Runs Of Homozygosity Research Articles

Genome-wide scan for selection signatures in Mexican Sardo Negro Zebu cattle.

The Sardo Negro cattle (SN) is the only zebu cattle breed developed in Mexico. Since its development, the selection could have led to an increase in the homozygosity level in some regions of the genome and made differentiation with other cattle populations. We aimed to identify and characterize selection signatures in SN using medium-density SNP data using four approaches: 1) Runs of homozygosity (ROH) 2) Nucleotide Diversity 3) Tajima's D and 4) the Wright's fixation index (FST). A sample of 555 SN animals genotyped for 65k SNPs was used to obtain ROH segments considered regions under selection. The FST values were estimated by comparing the sample of genotyped SN animals with samples of genotyped animals from the Gir, Brahman, and Ongole breeds. Only one region mapped to 35.78-42.51 Mb on BTA6 was considered a selection signature by the ROH method. This selection signature overlapped with the lowest diversity, negative values of Tajima's D and a diversification region between SN and the other Zebu breeds by FST. We found several candidate genes (LCORL, NCAPG, and SLIT2) related to growth and other economically important productive traits in this common region. Using the FST method, different regions, such as regions on BTA8 (8:93.4-93.9 Mb), BTA11 (11:99.2-99.7), and BTA14 (14: 26.1-26.8) related to growth and milk traits also were defined as candidate selection signatures. The selective signals identified in this study reflected the direction of the selection pressure that primarily involves the increase of live weight traits in the Sardo Negro cattle breeding program.

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.

Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact on ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, and with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.

Genetic Diversity in the Orenburg Goat Breed Revealed by Single-Nucleotide Polymorphism (SNP) Analysis: Initial Steps in Saving a Threatened Population

Background/Objectives: Orenburg goats are renowned for their soft down that acts as a substrate for warm clothing, particularly shawls that have an international reputation. As with many local livestock breeds, however, the Orenburg is presently at risk of extinction, an issue that can be addressed by assessing population genetic diversity and, thereafter, encouraging as much outbreeding as possible. Using single-nucleotide polymorphism (SNP)-based data, therefore, we analyzed the genetic diversity and population structure of modern Orenburg goats using samples collected from an expedition to Orenburg Oblast in 2024. Methods: We applied the Goat SNP50 BeadChip (Illumina, San Diego, CA, USA) for the genotyping of Orenburg goats from modern and archived populations. SNP genotypes of three Orenburg populations sampled in 2017 and 2019, Altai Mountain, Altai White, and Soviet Mohair breeds, were added to the dataset. Results: Principal component analysis and network and admixture analyses demonstrated that the genetic background inherent to the archived group of Orenburg goats was maintained in all modern populations. Values of genetic diversity indicators in modern populations were compatible with those obtained in comparison groups. Runs of homozygosity (ROH) were found in all the Orenburg goat populations (with a mean ROH length of 72.6–108.9 Mb and mean ROH number of 28–36). Genomic inbreeding based on ROH was low in all the Orenburg populations (FROH = 0.03–0.045). Conclusions: We showed that the ancestral background is retained in present-day Orenburg goats sampled in 2024. We provide the genetic basis through which certain breeder animals may be selected and bred traditionally or ex situ through a conservation program of gamete preservation.

Phylogenetic Relations and High-Altitude Adaptation in Wild Boar (Sus scrofa), Identified Using Genome-Wide Data.

The Qinghai-Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia, to explore their phylogenetic patterns and high-altitude adaptation based on genome-wide selection signal analysis and run of homozygosity (ROH) estimation. The findings demonstrate the alignment between the phylogenetic associations among wild boars and their geographical location. An ADMIXTURE analysis indicated a relatively close genetic relationship between QTP and southern Chinese wild boars. Analyses of the fixation index and cross-population extended haplotype homozygosity between populations revealed 295 candidate genes (CDGs) associated with high-altitude adaptation, such as TSC2, TELO2, SLC5A1, and SLC5A4. These CDGs were significantly overrepresented in pathways such as the mammalian target of rapamycin signaling and Fanconi anemia pathways. In addition, 39 ROH islands and numerous selective CDGs (e.g., SLC5A1, SLC5A4, and VCP), which are implicated in glucose metabolism and mitochondrial function, were discovered in QTP wild boars. This study not only assessed the phylogenetic history of QTP wild boars but also advanced our comprehension of the genetic mechanisms underlying the adaptation of wild boars to high altitudes.

Analysis of genetic evolutionary differences among four Tibetan pig populations in China

Tibetan pigs are a locally bred domestic pig breed originating from the Tibetan Plateau in China. They can be categorized into four distinct groups based on their geographical locations: Sichuan Tibetan pigs, Tibetan pigs from Tibet, Yunnan Tibetan pigs, and Gansu Tibetan pigs. This study aimed to explore population diversity, genetic structure and selection signals among Tibetan pigs in four Chinese national nature reserves. The results show that there is different observed heterozygosity among Tibetan pig populations (0.1957–0.1978). Ratio of runs of homozygosity (Froh) calculation of four Tibetan pig populations by runs of homozygosity (ROH) revealed the presence of inbreeding within the population (0.0336–0.0378). Analysis of the genetic structure demonstrated distinct population stratification among the four Tibetan pig populations, with each showing relatively independent evolutionary directions. Furthermore, Five methods (FST, Piratio, ROD, Tajima's D, XP-CLR) were used to artificially select evolutionary trajectories. The results mainly involved processes such as DNA repair, immune regulation, muscle fat deposition and adaptation to hypoxia. In conclusion, this study enhances our understanding of the genetic characteristics of Tibetan pig populations and provides a theoretical reference for the conservation of resources across different populations of Tibetan pigs.

A Novel Homozygous Variant in CPLANE1 Gene in a Patient with Developmental Deficits

Background: Oral-facial-digital syndrome (OFDS) type 6 is a rare subtype of Joubert syndrome characterized by orofacial anomalies and polydactyly with neurological features of Joubert syndrome. This rare syndrome is divided into thirteen subtypes, all of which demonstrate autosomal recessive inheritance, except for OFDS type 1 which demonstrates X-linked dominant inheritance. Case Presentation: A 19-year-old man with mild developmental delay was brought to a rural community clinic, as he had become irritable and angry, in the recent past. There was no history of prior medical conditions. In view of orofacial anomalies, and developmental deficits, a genetic analysis was requested. Karyotype analysis revealed a normal male karyotype (46,XY) in all 30 metaphase spreads analyzed. No numerical or structural chromosomal abnormalities were observed. Clinical exome sequencing and chromosomal microarray detected a variant of uncertain significance in exon 5 of CPLANE1 gene c.365T>G (p.Val122Gly) leading to substitution of Glycine for Valine. This was confirmed by Sanger sequencing. Parents were heterozygous, and the unaffected sibling was homozygous for the wild-type allele. This variant has not been reported earlier in the mutation databases or gnomAD. Runs of homozygosity (ROH) analysis showed a 3.2 Mb ROH around the CPLANE1 gene in the proband, which was absent in both parents and the unaffected sibling. Conclusion: We find a novel homozygous mutation in the CPLANE1 gene in a patient of non-consanguineous parentage with atypical orofacial features. This suggests that potentially deleterious, rare variants may occur in the heterozygous state in the population. Hence, sequencing of population samples might help understand the genetic epidemiology of rare syndromes.

Genomic Sequencing to Detect Cross-Breeding Quality in Dogs: An Example Studying Disorders in Sexual Development.

Disorders of sexual development (DSDs) in dogs, similar to humans, arise from genetic mutations, gonadal differentiation, or phenotypic sex development. The French Bulldog, a breed that has seen a surge in popularity and demand, has also shown a marked increase in DSD incidence. This study aims to characterize the genetic underpinnings of DSDs in a French Bulldog named Brutus, exhibiting ambiguous genitalia and internal sexual anatomy, and to explore the impact of breeding practices on genetic diversity within the breed. We utilized a comprehensive approach combining conventional cytogenetics, molecular techniques, and deep sequencing to investigate the genetic profile of Brutus. The sequence data were compared to three other male French Bulldogs' genome sequences with typical reproductive anatomy, including Brutus's father and the canine reference genome (CanFam6). We found a Robertsonian fusion involving chromosome 23 previously reported in dogs as a causative mutation responsible for sex reversal syndrome. Our findings revealed a 22% mosaicism (78,XX/77,XX), the absence of the sex-determining region (SRY) gene, and the presence of 43 unique Single Nucleotide Variants (SNVs) not inherited from the father. Notably, the run of homozygosity (ROH) analysis showed Brutus has a higher number of homozygous segments compared to other Bulldogs, with a total length of these fragments 50% greater than the average, strongly suggesting this dog is the product of the mating between siblings. Although no direct causative genes for the DSD phenotype were identified, four candidate loci warrant further investigation. Our study highlighted the need for a better annotated and curated reference dog genome to define genes causative of any specific phenotype, suggests a potential genetic basis for the DSD phenotype in dogs, and underscores the consequences of uncontrolled breeding practices in French Bulldogs. These findings highlight the importance of implementing strategic genetic management to preserve genetic health and diversity in canine populations.

Runs of Homozygosity Decipher Genetic Diversity in Cattle Breed Dwelling in the Colder Regions of the World

Background: Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs of homozygosity (ROHs). Yakutian cattle are adapted to Siberia’s harsh sub-arctic conditions, enduring temperatures below −70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in these cattle. Results: We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057, as compared to other breeds. Also, the different diversity indicators, namely, principal component analysis, heterozygosity, and effective population size analysis, revealed the prevalence of genetic diversity within the breed. Conclusion: Our findings on ROH are the first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity.

Whole genomes from the extinct Xerces Blue butterfly can help identify declining insect species

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80- to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue (Glaucopsyche lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (Glaucopsyche alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the former were significantly greater than in the later, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.

Whole genomes from the extinct Xerces Blue butterfly can help identify declining insect species.

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80- to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue (Glaucopsyche lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (Glaucopsyche alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the former were significantly greater than in the later, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.

Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations

Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5–5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P < 0.001), more total variants (P < 0.001), and lower individual inbreeding (FROH; P < 0.001) than horses in Group 2. However, the distribution of numbers of variants, allele frequency, and extent of ROH overlapped among all horses such that it was not possible to identify the group of origin of any single horse using these measures. Consequently, the Thoroughbred population would be better monitored by investigating changes in specific variants, rather than relying on broad measures of diversity. The WGS for these 185 horses is publicly available for comparison to other populations and as a foundation for modeling changes in population structure, breeding practices, or the appearance of deleterious variants.

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip.

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.

Whole-genome re-sequencing reveals genetic structure and selection signals of different populations in Megalobrama amblycephala

Characterization of genetic variants is crucial for understanding the molecular mechanisms behind selected traits and enhancing the rate of genetic gain through artificial selection. This study explored the genetic diversity and population structure of blunt snout bream Megalobrama amblycephala, a key freshwater fish in Chinese aquaculture. We conducted whole-genome re-sequencing of individuals from six populations, comprising three natural and three genetically improved strains, to assess genetic diversity, population structure and the impacts of selective breeding. We identified 17,009,590 high-quality biallelic single nucleotide polymorphism (SNP) loci. Genetic diversity assessments revealed low levels of polymorphism across populations, with genetically improved strains showing moderate to high genetic differentiation from their source populations. The study also highlighted runs of homozygosity (ROH) and analyzed linkage disequilibrium (LD) decay, indicating minimal recent inbreeding and diverse recombination events among populations. Selective sweep analyses uncovered significant selection loci associated with growth and hypoxia tolerance traits. Enrichment analyses identified genes involved in olfactory signal transduction, immune response, and metabolism pathways, which are closely related to these selective traits. These findings offer insights into the genetic basis of critical traits in M. amblycephala, contributing to the conservation of germplasm resources and supporting ongoing selective breeding efforts.

Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data.

Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found C. hyemalis to show more historical demographic stability, whereas M. fusca was affected particularly by the Last (Weichselian) Glaciation. This likely reflects C. hyemalis breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of M. fusca would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with F ROH from 0.012 to 0.063 in C. hyemalis and ranging from 0 to 0.047 in M. fusca. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.

Genetic Diversity, Selection Signatures, and Genome-Wide Association Study Identify Candidate Genes Related to Litter Size in Hu Sheep.

Hu sheep is a renowned prolific local sheep breed in China, widely distributed across the country due to its excellent reproductive performance. Deciphering the molecular mechanisms underlying the high fecundity of Hu sheep is crucial for improving the litter size of ewes. In this study, we genotyped 830 female Hu sheep using the Illumina OvineSNP50 BeadChip and performed genetic diversity analysis, selection signature detection, and a genome-wide association study (GWAS) for litter size. Our results revealed that the Hu sheep population exhibits relatively high genetic diversity. A total of 4927 runs of homozygosity (ROH) segments were detected, with the majority (74.73%) being short in length. Different genomic inbreeding coefficients (FROH, FHOM, FGRM, and FUNI) ranged from -0.0060 to 0.0126, showing low levels of inbreeding in this population. Additionally, we identified 91 candidate genomic regions through three complementary selection signature methods, including ROH, composite likelihood ratio (CLR), and integrated haplotype score (iHS), and annotated 189 protein-coding genes. Moreover, we observed two significant SNPs related to the litter size of Hu sheep using GWAS analysis based on a repeatability model. Integrating the selection signatures and the GWAS results, we identified 15 candidate genes associated with litter size, among which BMPR1B and UNC5C were particularly noteworthy. These findings provide valuable insights for improving the reproductive performance and breeding of high-fecundity lines of Hu sheep.

Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness.

This study investigates the genomic landscape of Sika deer populations, emphasizing the detection and characterization of runs of homozygosity (ROH) and their contribution towards components of fitness. Using 85,001 high-confidence SNPs, the investigation into ROH distribution unveiled nuanced patterns of autozygosity across individuals especially in 2 out of the 8 farms, exhibiting elevated ROH levels and mean genome coverage under ROH segments. The prevalence of shorter ROH segments (0.5-4Mb) suggests historical relatedness and potential selective pressures within these populations. Intriguingly, despite observed variations in ROH profiles, the overall genomic inbreeding coefficient (FROH) remained relatively low across all farms, indicating a discernible degree of genetic exchange and effective mitigation of inbreeding within the studied Sika deer populations. Consensus ROH (cROH) were found to harbor genes for important functions viz., EGFLAM gene which is involved in the vision function of the eye, SKP2 gene which regulates cell cycle, CAPSL involved in adipogenesis, SPEF2 which is essential for sperm flagellar assembly, DCLK3 involved in the heat stress. This first ever study on ROH in Sika deer, to shed light on the adaptive role of genes in these homozygous regions. The insights garnered from this study have broader implications in the management of genetic diversity in this vulnerable species.

The last days of Aporia crataegi (L.) in Britain: Evaluating genomic erosion in an extirpated butterfly.

Current rates of habitat degradation and climate change are causing unprecedented declines in global biodiversity. Studies on vertebrates highlight how conservation genomics can be effective in identifying and managing threatened populations, but it is unclear how vertebrate-derived metrics of genomic erosion translate to invertebrates, with their markedly different population sizes and life histories. The Black-veined White butterfly (Aporia crataegi) was extirpated from Britain in the 1920s. Here, we sequenced historical DNA from 17 specimens collected between 1854 and 1924 to reconstruct demography and compare levels of genomic erosion between extirpated British and extant European mainland populations. We contrast these results using modern samples of the Common Blue butterfly (Polyommatus icarus); a species with relatively stable demographic trends in Great Britain. We provide evidence for bottlenecks in both these species around the period of post-glacial colonization of the British Isles. Our results reveal different demographic histories and Ne for both species, consistent with their fates in Britain, likely driven by differences in life history, ecology and genome size. Despite a difference, by an order of magnitude, in historical effective population sizes (Ne), reduction in genome-wide heterozygosity in A. crataegi was comparable to that in P. icarus. Symptomatic of A. crataegi's disappearance were marked increases in runs-of-homozygosity (RoH), potentially indicative of recent inbreeding, and accumulation of putatively mildly and weakly deleterious variants. Our results provide a rare glimpse of genomic erosion in a regionally extinct insect and support the potential use of genomic erosion metrics in identifying invertebrate populations or species in decline.

Genome-Wide Selection Sweep Analysis to Identify Candidate Genes with Black and Brown Color in Tibetan Sibu Yaks.

Although coat color is an important economic phenotype in domesticated yaks (Bos grunniens), its genetic basis is not yet fully understood. In this study, a genome-wide selective sweep and high-frequency runs of homozygosity (ROH) identification were performed on 50 yaks with different coat colors to investigate candidate genes (CDGs) related to coat color. The results suggested that 2263 CDGs were identified from the 5% interaction windows of the FST and θπ ratio, along with 2801 and 2834 CDGs from black and brown yaks with iHS, respectively. Furthermore, 648 and 691 CDGs from black and brown yaks, which were widely enriched in pathways related to melanogenesis, melanocyte differentiation, and melanosome organization via GO and KEGG functional enrichment, respectively, were confirmed on the basis of the intersection of three parameters. Additionally, the genome of brown yaks presented more ROH, longer ROH fragments, and higher inbreeding levels than those of black yaks. Specifically, a large number of genes related to melanin synthesis and regulation (e.g., UST, TCF25, and AHRR) from the ROH islands were confirmed to be under strong selection. In summary, the results of this study enhance the understanding of the genetic basis for determining yak coat color.

Genomic characterisation and diversity assessment of eight endangered Belgian sheep breeds

Assessing the genetic diversity of local breeds is essential for conserving these unique breeds, which may possess unique traits. This study provides the genomic characterisation of eight indigenous sheep breeds in Belgium based on pedigree and single nucleotide polymorphism (SNP) analysis. A total of 687 sheep were genotyped and were subjected to a rigorous quality control, resulting in a set of 45 978 autosomal SNPs. Pedigree analysis showed breed-average inbreeding estimates between 3.3% and 11.3%. The genomic analysis included an assessment of runs of homozygosity (ROH) to examine the genomic inbreeding coefficient, with breed-average inbreeding coefficients estimated between 4.1% and 8.5%. Runs of homozygosity islands were identified in six of the eight breeds studied, with some exhibiting an incidence of up to 58%. Interestingly, several ROH islands overlapped with other breeds included in this study, as well as with international sheep breeds. Pedigree-based effective population sizes were estimated below 100 for all breeds, whereas genomic-based effective population sizes were below 24, indicating that these eight local sheep breeds are endangered. Principal component analysis, admixture analyses, and Fst computations were used to study the population structure and genetic differences. A neighbour−joining tree using 95 international sheep breeds positioned the eight local breeds in the group of milksheep, Texel sheep and the Scandinavian breeds. Additionally, the investigation of paternal oY1 genotypes revealed diverse lineage origins within the Belgian sheep population. This study refines and deepens our knowledge about the local sheep breeds in Belgium, thereby improving their management and conservation. Moreover, as these breeds are linked to other international breeds, these insights are significant for the global scientific community.