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

Genomic studies in domestic goats (Capra hircus L.): current advances and prospects (review] Геномные исследования домашних коз (Capra hircus L.): современное состояние и перспективы (обзор)

The domestic goat (Capra hircus) is a versatile small ruminant species spread on all continents, whose genomic features are becoming the subject of study by research teams from all over the world (A.M.A.M. Zonaed Siddiki et al., 2020; M.I. Selionova et al., 2021). The goal of this review is to elucidate the results of recent genomic studies on domestic goats using DNA chips and whole genome sequencing (WGS) analysis, and to compile a list of WGS-identified candidate genes associated with economically significant and adaption traits. This review summarizes and analyzes the results of WGS studies from 2020 to 2024. A list of candidate genes identified using WGS and associated with economically important and adaptive traits in goats is presented. An analysis of the methodological and bioinformatic approaches used to study WGS of domestic goats is executed. Using DNA chips, genetic relationships between different goat breeds and populations were established (T.E. Deniskova et al., 2021; V. Mukhina et al., 2022; A. Manunza et al., 2023), their genetic diversity was assessed (B.A. Vlaic et al., 2024; G. Chessari et al., 2024), and introgression from wild species of the genus Capra was studied (H. Asadollahpour Nanaei et al., 2023; N. Pogorevc et al., 2024). The decline in the WGS costs (B. Gu et al., 2022) has boosted an increase in the number of WGSs generated in goats (S. Belay et al., 2024). Genes under convergent selection pressure in sheep and goats have been identified, including DGKB, FAM155A, GRM5 (J. Yang et al., 2024) and CHST11 (L. Tao et al., 2021). An increase in the copy number of the GBP1 gene has been shown to be associated with immune resistance and prolificacy (R.Q. Zhang et al., 2019; R. Di Gerlando et al., 2020; M. Arslan, 2023). A large group of genes has been identified that affect milk productivity — ANPEP (J. Ni et al., 2024), ERBB4 (Z. Liu et al., 2024), NCAM2 (Z. Amiri Ghanatsaman et al., 2023) and GLYCAM1 (J. Xiong et al., 2023; H.B. Gebreselase et al., 2024), carcass quality — ACOX1, PGM1 (Z.X. An et al., 2024), ZNF385B and MYOT (H.B. Gebreselase et al., 2024), growth — HMGA2 and GJA3 (C. Li et al., 2024), live weight — STIM1 and ADM (R. Saif et al., 2021), and wool performance — CCNA2 (Y. Rong et al., 2024) and FGF5 (Q. Zhao et al., 2024). The TSHR and STC1 genes associated with domestication were discovered in Swiss breeds (H. Signer-Hasler et al., 2022). Genes involved in the formation of protective responses of the body to diseases and unfavorable climatic factors have been identified, including PIGR, TNFAIP2 (Q. Chen et al., 2021, 2022), KHDRBS2 (X. Sun et al., 2022), PPP2R3C (R. HuangFu et al., 2024), GNG2 (Z.X. An et al., 2024), HOXC12 and MAPK8IP2 (O. Sheriff et al., 2024). Genome-wide association studies (GWAS) based on WGS identified candidate genes associated with body size, including FNTB, CHURC1 (R. Yang et al., 2024), PSTPIP2 and SIPA1L (B. Gu et al., 2022), and milk production (H. Wu et al., 2023). To date, candidate genes have been identified on 21 of the 29 autosomes, with the largest number on CHI5 (9 genes), CHI18 (8 genes), CHI1, CHI3, CHI57 and CHI23 (7 genes on each chromosome). Thus, the compiled list of target candidate genes may be used in marker-assisted selection programs. Кошкина О.А., Денискова Т.Е., Романов М.Н., Зиновьева Н.А. Домашняя коза (Capra hircus L.) — это универсальный вид мелкого рогатого скота, разводимый на всех континентах, геномные особенности которого становятся предметом исследования для научных коллективов во всем мире (A.M.A.M. Zonaed Siddiki с соавт., 2020; М.И. Селионова с соавт., 2021). Цель обзора — отразить результаты недавних исследований геномов домашних коз с использованием ДНК-чипов и анализа последовательностей полных геномов (WGS) и составить список генов-кандидатов, выявленных с помощью WGS анализа, которые ассоциированы с экономически значимыми и адаптивными признаками у домашних коз. В настоящем обзоре обобщены и проанализированы результаты исследований WGS с 2020 по 2024 год. Представлен список генов-кандидатов, идентифицированных на основе WGS и ассоциированных с экономически значимыми и адаптивными признаками у домашних коз. Проведен анализ применяемых методических и биоинформатических подходов для изучения WGS домашних коз. С помощью ДНКчипов установлены генетические взаимосвязи различных пород и популяций коз (T.E. Deniskova с соавт., 2021; V. Mukhina с соавт., 2022; A. Manunza с соавт., 2023), оценено их генетическое разнообразие (B.A. Vlaic с соавт., 2024; G. Chessari с соавт., 2024), изучена интрогрессия с дикими видами рода Capra (H. Asadollahpour Nanaei с соавт., 2023; N. Pogorevc с соавт., 2024). Снижение стоимости WGS (B. Gu с соавт., 2022) стимулировало рост числа генерируемых WGS коз (S. Belay с соавт., 2024). Выявлены гены, находящиеся под давлением конвергентного отбора у овец и коз, включая DGKB, FAM155A, GRM5 (J. Yang с соавт., 2024) и CHST11 (L. Tao с соавт., 2021). Показано, что увеличение числа копий гена GBP1 связано с иммунорезистентностью и многоплодием (R.Q. Zhang с соавт., 2019; R. Di Gerlando с соавт., 2020; M. Arslan, 2023). Идентифицирована большая группа генов, влияющих на молочную продуктивность, — ANPEP (J. Ni с соавт., 2024), ERBB4 (Z. Liu с соавт., 2024), NCAM2 (Z. Amiri Ghanatsaman с соавт., 2023), GLYCAM1 (J. Xiong с соавт., 2023; H.B. Gebreselase с соавт., 2024), на качество туш — ACOX1, PGM1 (Z.X. An с соавт., 2024), ZNF385B и MYOT (H.B. Gebreselase с соавт., 2024), на рост — HMGA2 и GJA3 (C. Li с соавт., 2024), живую массу — STIM1 и ADM (R. Saif с соавт., 2021), а также шерстную продуктивность — CCNA2 (Y. Rong с соавт., 2024) и FGF5 (Q. Zhao с соавт., 2024). Обнаружены гены TSHR и STC1, связанные с одомашниванием у швейцарских пород (H. Signer-Hasler с соавт., 2022). Выявлены гены, вовлеченные в формирование защитных реакций при заболеваниях и действии неблагоприятных климатических факторов: PIGR, TNFAIP2 (Q. Chen с соавт., 2021, 2022), KHDRBS2 (X. Sun с соавт., 2022), PPP2R3C (R. HuangFu с соавт., 2024), GNG2 (Z.X. An с соавт., 2024), HOXC12 и MAPK8IP2 (O. Sheriff с соавт., 2024). При полногеномном поиске ассоциаций (GWAS) на основе WGS идентифицированы гены-кандидаты, ассоциированные с размерами туловища, включая гены FNTB, CHURC1 (R. Yang с соавт., 2024), PSTPIP2 и SIPA1L (B. Gu с соавт., 2022), и с молочной продуктивностью (H. Wu с соавт., 2023). Гены-кандидаты выявлены на 21 из 29 аутосом, при этом наибольшее их число к настоящему времени идентифицировано на CHI5 (9 генов), CHI18 (8 генов), CHI1, CHI3, CHI57 и CHI23 (по 7 генов на каждой хромосоме). Таким образом, сформирован список целевых генов-кандидатов, которые могут быть использованы в программах маркер-ориентированной селекции

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

[Genome-wide association study of testes development indicators in roosters (Gallus gallus L.)] Полногеномные ассоциативные исследования показателей развития семенников у петухов (Gallus gallus L.)

Reproductive ability is one of the main indicators of the male breeding value that depends primarily on the functional state of testes cells. Male fertility is defined by complex physiological processes affecting the formation of mature germ cells, i.e., spermatozoa in the process of spermatogenesis. The forming and accumulation of germ cells occur in the seminiferous tubules of the testes, therefore the gonad development can serve as an indicator characterizing spermatogenesis and the reproductive potential of males. A number of studies on farm animals, including poultry, have shown the genetic determinacy of this trait, with identification of respective single nucleotide polymorphisms (SNPs) and genes determining the male gonad growth and development. In the present investigation, a genome-wide association study (GWAS) of the testes development parameters in roosters (Gallus gallus L.) of the F2 resource population were conducted. For the first time, new significant SNPs and candidate genes (р < 1.05½104) determining gonad growth and development in roosters were identified. The aim of the research was to seek SNPs and identify genes associated with testes growth parameters in roosters. The object of the study were F2 roosters from a model resource population (n = 115) that was obtained by interbreeding two breeds, Russian White and White Cornish. DNA was extracted from feather pulp using a commercial kit DNK Extran-2 (OOO NPF Sintol, Russia) in accordance with the manufacturer’s protocol. Genotyping was carried out using the medium-density Illumina Chicken 60K SNP iSelect BeadChip chip. At the age of 63 days, the experimental birds were slaughtered and the mass and morphometric indices of testes (length and thickness) were examined. Based on the obtained genotypic and phenotypic data, the GWAS analysis was performed in F2 resource population roosters using PLINK 1.9 software. The examined population was characterized by a high coefficient of variation in the measured indices, 96.1 % for the testes mass and 39.1 % for the linear measurements. The mass and linear measurements of the left testis were 5-14 % higher (р 0.05) compared to the right testis. The GWAS analysis revealed 36 significant SNPs (р < 1.05½104) associated with testes growth and development parameters in 63-day-old cockerels, in particular with the mass, length and thickness of the testes, 3, 26 and 7 SNPs, respectively. SNPs were localized on chromosomes GGA1, GGA3, GGA6, GGA7, GGA12, GGA15, and GGA18. A total of 156 genes were identified in the regions of the detected SNPs, including 16 genes that coincided with the positions of these SNPs. In particular, the latter were one gene (WNT7A) associated with the testis mass, 13 genes (LHFPL1, GALNT3, TMEM198, CACNA2D3, CCDC66, CACNA1D, DENND6A, CELSR3, WNT7A, IP6K2, ERC2, ABHD6, and DEPDC5) associated with the testis length, and three genes (ESR1, POLE, and RNFT2) associated with the testis thickness. These data can be used in genomic selection of roosters aimed at increasing their reproductive potential

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

Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Background: It has been known for almost a century that the belted phenotype in cattle follows a pattern of dominant inheritance. In 2009, the approximate position of the belt locus in Brown Swiss cattle was mapped to a 922-kb interval on bovine chromosome 3 and, subsequently, assigned to a 336-kb haplotype block based on an animal set that included, Brown Swiss, Dutch Belted (Lakenvelder) and Belted Galloway individuals. A possible candidate gene in this region i.e. HES6 was investigated but the causal mutation remains unknown. Thus, to elucidate the causal mutation of this prominent coat color phenotype, we decided to remap the belted phenotype in an independent animal set of several European bovine breeds, i.e. Gurtenvieh (belted Brown Swiss), Dutch Belted and Belted Galloway and to systematically scan the candidate region. We also checked the presence of the detected causal mutation in the genome of belted individuals from a Siberian cattle breed. Results: A combined linkage disequilibrium and linkage analysis based on 110 belted and non-belted animals identified a candidate interval of 2.5 Mb. Manual inspection of the haplotypes in this region identified four candidate haplotypes that consisted of five to eight consecutive SNPs. One of these haplotypes overlapped with the initial 922-kb interval, whereas two were positioned proximal and one was positioned distal to this region. Next-generation sequencing of one heterozygous and two homozygous belted animals identified only one private belted candidate allele, i.e. a multiplication event that is located between 118,608,000 and 118,614,000 bp. Targeted locus amplification and quantitative real-time PCR confirmed an increase in copy number of this region in the genomes of both European (Belted Galloway, Dutch Belted and Gurtenvieh) and Siberian (Yakutian cattle) breeds. Finally, using nanopore sequencing, the exact breakpoints were determined at 118,608,362 and 118,614,132 bp. The closest gene to the candidate causal mutation (16 kb distal) is TWIST2. Conclusions: Based on our findings and those of a previously published study that identified the same multiplication event, a quadruplication on bovine chromosome 3 between positions 118,608,362 and 118,614,132 bp is the most likely candidate causal mutation for the belted phenotype in cattle

Elevated haplotypes frequencies reveal similarities for selection signatures in Western and Russian Simmental populations

This paper shows a straightforward, but surprisingly effective approach to detect genomic regions of importance, illustrated on two Simmental cattle populations. Medium density genomic data of 42 German/Austrian (denoted as “Western“) and 38 Russian Simmental cattle were used to identify the most frequent haplotypes within the two populations. The haplotypes were defined as non-overlapping segments of ten single nucleotide ploymorphisms (SNP). The phasing was done with the SHAPEIT software, with a follow up analysis of haplotypes using the GHap package. Despite the low sample size a number of high frequency haplotypes could be identified across the whole genome. The identified genes residing directly in these high frequency haplotypes were extremely relevant for the dual purpose Simmental cattle. A large part of these genes influenced growth rate and carcass traits, others were relevant for the milk production. A smaller proportion was connected to the reproduction, immune system and cellular processes, with indirect influence on production traits