weight, its volume and surface area. When taken as a whole, the results of our study can be regarded as the most thorough methodological approach to date for the execution of comprehensive investigations of quail egg quality. They will be applicable and instrumental in areas of food research and emerging technologies, including the aspects of storage, packing, and processing of quail eggs
Shared Ancestry and Signatures of Recent Selection in Gotland Sheep
Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (similar to 50%), Karakul (similar to 30%), Romanov (similar to 20%), and Fjallnas (similar to 10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation F-ST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the F-ST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep
Metabolic rate and egg production in Japanese quails can be predicted by assessing growth parameters of laying hens
Simple Summary:
Quails are becoming increasingly popular for their meat and eggs, and thus, the productivity of laying hens, and how that can be predicted, is of growing interest to quail producers. Because of this, we wanted to find out whether we could predict the performance of laying hens (typically expressed as the number of eggs produced multiplied by the egg weight—the so-called total egg mass) simply by looking at certain growth traits (i.e., body weight, surface area, and volume), as well as the metabolic rate among eight Japanese quail breeds. To succeed in this analysis, we developed a novel method for calculating the volume and surface area of a quail body. As a result, we derived a new mathematical formula called the metabolic index, which included the measurements of body weight, surface area, and volume. We discovered that the total egg mass in quails can be judged from these growth parameters, particularly when we examined the slope angles of the trend lines in the graphs pertaining to these parameters.
Abstract:
The aim of the current study was to assess the female metabolic rate and test the hypothesis that there is a relationship between the egg productivity of Japanese quails from eight breeds and their morphometric, or growth, parameters. Parameters measured were body weight (B), volume (V), and surface area (S), as well as the metabolism level expressed by the ratio S/V. The collected egg performance traits were as follows: the number of eggs produced (N), the average egg weight (W), and the total egg mass (M) (i.e., N multiplied by W). To measure the S and V values, a novel technique was developed that takes into account the similarity of the quail’s body to an ellipsoid. An analysis of the relationships between productivity indicators allowed us to introduce a new index called the metabolic index, B·S/V, based on all three main growth parameters in quails. Using the values of this index, we were then able to judge indirectly the level of quails’ egg productivity. We went on to assess the N, W, and M values, not only depending on the size of the bird’s growth parameters but also according to the degree of their changes during quail growth. These changes were expressed as the slope angles of trend lines describing the growth process data. This approach produced more accurate results for predicting the egg productivity in terms of W and M
Whole genome screening procures a holistic hold of the Russian chicken gene pool heritage and demographic history
Simple Summary:
A collection of native farm animal breeds can be considered as a gene pool and a national heritage. Long-term artificial selection in domesticated animals has certain effects on their genomes, which can be investigated using genome-wide screens for DNA sequence variation, that is, so-called single nucleotide polymorphism (SNP) screens. Here, we looked at the genomes of 19 Russian chicken gene pool breeds, both native and imported, evaluating the contrasting egg, meat and dual-purpose types. Based on genetic diversity statistics, we identified differences between the breeds using many DNA markers (SNPs) that may represent genomic regions that are being selected for, either within a specific breed or shared between breeds. Our research will be helpful for further understanding the genomic diversity and demographic history of Russian domestic chickens. This would be essential for their successful breeding.
Abstract:
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool
Dissecting selective signatures and candidate genes in grandparent lines subject to high selection pressure for broiler production and in a local Russian chicken breed of Ushanka
Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits
Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping
Background: Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip. Furthermore, to evaluate admixture contributions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data. Results: We recorded similar observed heterozygosity (0.354-0.395) and allelic richness (1.890-1.955) levels across the analyzed breeds and they are comparable with those observed in the worldwide breeds. Recent effective population sizes estimated from linkage disequilibrium five generations ago ranged from 65 to 543. Multi-dimensional scaling, admixture, and neighbor-net analyses consistently identified a two-step subdivision of the Russian local sheep breeds. A first split clustered the Russian sheep populations according to their wool type (fine wool, semi-fine wool and coarse wool). The Dagestan Mountain and Baikal fine-fleeced breeds differ from the other Merino-derived local breeds. The semi-fine wool cluster combined a breed of Romanian origin, Tsigai, with its derivative Altai Mountain, the two Romney-introgressed breeds Kuibyshev and North Caucasian, and the Lincoln-introgressed Russian longhaired breed. The coarse-wool group comprised the Nordic short-tailed Romanov, the long-fat-tailed outlier Kuchugur and two clusters of fat-tailed sheep: the Caucasian Mountain breeds and the Buubei, Karakul, Edilbai, Kalmyk and Tuva breeds. The Russian fat-tailed breeds shared co-ancestry with sheep from China and Southwestern Asia (Iran). Conclusions: In this study, we derived the genetic characteristics of the major Russian local sheep breeds, which are moderately diverse and have a strong population structure. Pooling our data with a worldwide genotyping set gave deeper insight into the history and origin of the Russian sheep populations
Whole‐genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats
After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.Deutscher Akademischer Austauschdienst
http://dx.doi.org/10.13039/501100001655Javna Agencija za Raziskovalno Dejavnost RS
http://dx.doi.org/10.13039/501100004329Ministry of Science and Higher Education of the Russian Federation
http://dx.doi.org/10.13039/501100012190Peer Reviewe
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