Runs of homozygosity: current knowledge and applications in livestock

Selection signatures and inbreeding: exploring genetic diversity in five native horse breeds

Horses have undergone extensive natural and artificial selection, shaping the diversity of breeds observed today. Native Italian breeds present unique traits influenced by natural selection, such as adaptation to harsh climates, or hoof strength, but face challenges due to population declines and the reduction of their original breeding purpose. This study focuses on five local Italian breeds: Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse, to understand how selection has shaped their populations. A total of 1620 individuals were genotyped with a medium-density SNP chip and remapped to EquCab3. After quality control, where data were filtered based on missing genotypes per SNP (> 0.10) and missing SNPs per sample (> 0.10), 1498 horses and 54,825 SNPs remained for analysis. Population structure and runs of homozygosity (ROH) were identified, and genomic inbreeding coefficients were calculated based on ROH coverage of autosomal SNPs. ROH islands shared by ≥ 70% of horses were identified as selection signatures, and candidate genes within these regions were annotated. The inbreeding coefficient (FROH) ranged from 0.15 to 0.23, with Bardigiano and Haflinger showing the highest values probably due to selective breeding, while Maremmano, Murgese, and Italian Heavy Draught Horse displayed lower FROH, reflecting a broader diversity. ROH islands were identified on 12 chromosomes, with 23 islands distributed among breeds. Cold-blooded breeds (Bardigiano, Haflinger, and Italian Heavy Draught Horse) showed the majority, particularly on Equine Chromosome 3 (ECA3). These islands overlapped with 83 quantitative trait loci (QTLs) and 76 genes associated with morphology and health. Health-related traits such as osteochondrosis and hoof health were linked to ROH patterns, particularly in Bardigiano and Haflinger, highlighting selection for disease resistance. Signature of selections were found in the proximity of MC1R and ASIP genes likely due to their role for coat color; especially in the Haflinger and Italian Heavy Draught Horse the genotype frequency of the BIEC2_816499 SNP which is in the vicinity of the causative mutation for chestnut coat color is due to linkage disequilibrium between the two. In conclusion, this study offered valuable insights that breeders could utilize to make sound decisions. This issue would ensure the maintenance of breed genetic diversity, and the preservation and improvement of the breed's distinct traits and health standards.

Distribution of runs of homozygosity in Lactuca species and its implications for plant breeding and evolutionary conservation

Runs of homozygosity (ROH) have been extensively investigated to uncover the genomic inbred regions that reflect past population and breeding histories. In this study, we have explored the distribution and number of ROH in different Lactuca species including the cultivated lettuce varieties and their wild relatives. Next generation sequencing (NGS) technology provides the unique opportunity to study the genomes with resolution up to per-base-pair and we could compute ROH in the highest accuracy using NGS data. Our study reveals that Lactuca sativa has the longest average ROH length and fewest number of ROHs, while wild species show shorter, more numerous ROHs as expected. We found that these cultivated varieties exhibit relatively stable number of ROH and ROH lengths, with the largest median ROH count observed in Oilseed and the largest average ROH length in Crisphead. There is a significant proportion of medium-length ROHs (100 kb-1 Mb) enriched in L. sativa and L. serriola, with the highest number observed in L. serriola, while L. saligna has more short ROHs (< 10 KB), and the highest number of ROHs in the 10 KB-100 KB range were observed in Butterhead, with Stalk and Oilseed showing fewer and shorter ROHs overall. It suggests that Stalk and Oilseed were still in a process of breeding. The comparison between PLINK computation and our developed in-house algorithm shows that PLINK tends to detect longer ROH, whereas our algorithm adopts a more conservative approach, resulting in fewer and shorter ROH segments detected with higher precision more suitable for NGS data. We further analyze the distribution of ROH hotspots with a higher frequency occurred across cultivated species genomes, which has identified key genes such as DREB2B, NHL12, RPV1, and EIX2, which play crucial roles in plant stress tolerance and immune responses, enhancing adaptability to extreme environments and providing resistance to various diseases. These findings provide fresh scientific insights into lettuce breeding, germplasm conservation, and sustainable production, highlighting the importance of understanding and managing genetic diversity in global agricultural practices.

A genomic tale of inbreeding in western Mediterranean human populations

Consanguineous marriages are common in many worldwide human populations, and the biological consequences for offspring can be relevant at the biomedical level. The current genomic revolution displayed through genome-wide studies is challenging the paradigm in the analysis of consanguinity. Here, we analyzed genomic inbreeding patterns in human populations located at the western edge of the Mediterranean region (Iberia and Morocco). Runs of Homozygosity (ROH) (autozygosity fragments) were identified in 139 autochthonous individuals originating from southern Iberia and Morocco via microarray data. All individuals analyzed carried at least one ROH in their genomes. The genomic inbreeding coefficient (FROH) and the presence of ROH islands (ROHi) revealed interesting patterns in the target populations as well as in the rest of the Mediterranean basin. Moroccan Berbers presented signals of recent inbreeding, relying on high coverage of long ROH (> 5 Mb) and FROH. The location and structure of ROHi among people in the western Mediterranean could be interpreted as a signature of common genetic links across the Strait of Gibraltar. We found a significant enrichment of some relevant biological functions in the estimated ROHi hotspots associated with the immune system and chemosensation. Genomic inbreeding approaches allow us to understand past population histories and can be used as a proxy to scan the genome in search of selection signals.

Whole-genome sequencing reveals patterns of runs of homozygosity underlying genetic diversity and selection in domestic rabbits

BACKGROUND

Runs of homozygosity (ROH) are continuous segments of homozygous genotypes inherited from both parental lineages. These segments arise due to the transmission of identical haplotypes. The genome-wide patterns and hotspot regions of ROH provide valuable insights into genetic diversity, demographic history, and selection trends. In this study, we analyzed whole-genome resequencing data from 117 rabbits to identify ROH patterns and inbreeding level across eleven rabbit breeds, including seven Chinese indigenous breeds and four exotic breeds, and to uncover selective signatures based on ROH islands.

RESULTS

We detected a total of 31,429 ROHs across the autosomes of all breeds, with the number of ROHs (NROH) per breed ranging from 1316 to 7476. The mean sum of ROHs length (SROH) per individual was 493.84 Mb, covering approximately 22.79% of the rabbit autosomal genome. The majority of the detected ROHs ranged from 1 to 2 Mb in length, with an average ROH length (LROH) of 1.84 Mb. ROHs longer than 6 Mb constituted only 0.83% of the detected ROHs. The average inbreeding coefficient derived from ROHs (FROH) was 0.23, with FROH values ranging from 0.14 to 0.38 across breeds. Among Chinese indigenous breeds, the Jiuyishan rabbit exhibited the highest values of NROH, SROH, LROH, and FROH, whereas the Fujian Yellow rabbit had the lowest FROH values. In exotic rabbit breeds, the Japanese White rabbit displayed the highest values for NROH, SROH, LROH, and FROH, while the Flemish Giant rabbit had the lowest values for these metrics. Additionally, we identified 17 ROH islands in Chinese indigenous breeds and 22 ROH islands in exotic rabbit breeds, encompassing 124 and 186 genes, respectively. In Chinese indigenous breeds, we identified prominent genes associated with reproduction, including CFAP206, RNF133, CPNE4, ASTE1, and ATP2C1, as well as genes related to adaptation, namely CADPS2, FEZF1, and EPHA7. In contrast, the exotic breeds exhibited a prevalence of genes associated with fat deposition, such as ELOVL3 and NPM3, as well as growth and body weight related genes, including FAM184B, NSMCE2, and TWNK.

CONCLUSIONS

This study enhances our understanding of genetic diversity and selection pressures in domestic rabbits, offering valuable implications for breeding management and conservation strategies.

Visualization of Runs of Homozygosity and Classification Using Convolutional Neural Networks

Runs of homozygosity (ROH) are key elements of the genetic structure of populations, reflecting inbreeding levels, selection history, and potential associations with phenotypic traits. This study proposes a novel approach to ROH analysis through visualization and classification using convolutional neural networks (CNNs). Genetic data from Large White (n = 568) and Duroc (n = 600) pigs were used to construct ROH maps, where each homozygous segment was classified by length and visualized as a color-coded image. The analysis was conducted in two stages: (1) classification of animals by breed based on ROH maps and (2) identification of the presence or absence of a phenotypic trait (limb defects). Genotyping was performed using the GeneSeek® GGP SNP80x1_XT chip (Illumina Inc., San Diego, CA, USA), and ROH segments were identified using the software tool PLINK v1.9. To visualize individual maps, we utilized a modified function from the HandyCNV package. The results showed that the CNN model achieved 100% accuracy, sensitivity, and specificity in classifying pig breeds based on ROH maps. When analyzing the binary trait (presence or absence of limb defects), the model demonstrated an accuracy of 78.57%. Despite the moderate accuracy in predicting the phenotypic trait, the high negative predictive value (84.62%) indicates the model's reliability in identifying healthy animals. This method can be applied not only in animal breeding research but also in medicine to study the association between ROH and hereditary diseases. Future plans include expanding the method to other types of genetic data and developing mechanisms to improve the interpretability of deep learning models.

Uncovering genomic diversity and signatures of selection in red Angus × Chinese red steppe crossbred cattle population

Crossbreeding is a cornerstone of modern livestock improvement, combining desirable traits to enhance productivity and environmental resilience. This study conducts the first comprehensive genomic analysis of Red Angus × Chinese Red Steppe (RACS) crossbred cattle, evaluating their genetic architecture, diversity, and selection signatures relative to founder breeds (Red Angus and Chinese Red Steppe) and global populations. A total of 119 cattle, comprising 104 RACS crossbreds and 15 Chinese Red Steppes cattle, were genotyped using the GGP Bovine 100k SNP array. Additionally, the public available genotypic data generated using the BovineSNP50 chip from 550 animals across eight beef breeds (Angus, Hereford, Limousin, Charolais, Mongolian, Shorthorn, Red Angus, and Simmental) and one dairy breed (Holstein) were incorporated into the analysis. We aimed to (1) define the population structure of RACS cattle, (2) quantify their genomic diversity and inbreeding levels, and (3) pinpoint regions under selection linked to adaptive and economic traits. We employed runs of homozygosity (ROH) and population differentiation (Fst) analyses to detect selection signals. The results revealed that the crossbred (RACS), Angus, and Red Angus breeds exhibited similar clustering patterns in principal component analysis (PCA), but the crossbred population showed the highest nucleotide diversity and lowest inbreeding coefficients compared to other breeds. Notably, candidate regions associated with immune response, cold adaptation, and carcass traits were identified within the RACS population. These findings enhance our understanding of the genetic makeup of crossbred beef cattle and highlight their potential for genetic improvement, informing future selection and breeding strategies aimed at optimizing beef production in challenging environments.

Population structure of Santa Inês sheep: the impact of genomic information

Information on genetic diversity and population structure among sheep breeds is essential for genetic improvement, understanding environmental adaptation, as well as the utilization and conservation of sheep breeds. This research aims to analyze the genomic population structure of Santa Inês sheep managed on different properties in northeastern Brazil. A total of 390 individuals were genotyped for 52,744 SNPs. The six flocks evaluated showed population differentiation indices (pairwise Fst) ranging from 0.0342 to 0.0938. Estimates of gene flow showed high values, ranging from 0.89 to 1 (Nm) between flocks 2 and 3, which are from the same town. The average value for inbreeding (Fis) and the overall genetic differentiation index (Fst) were -0.05 and 0.06 respectively, observed in the F statistic for each of the loci analyzed in the six flocks. These results indicate that diversity is concentrated within populations. After the simulations using the Bayesian clustering method, the most probable number of genetic groups (K) detected was 5, where flock 4 and 6 form a single group. It can be concluded that the samples from the six flocks form five genetic populations with a level of diversity that has been conserved. The results of this study can contribute with important genetic information and can adequately help diversity within the breed, which provides a good opportunity for the sustainable use and maintenance of improvements in genetic resources in Santa Inês sheep populations in Brazil.

Genomic insights into racing camels: inbreeding levels and positive selection linked to athletic traits

Racing dromedary camels are widely distributed across the Arabian Peninsula, predominantly concentrating in its northern and southeastern regions. Phenotypically, they are differentiated from other dromedary types, characterised by their smaller body size, longer limbs, reduced hump size, and thinner chest girth. In this study, the whole genome sequences of 34 racing camels were analysed to assess their genetic relationship with non-racing populations, estimate levels of inbreeding, calculate Wier and Cockerham's fixation index (Fst), assess effective population size (Ne), and identify candidate regions with signatures of positive selection. Both racing and non-racing camels exhibited comparable levels of genomic inbreeding (FROH = 0.21), with no significant genetic differentiation detected between them. The estimated Fst value between the two camel groups also revealed minimal genetic differentiation. A declining trend was observed in Ne estimations of both groups over the past 5 000 years, with slightly lower recent Ne in racing camels compared to their non-racing counterparts. Signatures of positive selection in the genomes of racing camels were identified through the application of two haplotype-based statistics, namely the integrated haplotype homozygosity score (iHS) and extended haplotype homozygosity between-populations (Rsb), along with runs of homozygosity (ROH) analysis. A total of 33 regions under selection were detected via iHS, 19 via Rsb, and 24 through ROH. Candidate regions under selection were found to overlap with genes involved in diverse biological pathways potentially linked to athletic performance, e.g., musculoskeletal development, lipid metabolism, stress response, bone integrity, as well as endurance and power. These findings provide a foundation for further exploration of the racing dromedary genome, with the goal of defining variants and haplotypes that might be associated with athletic traits. Such insights could assist the development of genetically informed breeding programmes aimed at developing specialised racing dromedary lines, contributing to the broader understanding and preservation of animal athletic performance and selection in domesticated species worldwide.

Runs of Homozygosity Preliminary Investigation in Pig Breeds

Runs of homozygosity (ROH) are contiguous homozygous genomic segments that provide valuable insights into population history, selection pressures, and inbreeding levels. However, the global distribution of ROH and their implications for pig domestication and breeding are not yet fully understood. In this study, we analyzed whole-genome resequencing data from 1203 pigs across 49 breeds to characterize ROH patterns worldwide. European commercial pigs exhibited longer and more numerous ROH segments than Asian indigenous breeds, indicative of stronger artificial selection and higher inbreeding. Crossbreeding led to a reduction in ROH burden, with greater reductions observed when parental genetic divergence was larger. Notably, Asian and European pigs displayed distinct ROH islands, reflecting divergent selection pressures. Functional analysis revealed that these ROH islands were associated with growth, immunity, and reproduction. These findings enhance our understanding of the genetic diversity and selection history of global pig populations, providing valuable insights for future breeding strategies.

Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse

BACKGROUND/OBJECTIVES

The Rhenish German draught horse is an endangered German horse breed, originally used as working horse in agriculture. Therefore, the objective of this study was to evaluate the breed's genetic diversity using pedigree and genomic data in order to analyze classical and ancestral pedigree-based inbreeding, runs of homozygosity, ROH islands, and consensus ROH.

METHODS

We studied the genome-wide genotype data of 675 Rhenish German draught horses and collated pedigree-based inbreeding coefficients for these horses. The final dataset contained 64,737 autosomal SNPs.

RESULTS

The average number of ROH per individual was 43.17 ± 9.459 with an average ROH length of 5.087 Mb ± 1.03 Mb. The average genomic inbreeding coefficient FROH was 0.099 ± 0.03, the pedigree-based classical inbreeding coefficient FPED 0.016 ± 0.021, and ancestral inbreeding coefficients ranged from 0.03 (Fa_Kal) to 0.51 (Ahc). Most ROH (55.85%) were classified into the length category of 2-4 Mb, and the minority (0.43%) into the length category of >32 Mb. The effective population size (Ne) decreased in the last seven generations (~65 years) from 189.43 to 58.55. Consensus ROH shared by 45% of the horses were located on equine chromosomes 3 and 7, while ROH islands exceeding the 99th percentile threshold were identified on chromosomes 2, 3, 5, 7, 9, 10, and 11. These ROH islands contained genes associated with morphological development (HOXB cluster), fertility (AURKC, NLRP5, and DLX3), muscle growth, and skin physiology (ZNF gene cluster).

CONCLUSIONS

This study highlights how important it is to monitor genetic diversity in endangered populations with genomic data. The results of this study will help to develop breeding strategies to ensure the conservation of the German Rhenish draught horse population and show whether favorable alleles from the overrepresented candidate genes within ROH were transmitted to the next generation.

Genome-Wide Runs of Homozygosity Reveal Inbreeding Levels and Trait-Associated Candidate Genes in Diverse Sheep Breeds

BACKGROUND

Quantifying and controlling the inbreeding level in livestock populations is crucial for the long-term sustainability of animal husbandry. However, the extent of inbreeding has not been fully understood in sheep populations on a global scale.

METHODS

Here, we analyzed high-depth genomes of 210 sheep from 20 worldwide breeds to identify the pattern and distribution of genome-wide runs of homozygosity (ROH) and detect candidate selected genes in ROH islands for agronomic and phenotypic traits.

RESULTS

Leveraging whole-genome sequencing data, we found a large number of short ROH (e.g., <1.0 Mb) in all breeds and observed the overall higher values of ROH statistics and inbreeding coefficient in European breeds than in Asian breeds and Dorper sheep. We identified some well-known candidate genes (e.g., CAMK4, HOXA gene family, ALOX12, FGF11, and MTOR) and 40 novel genes (e.g., KLHL1, FGFRL1, WDR62, GDF6, KHDRBS2, and PAX1) that are functionally associated with fecundity, body size, and wool-related traits in sheep. Based on the candidate genes, we revealed different genetic bases for the fecundity traits of European and Asian sheep.

CONCLUSIONS

This study improves the resolution of ROH detection and provides new insights into genomic inbreeding and trait architecture in sheep as well as useful markers for future breeding practice.

Genome-wide landscape of genetic diversity, runs of homozygosity, and runs of heterozygosity in five Alpine and Mediterranean goat breeds

BACKGROUND

Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments. Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity, especially as we are facing important climate and agriculture challenges. To this aim the genomic architecture of 480 goats belonging to five breeds (i.e., Saanen [SAA], Camosciata delle Alpi [CAM], Murciano-Granadina [MUR], Maltese [MAL], Sarda [SAR]) reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits. Inbreeding, runs of homozygosity (ROH) and runs of heterozygosity (ROHet) were identified. Finally, candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.

RESULTS

In total, we detected 10,341 ROH in the SAA genome, 11,063 ROH in the CAM genome, 12,250 ROH in the MUR genome, 8,939 ROH in the MAL genome, and 18,441 ROH in the SAR genome. Moreover, we identified 4,087 ROHet for SAA, 3,360 for CAM, 2,927 for MUR, 3,701 for MAL, and 3,576 for SAR, with SAR having the highest heterozygosity coefficient. Interestingly, when computing the inbreeding coefficient using homozygous segment (FROH), SAA showed the lowest value while MAL the highest one, suggesting the need to improve selecting strategies to preserve genetic diversity within the population. Among the most significant candidate genes, we identified several ones linked to different physiological functions, such as milk production (e.g., DGAT1, B4GALT1), immunity (GABARAP, GPS2) and adaptation to environment (e.g., GJA3, GJB2 and GJB6).

CONCLUSIONS

This study highlighted the genetic diversity within and among five goat breeds. The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation, which might negatively impact the animal population. Conversely, high levels of ROHet might indicate regions of the genetic diversity, beneficial for breed health and resilience. Therefore, these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.

Integration of whole genome resequencing and transcriptome sequencing to identify candidate genes for tall and short traits in Baicheng Fatty chickens

The tall and short traits of chickens are significant indicators for evaluating their growth and development. Tall chickens have longer growth cycles, allowing them to accumulate sufficient nutrients and resulting in superior meat quality. This study aims to investigate the tall and short traits of Baicheng Fatty chickens and to identify relevant candidate genes. A total of 25 Baicheng Fatty chickens were selected for this research, where whole genome resequencing was performed on all samples to uncover genetic variations influencing tall and short traits. Additionally, transcriptome sequencing was conducted on 15 of these chickens to identify important genes affecting these traits through combined analysis. Using methods such as population genetic structure analysis, principal component analysis (PCA), linkage disequilibrium analysis (LD), runs of homozygosity (ROH) analysis, as well as genetic differentiation index (FST ) and nucleotide diversity (θπ), a total of 1,019 candidate genes were identified through whole genome resequencing analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on these candidates. From the transcriptome data, 253 differentially expressed genes (DEGs) were identified, including 229 upregulated and 24 downregulated genes. GO and KEGG enrichment analyses were conducted on these differential genes, and a protein-protein interaction network for the DEGs was constructed. Through the combined analysis of whole genome resequencing and transcriptome data, six intersecting genes were identified: KLF15, NRXN1, LOC107050638, MHCY11, HAO1, and BORCS6. KEGG enrichment analysis revealed significant involvement in the Glyoxylate and Dicarboxylate Metabolism pathway, Peroxisome pathway, Carbon Metabolism, and Cell Adhesion Molecules (CAMs) pathway. These genes may influence the growth and developmental patterns of skeletal structures, though their regulatory mechanisms require further investigation. This study provides new insights for further research into the genetic mechanisms underlying chicken skeletal development and growth, as well as potential molecular markers for poultry breeding.

Genome-wide insights into selection signatures for transcription factor binding sites in cattle ROH regions

Runs of Homozygosity (ROH) regions are characterized by homozygous genotypes inherited from a common ancestor, often arising from positive selection for adaptive traits. These homozygous regions may arise due to inbreeding, selective breeding, or demographic events like population bottlenecks. Transcription factor binding sites (TFBS) are short, specific DNA sequences where transcription factors bind to regulate the expression of nearby genes. These sites are essential for controlling biological processes such as development, metabolism, and immune response. TFBS act as key regulatory elements, and their variations can influence gene activity, contributing to phenotypic differences and adaptation. ROH often encompass regulatory elements, including TFBS, suggesting a functional connection between these genomic features. This study investigates TFBS within ROH regions in 297 animals of six cattle breeds: Gir (48), Tharparkar (72), Vrindavani (72), Frieswal (14), Holstein Friesian (63), and Jersey (28). Utilizing genotyped data of these animals, we identified genomic regions enriched with ROH. We focused on the central 10 kb regions of 50 ROH regions common across all breeds. Within these regions, 450 motifs were examined, identifying 168 transcription factors potentially binding to these regions. The results emphasize the role of TFBS in gene regulation and adaptive processes. By linking ROH patterns to regulatory elements, this study enhances our understanding of the genetic architecture underlying phenotypic traits and their adaptation to environmental pressures. These findings provide insights into the molecular mechanisms influencing genetic variation in cattle populations.

Identification of selection signatures and genetic diversity in the sheep

In the study, data obtained from OvineSNP50K SNP chips using the Illumina® iScan platform for Eşme sheep were used. The integrated haplotype score (iHS) and runs of homozygosity (ROH) statistical approaches were used to identify selection signatures. Using the iHS analysis, it was discovered that there are 10 genomic regions and 51 genes on ovine chromosomes 1, 9, 11, and 12 that are under selection. Three genomic regions and 97 genes on ovine chromosomes 6 and 11 were found to be under selection using the ROH analysis. Candidate genes associated with economic and ecological traits were detected using both approaches. Among the genetic diversity parameters considered in this study, the minor allele frequency (MAF), the genetic distance between individuals (D), as well as observed (Ho) and expected heterozygosities (He) values were 0.300, 0.309, 0.388, and 0.390, respectively. The obtained Ho, He and D values indicate a moderate level of genetic diversity. The ratio of polymorphic SNPs (PN) was 0.947, and the average values of FROH and FHOM were 0.030 and 0.029, respectively. Considering the PN value obtained in the study, it is evident that the SNPs in the population exhibit a high level of polymorphism at 94.7%. While the FROH value obtained indicates high genetic diversity among the individuals in the present study, the FHOM value suggests that the population is predominantly composed of heterozygous individuals. As a result, evidence indicating genetic advancements have been made for target traits in breeding programs within the population. Additionally, candidate genes suitable for future molecular marker-supported breeding programs have been identified. In addition, a better understanding of the genetic structure and production potential of the population has been achieved. Findings have shown that Eşme sheep are a breed with high meat production potential and strong adaptation abilities.

Performance of homozygosity by descent in two mice lines divergently selected for birth weight environmental variability

Inbreeding can have negative effects, such as increasing the expression of deleterious alleles or reducing fitness. A method based on Hidden Markov Models (HMM) was developed to determine the probability of an individual genome in a homozygous-by-descent state (HBD). As a result of an experiment of divergent selection for birth weight environmental variability two lines were created: high variability line (H-Line) and low variability line (L-Line). The L-Line demonstrated a better performance in traits related with robustness than the H-Line. From a selection period of 20 generations, a total of 655 individuals from the H-Line and 675 individuals from the L-Line were genotyped with a high-density SNP array. We used a predefined multiclass HMM with a total of 9 age related HBD classes and 1 non HBD class. The sum of the probabilities of each HBD class was defined as the total HBD inbreeding (FHBD). In addition, FHBD was divided into age related groups as recent and ancient. Moreover, recent pedigree inbreeding (FPEDR) was defined using different generation thresholds (4 to 14). The evolution of FHBD across generations was similar in both selected lines. However, the distribution in each age-related class was different between lines in more recent generations. The H-Line presented twice as much FHBD by ancestors from 8 generations ago than the L-Line. Moreover, the correlations between recent FHBD and FPEDR obtained with different generation thresholds were greater in the H-Line when very recent FHBD was calculated from classes related with ancestors from 1 to 8 generations ago. However, in the L-Line, considering more than 4 generations ago to define very recent inbreeding did not affect the correlations with FPEDR. The HBD was the first methodology that could detect differences in the inbreeding pattern between the selected lines that could be related with the divergent selection, despite being under the identical mating policy and similar intensity of selection.

The effects of runs-of-homozygosity on pig domestication and breeding

BACKGROUND

Since their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations and the increase of runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand the genetic underpinnings of inbreeding depression.

RESULTS

Here we integrated a comprehensive dataset comprising 7239 domesticated pigs and wild boars genotyped by single nucleotide polymorphism (SNP) chips, along with phenotypic data encompassing growth, reproduction and disease-associated traits. Our study revealed differential ROH landscapes during domestication and artificial selection of Eurasian pigs. We observed associations between ROH burden and phenotypic traits such as body conformation and susceptibility to diseases like scrotal hernia. By examining associations of whole-genome and regional ROH burden with gene expression, we identified specific genes and pathways affected by inbreeding depression. Associations of regional ROH burden with gene expression also enabled the discovery of novel regulatory elements. Lastly, we inferred recessive lethal mutations by examining depletion of ROH in an inbred population with relatively small sample size, following by fine mapping with sequencing data.

CONCLUSIONS

These findings suggested that both phenotypic and genetic variations have been reshaped by inbreeding, and provided insights to the genetic mechanisms underlying inbreeding depression.

Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits

Runs of homozygosity (ROH) are contiguous stretches of identical genomic regions inherited from both parents. Assessment of ROH in livestock species contributes significantly to our understanding of genetic health, population genetic structure, selective pressure and conservation efforts. In this study, whole genome re-sequencing data from 140 birds of 10 Iranian indigenous chicken ecotypes, 3 commercial chicken breeds and 1 red junglefowl (RJF) population were used to investigate their population genetic structure, ROH characteristics (length and frequency) and genomic inbreeding coefficients (FROH). Additionally, we examined ROH islands for selection footprints in the indigenous chicken populations. Our results revealed distinct genetic backgrounds, among which the White Leghorn breed exhibited the greatest genetic distance from other populations, while the gamecock populations formed a separate cluster. We observed significant differences in ROH characteristics, in which the commercial breeds showed a higher number of ROH compared to indigenous chickens and red junglefowls. Short ROH ranging from 0.1 to 1 Mb were dominant among the populations. The Arian line had the highest mean length of ROH, while the White Leghorn breed showed the highest number of ROH. Among indigenous chickens, the Lari-Afghani ecotype exhibited the highest FROH, but the Sari inherited the richest genetic diversity. Interestingly, GGA16 carried no ROH in the red junglefowls, whereas GGA22 had the highest FROH across all populations, except in the Isfahan ecotype. We also identified ROH islands associated with genetic adaptations in indigenous ecotypes. These islands harboured immune-related genes contributing to disease resistance (TLR2, TICAM1, IL22RA1, NOS2, CCL20 and IFNLR1), heat tolerance and oxidative stress response (NFKB1, HSF4, OSGIN1 and BDNF), and muscle development, lipid metabolism and reproduction (MEOX2, CEBPB, CDS2 and GnRH-I). Overall, this study highlights the genetic potential of indigenous chickens to survive and adapt to their respective environments.

Analysis of genetic structure and identification of important genes associated with muscle growth in Fujian Muscovy duck

Fujian Muscovy duck is a well-known meat waterfowl in Fujian Province due to its high meat production, superior breeding potential, and strong resistance. To fully explore the genetic characteristics of these advantages, Fujian black Muscovy duck and white Muscovy duck were used for whole-genome re-sequencing and transcriptome analyses. Population structure analysis showed significant differentiation between the two feather strains. Runs of homozygosity analysis indicated a stronger artificial influence on the black-feathered strain, with ROH island genes notably enriched in muscle tissue-related terms and pathways. Selective sweep and transcriptome analysis revealed a significant enrichment of genes linked to muscle tissue and muscle fiber-related terms and pathways. Key candidate genes identified, such as MEF2C, MYOZ2, and METTL21C, are believed to play crucial roles in meat production in Fujian Muscovy duck. This study offers a new perspective on improving meat production in Fujian Muscovy duck, which can benefit breeding strategies and production management.

Genomic inbreeding analysis reveals resilience and genetic diversity in Indian yak populations

The yak (Bos grunniens), renowned for its adaptability to extreme cold and hypoxic conditions, stands as a remarkable domestic animal crucial for sustaining livelihoods in harsh climates. We conducted a comprehensive analysis of the whole genome sequence data from three distinct Indian yak populations: Arunachali yak (n = 10), Himachali yak (n = 10), and Ladakhi yak (n = 10). The genomic data for Indian yaks were meticulously generated by our laboratory and compared with their Chinese counterpart, the Jinchuan yak (n = 8), for a more nuanced understanding. Our investigation revealed a total of 37,437 runs of homozygosity (ROH) segments in 34 animals representing four distinct yak populations. The Jinchuan yak population exhibited the highest proportion, constituting 80.8 % of total ROHs, predominantly as small segments (<0.1 Mb), accounting for 63 % of the overall ROHs. Further analysis uncovered a significantly higher degree of inbreeding in Chinese yaks compared to their Indian counterparts. The Indian yak populations, in contrast, demonstrated relatively lower and consistent levels of inbreeding. Moreover, we identified ROH hotspots that covered at least 60 % of individuals in our study, indicating their pivotal role in environmental adaptation. A total of five hotspot regions were detected, housing genes such as ENSBGRG00000015023 (WNT2), YIPF4, SPAST, TLN2, and DSG4. These genes are associated with traits including hair follicle initiation, nutrient stress response, microtubule assembly, development of cardiac muscle, hair follicle, and coat color. This observation strongly suggests that there is substantial selection acting on these genes, emphasizing their important role in environmental adaptation among yak populations.

Signatures of selection analyses reveal genomic differences among three heavy pig breeds that constitute the genetic backbone of a dry-cured ham production system

The Italian pig farming industry is unique in its focus on raising heavy pigs primarily for the production of high-quality dry-cured hams. These products require pigs to be slaughtered at a live weight of around 170 kg at 9 months of age. The primary breeds used in this system are Italian Duroc, Italian Landrace, and Italian Large White which are crossed to produce lines that meet standard requirements. Over the past four decades, selection and breeding programmes for these breeds have been subjected to distinct selective pressures to highlight the characteristics of each breed. In this study, we investigated the genome of these breeds by analysing high-density single nucleotide polymorphism data from over 9 000 pigs to scan for signatures of selection using four different methods, two within breeds and two across breeds. This allowed to identify the genomic regions that differentiate these breeds as well as any relevant genes and biological terms. On a global scale, we found that the Italian Duroc breed exhibited a higher genetic differentiation from the Italian Landrace and Italian Large White breeds, with a pairwise FST value of 0.20 compared with the 0.13 between Italian Landrace and Italian Large White. This may reflect either their different origins or the different breeding goals, which are more similar for the Italian Landrace and Italian Large White breeds. Despite these genetic differences at a global level, few signatures of selection regions reached complete fixation, possibly due to challenges in detecting selection linked to quantitative polygenic traits. The differences among the three breeds are confirmed by the low level of overlap in the regions detected. Genetic enrichment analyses of the three breeds revealed pathways and genes related to various productive traits associated with growth and fat deposition. This may indicate a common selection direction aimed at enhancing specific production traits, though different biological mechanisms are likely targeted by the same directional selection in these three breeds. Therefore, these genes may play a critical role in determining the distinctive characteristics of Italian Duroc, Italian Landrace, and Italian Large White, and potentially influence the traits in crossbred pigs derived from them. Overall, the insights gained from this study will contribute to understanding how directional selection has shaped the genome of these heavy pig breeds and to better address selection strategies aimed at enhancing the meat processing industry linked with dry-cured ham production chains.

Reducing foreign genetic contributions to the YDH pig population by segment-based advanced optimum contribution selection

Yuedonghei (YDH) is the only local pig breed with full black hair among the four well-known local pig breeds originated and distributed in Guangdong province, China, which caters to the consumers' preference of the local market of 127 million residents and thus brings a significantly above-average price. However, considerable genetic introgression (GI) has been reported for the YDH population, i.e., gene flow into YDH from other pig breeds, which is mainly due to the recent crossbreeding with several mainstream breeds for upgrading reasons. Therefore, this study aimed to evaluate the GI as well as the conservation status in the current YDH population and test the feasibility of advanced optimum contribution selection (aOCS) in alleviating GI in YDH. We first analysed the genetic diversity, ancestral structure, population structure, and phylogeny of 360 YDH relative to 782 publicly downloaded pigs of 42 Eurasian or American breeds and wild boars, based on single nucleotide polymorphism chip data. Then, we selected 304 initial YDH and stochastically simulated a practical conservation programme that spanned 10 discrete generations and implemented haplotype segment-based aOCS in every generation. The expected and observed heterozygosity of 360 YDH were 0.344 and 0.336. The linkage disequilibrium-based recent effective population size (Ne) was 32.89. Considerable GI amounting to 32.9% foreign ancestry was found in 28 lowly related YDH individuals using admixture analysis. In the simulated YDH conservation programme, the average native genomic contribution was increased from 50.4 to 71.4% while maintaining a Ne of 100 by controlling classic kinship and native kinship. Our study showed that segment-based aOCS that required only genomic data can be used to alleviate GI in the current YDH population and meanwhile increase its Ne, which provided strategic insights into the sustainable conservation of local genetic resources of livestock.

Genome-Wide Association Studies and Runs of Homozygosity Reveals Genetic Markers Associated with Reproductive Performance in Korean Duroc, Landrace, and Yorkshire Breeds

BACKGROUND

Reproductive performance is critical in the pig industry, and improved sow performance could lead to increased economic benefits. GWAS and ROH analyses based on SNP array data were conducted to identify the breed-specific genetic architecture underlying the variation in NBA and TNB.

METHODS

A total of 7488 breeding pigs with phenotypic data from 1586 Duroc, 2256 Landrace, and 3646 Yorkshire breeds, along with 76,756 SNP markers from Korean grand-grand-parent (GGP) breeding farms, were used.

RESULTS

In the Duroc breeds, SNPs on SSC 9 and 17 were found to be associated with the SIDT2 and TGM2 genes, respectively. In the Landrace breed, PPP1R9A, LMTK2, and GTF2H3 on SSCs 9, 3, and 14, respectively, were associated with both TNB and NBA. With the Yorkshire breed genome, GRID1, DLGAP2, ZZEF1, PARG, RNF17, and NDUFAF5 in SSCs 14, 15, 12, 14, 11, and 17, respectively, were associated with NBA and TNB traits. These genes have distinct functions, ranging from synaptic transmission and cytoskeletal organization to DNA repair and cellular energy production. In the Duroc breed, six genes identified in the ROH islands were associated with various biological pathways, molecular functions, and cellular components. NT5DC1 was associated with metaphyseal chondrodysplasia, CRTAC1 with ion binding, CFAP43 with spermatogenic failure, CASC3 with intracellular mRNA localization, ERC2 with cellular component organization, and FOCAD with Focadhesin. In the Landrace and Yorkshire breeds, PDE6D was associated with GTPase inhibitor activity.

CONCLUSIONS

Through GWAS and ROH analyses, we identified breed-specific SNP markers associated with NBA and TNB in three breed genotypes, providing insights for improving reproductive performance efficiency and contributing to future breeding strategies.

Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs

The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570-27186456 and SSC11:7220366-14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.

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.

Runs of homozygosity analysis for selection signatures in the Yellow Korean native chicken

OBJECTIVE

Yellow Korean native chicken (KNC-Y) is one of the five pure Korean indigenous chicken breeds that were restored through a government project in 1992. KNC-Y is recognized for its superior egg production performance compared to other KNC lines. In this study, we performed runs of homozygosity (ROH) analysis to discover selection signatures associated with egg production traits in the KNC-Y population.

METHODS

A total of 675 DNA samples from KNC-Y were genotyped to generate single nucleotide polymorphism (SNP) data using custom 60K Affymetrix SNP chips. ROH analysis was performed using PLINK software, with predefined parameters set for the analysis. The threshold of ROH island was defined as the top 1% frequency of SNPs withing the ROH among the population.

RESULTS

In the KNC-Y population, a total of 29,958 runs of homozygosity (ROH) fragments were identified. The average total length of ROH was 120.84 Mb, with each ROH fragment having an average length of 2.71 Mb. The calculated ROH-based inbreeding coefficient (FROH) was 0.13. Furthermore, we revealed the presence of ROH islands on chromosomes 1, 2, 4, 5, 7, 8, and 11. Within the identified regions, a total of 111 genes were annotated, and among them were genes related to economic traits, including PRMT3, ANO5, HDAC4, LSS, PLA2G4A, and PTGS2. Most of the overlapping quantitative trait locus regions with ROH islands were found to be associated with production traits.

CONCLUSION

This study conducted a comprehensive analysis of ROH in the KNC-Y population. Notably, among the findings, the PTGS2 gene is believed to play a crucial role in influencing the laying performance of KNC-Y.

Genetic characterization of cashmere goat (Capra hircus) populations in Mongolia

Objective

Characterization studies of the phenotypic and genetic diversity of Mongolian goats are limited, despite several goat breeds being registered in the country. This study aimed to evaluate the phenotypic and genetic diversity of 14 cashmere goat populations in Mongolia, consisting largely of identified goat breeds.

Methods

Body weight, cashmere quality, and coat color were the phenotypic traits considered in this study. A linear model was used to fit body weight and cashmere traits, and least squares means (LSMs) were estimated for the region and location classes. Genetic diversity and structure were assessed using a goat 50K SNP array.

Results

The studied populations exhibited greater phenotypic diversity at the regional level. A very small overall differentiation index (Fst: 0.017) was revealed by Wright's Fst and a very small overall inbreeding index (F ROH1 :0.019) was revealed based on runs of homozygosity. Genetic clustering of populations by principal components showed large variances for the two goat populations of the Russian admixture (Gobi Gurvan Saikhan and Uuliin Bor), and smaller but differentiated clusters for the remaining populations. Similar results were observed in the admixture analysis, which identified populations with the highest (Govi Gurvan Saikhan and Uuliin Bor) and lowest (Tsagaan Ovoo Khar) exotic admixtures. A genomewide association study (GWAS) of body weight and cashmere traits identified a few significant variants on chromosomes 2, 4, 5, 9, and 15, with the strongest variant for cashmere yield on chromosome 4. The GWAS on coat color yielded nine significant variants, with the strongest variants located on chromosomes 6, 13, and 18 and potential associations with KIT, ASIP, and MC1R genes. These signals were also found in other studies on coat color and patterns in goats.

Conclusion

Mongolian cashmere goats showed relatively low genetic differentiation and low inbreeding levels, possibly caused by the traditional pastoral livestock management system and the practice of trading breeding bucks across provinces, along with a recent increase in the goat population. Further investigation of cashmere traits using larger samples and alternative methods may help identify the genes or genomic regions underlying cashmere quality in goats.

Genomic and Conventional Inbreeding Coefficient Estimation Using Different Estimator Models in Korean Duroc, Landrace, and Yorkshire Breeds Using 70K Porcine SNP BeadChip

The purpose of this study was to estimate the homozygosity distribution and compute genomic and conventional inbreeding coefficients in three genetically diverse pig breed populations. The genomic and pedigree data of Duroc (1586), Landrace (2256), and Yorkshire (3646) were analyzed. We estimated and compared various genomic and pedigree inbreeding coefficients using different models and approaches. A total of 709,384 ROH segments in Duroc, 816,898 in Landrace, and 1,401,781 in Yorkshire, with average lengths of 53.59 Mb, 56.21 Mb, and 53.46 Mb, respectively, were identified. Relatively, the Yorkshire breed had the shortest ROH segments, whereas the Landrace breed had the longest mean ROH segments. Sus scrofa chromosome 1 (SSC1) had the highest chromosomal coverage by ROH across all breeds. Across breeds, an absolute correlation (1.0) was seen between FROH total and FROH1-2Mb, showing that short ROH were the primary contributors to overall FROH values. The overall association between genomic and conventional inbreeding was weak, with values ranging from 0.058 to 0.140. In contrast, total genomic inbreeding (FROH) and ROH classes showed a strong association, ranging from 0.663 to 1.00, across the genotypes. The results of genomic and conventional inbreeding estimates improve our understanding of the genetic diversity among genotypes.

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

Genome-wide association analyses reveal copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle

This study aimed to evaluate the impact of copy number variants (CNV) on 13 reproduction and 12 disease traits in Holstein cattle. Intensity signal files containing log R ratio and B allele frequency information from 13,730 Holstein animals genotyped with a 95K SNP panel, and 8,467 Holstein animals genotyped with a 50K SNP panel were used to identify the CNVs. Subsequently, the identified CNVs were validated using whole-genome sequence data from 126 animals, resulting in 870 high-confidence copy number variant regions (CNVR) on 12,131 animals. Out of these, 54 CNVR had frequencies higher than or equal to 1% in the population and were used in the genome-wide association analysis (one CNVR at a time, including the G matrix). Results revealed that 4 CNVR were significantly associated with at least one of the traits analyzed in this study. Specifically, 2 CNVR were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and nonreturn rate), and 2 CNVR were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVR harbored genes implicated in immune response, cellular signaling, and neuronal development, supporting their potential involvement in these traits. Further investigations to unravel the mechanistic and functional implications of these CNVR on the mentioned traits are warranted.

Genetic diversity, population structure and origin of the native goats in Central Laos

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

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.

Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle

An increasing trend in ancestral and classical inbreeding coefficients as well as inbreeding depression for longevity were found in the German Brown population. In addition, the proportion of US Brown Swiss genes is steadily increasing in German Browns. Therefore, the aim of the present study was to analyze the presence and genomic localization of runs of homozygosity (ROH) in order to evaluate their associations with the proportion of US Brown Swiss genes and survival rates of cows to higher lactations. Genotype data were sampled in 2364 German Browns from 258 herds. The final data set included 49,693 autosomal SNPs. We identified on average 35.996 ± 7.498 ROH per individual with a mean length of 8.323 ± 1.181 Mb. The genomic inbreeding coefficient FROH was 0.122 ± 0.032 and it decreased to 0.074, 0.031 and 0.006, when genomic homozygous segments > 8 Mb (FROH>8), >16 Mb (FROH>16) and >32 Mb (FROH>32) were considered. New inbreeding showed the highest correlation with FROH>32, whereas ancestral inbreeding coefficients had the lowest correlations with FROH>32. The correlation between the classical inbreeding coefficient and FROH was 0.572. We found significantly lower FROH, FROH>4, FROH>8 and FIS for US Brown Swiss proportions <60% compared to >80%. Cows surviving to the 2nd, 4th, 6th, 8th, and 10th lactation had lower genomic inbreeding for FROH and up to FROH>32, which was due to a lower number of ROH and a shorter average length of ROH. The strongest ROH island and consensus ROH shared by 50% of the animals was found on BTA 6 at 85-88 Mb. The genes located in this genomic region were associated with longevity (NPFFR2 and ADAMTS3), udder health and morphology (SLC4A4, NPFFR2, GC and RASSF6), milk production, milk protein percentage, coagulation properties of milk and milking speed (CSN3). On BTA 2, a ROH island was detected only in animals with <60% US Brown Swiss genes. Genes within this region are predominantly important for dual-purpose cattle breeds including Original Browns. For cows reaching more than 9 lactations, an exclusive ROH island was identified on BTA 7 with genes assumed to be associated with longevity. The analysis indicated that genomic homozygous regions important for Original Browns are still present and also ROH containing genes affecting longevity may have been identified. The breeding of German Browns should prevent any further increase in genomic inbreeding and run a breeding program with balanced weights on production, robustness and longevity.

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

BACKGROUND

The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.

RESULTS

HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).

CONCLUSIONS

Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Genomic analysis of inbreeding and coancestry in Nordic Jersey and Holstein dairy cattle populations

In recent years, genomic selection (GS) has accelerated genetic gain in dairy cattle breeds worldwide. Despite the evident genetic progress, several dairy populations have also encountered challenges such as heightened inbreeding rates and reduced effective population sizes. The challenge has been to find a balance between achieving substantial genetic gain while managing genetic diversity within the population, thereby mitigating the negative effects of inbreeding depression. This study aims to elucidate the impact of GS on pedigree and genomic rates of inbreeding (ΔF) and coancestry (ΔC) in Nordic Jersey (NJ) and Holstein (NH) cattle populations. Furthermore, key genetic metrics, including the generation interval (L), effective population size (Ne), and future effective population size (FNe) were assessed between 2 time periods, before and after GS, and across distinct animal cohorts in both breeds: females, bulls, and approved semen-producing bulls (AI-sires). Analysis of ΔF and ΔC revealed distinct trends across the studied periods and animal groups. Notably, there was a consistent increase in yearly ΔF for most animal groups in both breeds. An exception was observed in NH AI-sires, which demonstrated a slight decrease in yearly ΔF. Moreover, NJ displayed minimal changes in yearly ΔC between the periods, whereas NH exhibited elevated ΔC values across all animal groups. Particularly striking was the substantial increase in yearly ΔC within the NH female population, surging from 0.02% to 0.39% between the periods. Implementation of GS resulted in a reduction of the generation interval across all animal cohorts in both NJ and NH breeds. However, the extent of reduction was more pronounced in males compared with females. This reduction in generation interval influenced generational changes in ΔF and ΔC. Bulls and AI-sires of both breeds exhibited reduced generational ΔF between periods, in contrast to females that demonstrated an opposing pattern. Between the periods, NJ maintained a relatively stable Ne (29.4 before and 30.3 after GS), whereas NH experienced a notable decline from 54.3 to 42.8. Female groups in both breeds displayed a negative Ne trend, whereas males demonstrated either neutral or positive Ne developments. Regarding FNe, NJ exhibited positive FNe development with an increase from 40.7 to 57.2. The opposite was observed in NH, where FNe decreased from 198.8 to 42.7. In summary, it was evident that the genomic methods could detect differences between the populations and changes in ΔF and ΔC more efficiently than pedigree methods. Implementation of GS yielded positive outcomes within the NJ population regarding the rate of coancestry but the opposite was observed with NH. Moreover, analysis of ΔC data hints at the potential to decrease future ΔF through informed mating strategies. Conversely, NH faces more pressing concerns, even though ΔF remains comparatively modest in contrast to what has been observed in other Holstein populations. These findings underscore the necessity of genomic control of inbreeding and coancestry with strategic changes in the Nordic breeding schemes for dairy to ensure long-term sustainability in the forthcoming years.

Genome-wide detection of runs of homozygosity and heterozygosity in Tunchang pigs

Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures and humidity. Runs of homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals and selection signals that may reveal candidate genes associated with key functional traits. Runs of heterozygosity (ROHet) are commonly associated with balance selection, which can help us understand the adaptive evolutionary history of domestic animals. In this study, we investigated ROHs and ROHets in 88 Tunchang pigs. We also compared the estimates of inbreeding coefficients in individuals calculated based on four methods. In summary, we detected a total of 16 ROH islands in our study, and 100 genes were found within ROH regions. These genes were correlated with economically important traits such as reproduction (e.g., SERPIND1, HIRA), meat quality (e.g., PI4KA, TBX1), immunity (e.g., ESS2, RANBP1), adaption to heat stress (TXNRD2 and DGCR8), and crude food tolerance (TRPM6). Moreover, we discovered 18 ROHet islands harbouring genes associated with reproduction (e.g., ARHGEF12, BMPR2), immune system (e.g., BRD4, DNMT3B). These findings may help us design effective breeding and conservation strategies for this unique breed.

Runs of homozygosity analysis and genomic inbreeding estimation in Sumba Ongole cattle (Bos indicus) using a BovineSNP50K BeadChip

Background and Aim

Runs of homozygosity (ROH) is a biocomputational technique for identifying homozygous regions in the genomics of livestock. This study aimed to determine the ROH in Sumba Ongole (SO) bulls (n = 48) using the BovineSNP50K BeadChip.

Materials and Methods

GenomeStudio 2.0 software was used to generate the BovineSNP50K BeadChip output. The ROH and ROH-based inbreeding coefficients (FROH) were determined using the detect RUNS R v4.1.0 package. Using the following filtering criteria, PLINK v1.90 software was used to perform genotype quality control: (1) Individuals and single-nucleotide polymorphism (SNPs) had call rates >0.95; (2) more than 0.05 was the minor allele frequency; (3) the list contained only SNPs linked to autosomes; and (4) SNPs that strongly deviated (p < 1e-6) from Hardy-Weinberg equilibrium were removed. Subsequently, 25,252 autosomal SNP markers were included in the ROH and FROH analyses.

Results

In general, the number and length of ROH segments in pool animals were 149.77 ± 16.02 Mb and 486.13 ± 156.11 Mb, respectively. Furthermore, the ROH segments in the animals under study can be discriminated into two classes of 1-4 Mb (83.33%) and 4-8 Mb (16.67%). Subsequently, Bos taurus autosomes (BTA) 1, BTA6, and BTA14 had significant homozygous segments comprising 13 genes. Despite this, the average FROH in pool animals was 0.20 ± 0.06.

Conclusion

These findings indicate that a recent inbreeding event in SO cattle occurred many generations ago. Furthermore, the candidate genes identified from the ROH analysis indicate phenotypic attributes associated with environmental adaptation and economic traits.

Genetic analysis of a Kaijiang duck conservation population through genome-wide scan

1. The Kaijiang duck is a native Chinese breed known for its excellent egg laying performance, killing-out percentage (88.57%), and disease resistance. The assessment of population genetic structure is the basis for understanding the genetics of indigenous breeds and for their protection and management.2. In this study, whole-genome sequencing was performed on 60 Kaijiang ducks to identify genetic variations and investigate the population structure. Homozygosity (ROH) analysis was conducted to assess inbreeding levels in the population.3. The study revealed a moderate level of inbreeding, indicated by an average inbreeding coefficient of 0.1043. This may impact the overall genetic diversity.4. Genomic Regions of Interest identified included 168 genomic regions exhibiting high levels of autozygosity. These regions were associated with processes including muscle growth, pigmentation, neuromodulation, and growth and reproduction.5. The significance of these pathways indicated their potential role in shaping the desirable traits of the Kaijiang duck. These findings provide insights into the genetic basis of the Kaijiang duck's desirable traits and can inform future breeding and conservation efforts.

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

BACKGROUND

Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators ([Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]), as well as two segment-based estimators of runs of homozygosity (ROH, [Formula: see text]) and homozygous-by-descent (HBD, [Formula: see text]). Functional implications were analyzed for the positional candidate genes located within the related genomic regions.

RESULTS

A total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs ([Formula: see text]), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of [Formula: see text] and [Formula: see text], however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals.

CONCLUSIONS

We successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations.

Genome-Wide Association Studies of Growth Trait Heterosis in Crossbred Meat Rabbits

The application of heterosis can not only effectively improve the disease resistance and meat quality of livestock, but also significantly enhance the reproduction and growth of livestock and poultry. We conducted genome-wide association studies using data from F2 crossbred meat rabbits to screen out candidate genes with significant dominant effects associated with economic trait variation. High-throughput sequencing technology was used to obtain SNPs covering the whole genome to evaluate the homozygosity of the population genome, and analyze the number, length, frequency, and distribution of ROHs in the population. Candidate genes related to economic traits of meat rabbits were searched based on high-frequency ROH regions. After quality control filtering of genotype data, 380 F2 crossbred rabbits were identified with 78,579 SNPs and 42,018 ROHs on the autosomes. The fitting of the Logistic growth curve model showed that 49-day-old rabbits were a growth inflection point. Then, through genome-wide association studies, 10 SNP loci and seven growth trait candidate genes were found to be significantly related to body weight in meat rabbits at 84 days of age. In addition, we revealed the functional roles and locations of 20 candidate genes in the high-frequency ROH region associated with economic traits in meat rabbits. This study identified potential genes associated with growth and development in the high-frequency ROH region of meat rabbits. In this study, the identified candidate genes can be used as molecular markers for assisted selection in meat rabbits. At the same time, the inbreeding situation based on ROH assessment can provide reference for breeding and breeding preservation of meat rabbits.

Identification of consensus homozygous regions and their associations with growth and feed efficiency traits in American mink

The recent chromosome-based genome assembly and the newly developed 70K single nucleotide polymorphism (SNP) array for American mink (Neogale vison) facilitate the identification of genetic variants underlying complex traits in this species. The objective of this study was to evaluate the association between consensus runs of homozygosity (ROH) with growth and feed efficiency traits in American mink. A subsample of two mink populations (n = 2,986) were genotyped using the Affymetrix Mink 70K SNP array. The identified ROH segments were included simultaneously, concatenated into consensus regions, and the ROH-based association studies were carried out with linear mixed models considering a genomic relationship matrix for 11 growth and feed efficiency traits implemented in ASReml-R version 4. In total, 298,313 ROH were identified across all individuals, with an average length and coverage of 4.16 Mb and 414.8 Mb, respectively. After merging ROH segments, 196 consensus ROH regions were detected and used for genome-wide ROH-based association analysis. Thirteen consensus ROH regions were significantly (P < 0.01) associated with growth and feed efficiency traits. Several candidate genes within the significant regions are known for their involvement in growth and body size development, including MEF2A, ADAMTS17, POU3F2, and TYRO3. In addition, we found ten consensus ROH regions, defined as ROH islands, with frequencies over 80% of the population. These islands harbored 12 annotated genes, some of which were related to immune system processes such as DTX3L, PARP9, PARP14, CD86, and HCLS1. This is the first study to explore the associations between homozygous regions with growth and feed efficiency traits in American mink. Our findings shed the light on the effects of homozygosity in the mink genome on growth and feed efficiency traits, that can be utilized in developing a sustainable breeding program for mink.

Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates

Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also create long ROHs. While ROHs are frequently used to understand inbreeding in the context of conservation and selective breeding, as well as for consanguinity of populations and their demographic history, it remains unclear how ROH characteristics are altered by selfing and if this confounds expected signatures of inbreeding due to demographic change. Using simulations, we study the impact of the mode of reproduction and demographic history on ROHs. We apply random forests to identify unique characteristics of ROHs, indicative of different sources of inbreeding. We pinpoint distinct features of ROHs that can be used to better characterize the type of inbreeding the population was subjected to and to predict outcrossing rates and complex demographic histories. Using additional simulations and four empirical datasets, two from highly selfing species and two from mixed-maters, we predict the selfing rate and validate our estimations. We find that self-fertilization rates are successfully identified even with complex demography. Population genetic summary statistics improve algorithm accuracy particularly in the presence of additional inbreeding, e.g. from population bottlenecks. Our findings highlight the importance of ROHs in disentangling confounding factors related to various sources of inbreeding and demonstrate situations where such sources cannot be differentiated. Additionally, our random forest models provide a novel tool to the community for inferring selfing rates using genomic data.

Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding

BACKGROUND

The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding.

RESULTS

In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight.

CONCLUSIONS

In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.

Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data

Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed of south China's tropical island province of Hainan, possess distinctive traits such as black hair, a moderate growth rate, good meat quality, and small body size. However, they exhibit exceptional resilience to rough feeding conditions, possess high-quality meat, and show remarkable resistance to stress and heat. In this study, we resequenced the whole genome of Hainan black goats to study the economic traits and genetic basis of these goats, we leveraged whole-genome sequencing data from 33 Hainan black goats to analyze single nucleotide polymorphism (SNP) density, Runs of homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) and selection characteristics. Our findings revealed that Hainan black goats harbor a substantial degree of genetic variation, with a total of 23 608 983 SNPs identified. Analysis of ROHs identified 53 710 segments, predominantly composed of short fragments, with inbreeding events mainly occurring in ancient ancestors, the estimates of inbreeding based on ROH in Hainan black goats typically exhibit moderate values ranging from 0.107 to 0.186. This is primarily attributed to significant declines in the effective population size over recent generations. Moreover, we identified 921 candidate genes within the intersection candidate region of ROH and iHS. Several of these genes are associated with crucial traits such as immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE and PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 and LEPR), meat quality (ACOX1, SSTR1, CAMK2B, PPP2CA and PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 and CDK19), and stress resistance (TLR2, IFI44, ENPP1, STK3 and NFATC1). The presence of these genes may be attributed to the genetic adaptation of Hainan black goats to local climate conditions. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of Hainan black goats and their valuable genetic resources.

Integrating Bioinformatics and Machine Learning for Genomic Prediction in Chickens

Genomic prediction plays an increasingly important role in modern animal breeding, with predictive accuracy being a crucial aspect. The classical linear mixed model is gradually unable to accommodate the growing number of target traits and the increasingly intricate genetic regulatory patterns. Hence, novel approaches are necessary for future genomic prediction. In this study, we used an illumina 50K SNP chip to genotype 4190 egg-type female Rhode Island Red chickens. Machine learning (ML) and classical bioinformatics methods were integrated to fit genotypes with 10 economic traits in chickens. We evaluated the effectiveness of ML methods using Pearson correlation coefficients and the RMSE between predicted and actual phenotypic values and compared them with rrBLUP and BayesA. Our results indicated that ML algorithms exhibit significantly superior performance to rrBLUP and BayesA in predicting body weight and eggshell strength traits. Conversely, rrBLUP and BayesA demonstrated 2-58% higher predictive accuracy in predicting egg numbers. Additionally, the incorporation of suggestively significant SNPs obtained through the GWAS into the ML models resulted in an increase in the predictive accuracy of 0.1-27% across nearly all traits. These findings suggest the potential of combining classical bioinformatics methods with ML techniques to improve genomic prediction in the future.

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

BACKGROUND

Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding.

RESULTS

To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively.

CONCLUSION

Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.

Exploring genomic inbreeding and selection signatures in a commercial Brangus herd through functional annotation

Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year. A total of 4035 commercial Brangus cattle were genotyped using the GGP-F250K array. Runs of Homozygosity (ROH) were used to identify signatures of selection and calculate genomic inbreeding. Quantitative trait loci (QTL) enrichment analysis and literature search identified phenotypic traits linked to ROH islands. Genomic inbreeding averaged 5%, primarily stemming from ancestors five or more generations back. A total of nine ROH islands were identified, QTL enrichment analysis revealed traits related to growth, milk composition, carcass, reproductive, and meat quality traits. Notably, the ROH island on BTA14 encompasses the pleiomorphic adenoma (PLAG1) gene, which has been linked to growth, carcass, and reproductive traits. Moreover, ROH islands associated with milk yield and composition were more pronounced in selected replacement heifers of the population, underscoring the importance of milk traits in cow-calf production. In summary, our research sheds light on the changing genetic landscape of the Brangus breed due to selection pressures and reveals key genomic regions impacting production traits.

Unraveling inbreeding patterns and selection signals in Alpine Grey cattle

Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.

Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park

Theodore Roosevelt National Park (TRNP) manages a herd of feral horses (Equus caballus) which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, we used genome-wide markers to examine the population structure of a combined dataset containing common established breeds. Using the Illumina Equine 70k BeadChip, we sampled SNPs across the genome for 118 TRNP horses and evaluated the inbreeding coefficient f and runs of homozygosity (RoH). To identify breed relationships, we compared 23 representative TRNP samples with 792 horses from 35 different breeds using genomic population structure analyses. Mean f of TRNP horses was 0.180, while the mean f for all other breeds in the dataset was 0.116 (SD 0.079). RoH analysis indicates that the TRNP population has experienced recent inbreeding in a timeframe consistent with their management. With Bayesian clustering, PCA, and maximum likelihood phylogeny, TRNP horses show genetic differentiation from other breeds, likely due to isolation, historical population bottlenecks, and genetic drift. However, maximum likelihood phylogeny places them with moderate confidence (76.8%) among draft breeds, which is consistent with the known history of breeds used on early North Dakota ranches and stallions subsequently introduced to the park herd. These findings will help resolve speculation about the origins of the herd and inform management decisions for the TRNP herd.