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

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

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

Genetic diversity in the Orenburg goat breed revealed by single-nucleotide polymorphism (SNP) analysis: Initial steps in saving a threatened population

Background/Objectives: For genomic selection to enhance the efficiency of broiler production, finding SNPs and candidate genes that define the manifestation of main selected traits is essential. We conducted a genome-wide association study (GWAS) for growth and meat productivity traits of roosters from a chicken F2 resource population (n = 152). Methods: The population was obtained by crossing two breeds with contrasting phenotypes for performance indicators, i.e., Russian White (slow-growing) and Cornish White (fast-growing). The birds were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. After LD filtering of the data, 54,188 SNPs were employed for the GWAS analysis that allowed us to reveal significant specific associations for phenotypic traits of interest and economic importance. Results: At the threshold value of p < 9.2 × 10−7, 83 SNPs associated with body weight at the age of 28, 42, and 63 days were identified, as well as 171 SNPs associated with meat qualities (average daily gain, slaughter yield, and dressed carcass weight and its components). Moreover, 34 SNPs were associated with a group of three or more traits, including 15 SNPs significant for a group of growth traits and 5 SNPs for a group of meat productivity indicators. Relevant to these detected SNPs, nine prioritized candidate genes associated with the studied traits were revealed, including WNT2, DEPTOR, PPA2, UNC80, DDX51, PAPPA, SSC4D, PTPRU, and TLK2. Conclusions: The found SNPs and candidate genes can serve as genetic markers for growth and meat performance characteristics in chicken breeding in order to achieve genetic improvement in broiler production

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667–248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication

Data from: Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)

Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographical pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor-Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population–TIK, and maximum values were observed in the most southern population–SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the late Pleistocene glaciations of Verkhoyansk Range

Complete mitochondrial genomes of Karchaev goat (Capra hircus)

Karachaev goat (Capra hircus) is a local breed from North-Caucasus region, Russia. Here we present complete mitochondrial genome of Karachaev goat from the republic of Karachaevo-Cherkessia, Russia. The length of the studied sequence was 16,624 bp in size. It was shown that the studied specimen belonged to haplogroup A

Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

BACKGROUND: The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references. RESULTS: The observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337–0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource. CONCLUSIONS: Whole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies

Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples

The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people\u27s pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs