Extended tracts of homozygosity in outbred human populations

Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

BACKGROUND

Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes.

RESULTS

Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation.

CONCLUSIONS

The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.

Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle

In this study, runs of homozygosity (ROH) and quantitative trait locus/association (QTL) for semen parameters in selected Chinese and South African beef cattle breed were estimated. The computed results showed 7516 ROH were observed between classes 0−5 Mb with no ROH observed in classes >40 Mb. Distribution of ROH showed high level of genomic coverage for ANG, NGU, CSI, and BEL breeds. Approximately 13 genomic regions with QTL were controlling sperm motility, sperm concentration, semen volume, sperm count, sperm head abnormalities, sperm tail abnormalities, sperm integrity, and percentage of abnormal sperm traits. Nine candidate genes, CDF9, MARCH1, WDR19, SLOICI, ST7, DOP1B, CFAF9, INHBA, and ADAMTS1, were suggested to be associated with above mentioned QTL traits. The results for inbreeding coefficient showed moderate correlation between FROH vs FHOM at 0.603 and high correlation between FROH 0−5 Mb 0.929, and lowest correlation for 0−>40 Mb 0.400. This study suggested recent inbreeding in CSI, BEL, ANG, BON, SIM, and NGU breeds. Furthermore, it highlighted varied inbreeding levels and identified QTL for semen traits and genes of association. These results can assist in implementation of genetic improvement strategies for bulls and provide awareness and proper guidelines in developing breeding programs.

Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data

Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.

Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

Background

Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (F_ROH) and homozygosity (F_HOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein.

Results

The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. F_ROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, F_ROH and F_HOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits.

Conclusion

Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08583-9.

Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.

Homozygous might be hemizygous: CRISPR/Cas9 editing in iPSCs results in detrimental on-target defects that escape standard quality controls

The ability to precisely edit the genome of human induced pluripotent stem cell (iPSC) lines using CRISPR/Cas9 has enabled the development of cellular models that can address genotype to phenotype relationships. While genome editing is becoming an essential tool in iPSC-based disease modeling studies, there is no established quality control workflow for edited cells. Moreover, large on-target deletions and insertions that occur through DNA repair mechanisms have recently been uncovered in CRISPR/Cas9-edited loci. Yet the frequency of these events in human iPSCs remains unclear, as they can be difficult to detect. We examined 27 iPSC clones generated after targeting 9 loci and found that 33% had acquired large, on-target genomic defects, including insertions and loss of heterozygosity. Critically, all defects had escaped standard PCR and Sanger sequencing analysis. We describe a cost-efficient quality control strategy that successfully identified all edited clones with detrimental on-target events and could facilitate the integrity of iPSC-based studies.

Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history

Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In-depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.

Genome-wide analysis of runs of homozygosity in Italian Mediterranean buffalo

Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted for approximately 72.29% of all ROH. In contrast, the larger ROH (>8 Mb) class accounted for only 7.97% of all ROH segments. Estimated inbreeding coefficients from ROH (F_ROH) ranged from 0.0201 to 0.0371. Pearson correlations between F_ROH and genomic relationship matrix increased with the increase of ROH length. We identified ROH hotspots in 12 genomic regions, located on chromosomes 1, 2, 3, 5, 17, and 19, harboring a total of 122 genes. Protein-protein interaction (PPI) analysis revealed the clustering of these genes into 7 PPI networks. Many genes located in these regions were associated with different production traits. In addition, 5 ROH islands overlapped with cattle quantitative trait loci that were mainly associated with milk traits. These findings revealed the genome-wide autozygosity patterns and inbreeding levels in Mediterranean buffalo. Our study identified many candidate genes related to production traits that could be used to assist in selective breeding for genetic improvement of buffalo.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.

Increased runs of homozygosity in the autosomal genome of Brazilian individuals with neurodevelopmental delay/intellectual disability and/or multiple congenital anomalies investigated by chromosomal microarray analysis

Runs of homozygosity (ROH) in the human genome may be clinically relevant. The aim of this study was to report the frequency of increased ROH of the autosomal genome in individuals with neurodevelopmental delay/intellectual disability and/or multiple congenital anomalies, and to compare these data with a control group. Data consisted of calls of homozygosity from 265 patients and 289 controls. In total, 7.2% (19/265) of the patients showed multiple ROH exceeding 1% of autosomal genome, compared to 1.4% (4/289) in the control group (p=0.0006). Homozygosity ranged from 1.38% to 22.12% among patients, and from 1.53 to 2.40% in the control group. In turn, 1.9% (5/265) of patients presented ROH ≥10Mb in a single chromosome, compared to 0.3% (1/289) of individuals from the control group (p=0.0801). By excluding cases with reported consanguineous parents (15/24), the frequency of increased ROH was 3.4% (9/250) among patients and 1.7% (5/289) in the control group, considering multiple ROH exceeding 1% of the autosome genome and ROH ≥10Mb in a single chromosome together, although not statistically significant (p=0.1873). These results reinforce the importance of investigating ROH, which with complementary diagnostic tests can improve the diagnostic yield for patients with such conditions.

Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1

Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.

Genetic diversity and selection in Puerto Rican horses

Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the "Criollo") horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the "gait-keeper" DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the "gait-keeper" DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant "gait-keeper" allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.

Rank-invariant estimation of inbreeding coefficients

The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.

Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (F_PED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.

ROHMM-A flexible hidden Markov model framework to detect runs of homozygosity from genotyping data

Runs of long homozygous (ROH) stretches are considered to be the result of consanguinity and usually contain recessive deleterious disease-causing mutations. Several algorithms have been developed to detect ROHs. Here, we developed a simple alternative strategy by examining X chromosome non-pseudoautosomal region to detect the ROHs from next-generation sequencing data utilizing the genotype probabilities and the hidden Markov model algorithm as a tool, namely ROHMM. It is implemented purely in java and contains both a command line and a graphical user interface. We tested ROHMM on simulated data as well as real population data from the 1000G Project and a clinical sample. Our results have shown that ROHMM can perform robustly producing highly accurate homozygosity estimations under all conditions thereby meeting and even exceeding the performance of its natural competitors.

Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses

Background

The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance.

Results

There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP.

Conclusions

Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00676-5.

Runs of homozygosity analysis reveals population characteristics of yellow-feathered chickens using re-sequencing data

1. To evaluate the inbreeding of yellow-feathered chickens (YFCs) and identify genes related to their unique characteristics, whole-genome re-sequencing data were applied to detect runs of homozygosity (ROH) in the genomes of ten YFC breeds. The number, length, distribution of ROH, and inbreeding coefficient in different YFC populations were calculated. Genomic regions with high frequency in ROH were annotated.2. In total, 25,547 ROH with an average length of 335 kb were detected, with most being <1 Mb. The domination of short ROH reflected the long breeding history of this chicken. The number, length, frequency, and distribution of ROH varied among chicken populations, and high genetic diversity was maintained.3. Numerous genes related to YFC characteristics were identified in the high-frequency ROH regions. Among these, IFNA, IFNB, IL11RA, IL22RA1, IFNLR1, and TRIF genes were involved in disease resistance. The AMY, G6PC, SDHB, GCNT4, and ACO genes were associated with energy material metabolism; and FABPL, AQP7, ACAA2, and RYR2 were related to meat quality and flavour. The KITLG, CREB3, RYR2, and LGR4 genes, related to pigmentation, were detected.4. This ROH-based inbreeding evaluation laid the foundation for breeding and conservation of YFC populations, and the candidate genes identified can be used for marker-assisted selection.

Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning

Dianzhong cattle is a classic Chinese indigenous cattle breed with historical records dating back to 200 BC. But with its genomic differences having not been clearly elucidated, the quest for genomic characterization will be an essential step towards understanding the genomic basis of productivity and adaptation to survival under Chinese farming systems. Here we compared 10 Dianzhong cattle (four newly sequenced and six downloaded) with 29 published genomes of three underlying ancestral populations (Chinese zebu, Indian zebu, and Yanbian cattle) to characterize the genomic variations of Dianzhong cattle. Dianzhong cattle has a high nucleotide diversity (0.0034), second only to Chinese zebu. Together with analyses of linkage disequilibrium decay and runs of homozygosity, Dianzhong cattle displayed higher genomic diversity and weaker artificial selection compared with Yanbian cattle. From a selective sweep analysis by four methods (Fst, π-ratio, XP-CLR, and XP-EHH), the positive selective signals were mainly manifested in candidate genes and pathways related to heat resistance, growth and development, fat deposition, and male reproduction. Missense mutations were detected in candidate genes, SDS (c.944C > A and p.Ala315Glu), PDGFD (c.473A > G and p.Lys158Arg), and DDX4 (rs460251486, rs722912933, and rs517668236), which related to heat resistance, fat deposition, and spermatogenesis, respectively. Our findings unravel, at the genome-wide level, the unique diversity of Dianzhong cattle while emphasizing the opportunities for improvement of livestock productivity in further breeding programs.

Genetic structure analysis in several populations of cattle using SNP genotypes

Parameters such as effective population size (Ne), runs of homozygosity (ROH), and inbreeding based on ROH (FROH) can give new insight into the level of genetic diversity for the population under selection. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), Haplotype Block Structure, and runs of homozygosity (ROHs) in several populations of cattle using SNP genotypes. In this study, that the average r² decreased with the increasing distance of SNP pairs. A general decrease in Ne can be seen for all four populations, indicating a loss of genetic diversity. The Iranian Holstein had the lowest level of genomic inbreeding at an ROH of 1, 5, 10 Mb, while the French Holstein had the highest. The maximum number of ROH is seen at a distance of less than 1 Mb, and the lowest number of ROH is seen at a distance of 10 Mb. The number of ROH decreases with increasing distance due to the increased recombination rate. This is a concern as an increase in inbreeding leads to a reduction in the effective population size, which was also evident in the study populations.

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

Genomic diversity and breed composition of Vietnamese smallholder dairy cows

Vietnamese smallholder dairy cows (VDC) are the result of crossbreeding between different zebu (ZEB) and taurine dairy breeds through many undefined generations. Thus, the predominant breed composition of VDC is currently unknown. This study aimed to evaluate the level of genetic diversity and breed composition of VDC. The SNP data of 344 animals from 32 farms located across four dairy regions of Vietnam were collected and merged with genomic reference data, which included three ZEB breeds: Red Sindhi, Sahiwal and Brahman, three taurine breeds: Holstein (HOL), Jersey (JER) and Brown Swiss (BSW), and a composite breed: Chinese Yellow cattle. Diversity and admixture analyses were applied to the merged data set. The VDC were not excessively inbred, as indicated by very low inbreeding coefficients (Wright's F_IS ranged from -0.017 to 0.003). The genetic fractions in the test herds suggested that the VDC are primarily composed of HOL (85.0%); however, JER (6.0%), BSW 5.3%) and ZEB (4.5%) had also contributed. Furthermore, major genotype groupings in the test herds were pure HOL (48%), B3:15/16HOL_1/16ZEB (22%) and B2:7/8HOL_1/8ZEB (12%). The genetic makeup of the VDC is mainly components of various dairy breeds but also has a small percentage of ZEB; thus, the VDC could be a good genetic base for selecting high milk-producing cows with some degree of adaptation to tropical conditions.

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

BACKGROUND

Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle.

RESULTS

We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher's exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle.

CONCLUSIONS

Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

Investigating inbreeding in the turkey (Meleagris gallopavo) genome

The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an individual. The estimation of inbreeding coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of pedigree-based inbreeding coefficients (F_PED) with genomic-based inbreeding coefficients estimated from ROH (F_ROH) and the genomic relationship matrix (F_GRM). A total of 2,616,890 pedigree records were available. Of these records, 6,371 genotyped animals from three purebred turkey (Meleagris gallopavo) lines between 2013 and 2019 were available, and these were obtained using a dense single nucleotide polymorphism array (56,452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a mean number of 84.87 ± 8.79 ROH per animal. Short ROH with lengths of 1 to 2 Mb long were the most abundant throughout the genome. Mean ROH coverage differed greatly between chromosomes and lines. Considering inbreeding coefficient means across all lines, genomic derived inbreeding coefficients (F_ROH = 0.27; F_GRM = 0.32) were higher than coefficients estimated from pedigree records (F_PED = 0.14). Correlations between F_ROH and F_PED, F_ROH and F_GRM, and F_PED and F_GRM ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between F_ROH from different lengths and F_PED substantially increased with ROH length from -0.06 to 0.33. Results of the current research, including the distribution of ROH throughout the genome and ROH-derived inbreeding estimates, can provide a more comprehensive description of inbreeding in the turkey genome. This knowledge can be used to evaluate genetic diversity, a requirement for genetic improvement, and develop methods to minimize inbreeding in turkey breeding programs.

Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

Donkey (Equus asinus) is an important livestock animal in China because of its draft and medicinal value. After a long period of natural and artificial selection, the variety and phenotype of donkeys have become abundant. We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds. According to population structure, most Chinese domestic donkeys showed a dominant ancestral type. However, the Chinese donkeys still represented a significant geographical distribution trend. In the selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small donkey groups, we identified selective signals, including NCAPG and LCORL, which are related to rapid growth and large body size. Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.

Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (N_e), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, N_e, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low N_e values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi

Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

The use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

A Mix of Old British and Modern European Breeds: Genomic Prediction of Breed Composition of Smallholder Pigs in Uganda

Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of 22.8% with a range of 2-50% while "local" blood contributed 69.2% (36.9-95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.

Genome-wide homozygosity and risk of four non-Hodgkin lymphoma subtypes

AIM

Recessive genetic variation is thought to play a role in non-Hodgkin lymphoma (NHL) etiology. Runs of homozygosity (ROH), defined based on long, continuous segments of homozygous SNPs, can be used to estimate both measured and unmeasured recessive genetic variation. We sought to examine genome-wide homozygosity and NHL risk.

METHODS

We used data from eight genome-wide association studies of four common NHL subtypes: 3061 chronic lymphocytic leukemia (CLL), 3814 diffuse large B-cell lymphoma (DLBCL), 2784 follicular lymphoma (FL), and 808 marginal zone lymphoma (MZL) cases, as well as 9374 controls. We examined the effect of homozygous variation on risk by: (1) estimating the fraction of the autosome containing runs of homozygosity (FROH); (2) calculating an inbreeding coefficient derived from the correlation among uniting gametes (F3); and (3) examining specific autosomal regions containing ROH. For each, we calculated beta coefficients and standard errors using logistic regression and combined estimates across studies using random-effects meta-analysis.

RESULTS

We discovered positive associations between FROH and CLL (β = 21.1, SE = 4.41, P = 1.6 × 10-6) and FL (β = 11.4, SE = 5.82, P = 0.02) but not DLBCL (P = 1.0) or MZL (P = 0.91). For F3, we observed an association with CLL (β = 27.5, SE = 6.51, P = 2.4 × 10-5). We did not find evidence of associations with specific ROH, suggesting that the associations observed with FROH and F3 for CLL and FL risk were not driven by a single region of homozygosity.

CONCLUSION

Our findings support the role of recessive genetic variation in the etiology of CLL and FL; additional research is needed to identify the specific loci associated with NHL risk.

An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly

The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database.

Long tracks of homozygosity predict the severity of alcohol use disorders in an American Indian population

Runs of homozygosity (ROH) arise when an individual inherits two copies of the same haplotype segment. While ROH are ubiquitous across human populations, Native populations-with shared parental ancestry arising from isolation and endogamy-can carry a substantial enrichment for ROH. We have been investigating genetic and environmental risk factors for alcohol use disorders (AUD) in a group of American Indians (AI) who have higher rates of AUD than the general U. S. population. Here we explore whether ROH might be associated with incidence and severity of AUD in this admixed AI population (n = 742) that live on geographically contiguous reservations, using low-coverage whole genome sequences. We have found that the genomic regions in the ROH that were identified in this population had significantly elevated American Indian heritage compared with the rest of the genome. Increased ROH abundance and ROH burden are likely risk factors for AUD severity in this AI population, especially in those diagnosed with severe and moderate AUD. The association between ROH and AUD was mostly driven by ROH of moderate lengths between 1 and 2 Mb. An ROH island on chromosome 1p32.3 and a rare ROH pool on chromosome 3p12.3 were found to be significantly associated with AUD severity. They contain genes involved in lipid metabolism, oxidative stress and inflammatory responses; and OSBPL9 was found to reside on the consensus part of the ROH island. These data demonstrate that ROH are associated with risk for AUD severity in this AI population.

Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

Background

Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, using computerized genotype phasing, reported haplotype data. In contrast, we identified long reference sequences by analyzing the homozygous genomic regions in this online database, a concept that has rarely been reported since next generation sequencing data became available.

Study design and methods

Phased genotype data for a 80.6 kb region of chromosome 1 was downloaded for all 2,504 unrelated individuals of the 1000 Genome Project Phase 3 cohort. The data was centered on the ACKR1 gene and bordered by the CADM3 and FCER1A genes. Individuals with heterozygosity at a single site or with complete homozygosity allowed unambiguous assignment of an ACKR1 haplotype. A computer algorithm was developed for extracting these haplotypes from the 1000 Genome Project in an automated fashion. A manual analysis validated the data extracted by the algorithm.

Results

We confirmed 902 ACKR1 haplotypes of varying lengths, the longest at 80,584 nucleotides and shortest at 1,901 nucleotides. The combined length of haplotype sequences comprised 19,895,388 nucleotides with a median of 16,014 nucleotides. Based on our approach, all haplotypes can be considered experimentally confirmed and not affected by the known errors of computerized genotype phasing.

Conclusions

Tracts of homozygosity can provide definitive reference sequences for any gene. They are particularly useful when observed in unrelated individuals of large scale sequence databases. As a proof of principle, we explored the 1000 Genomes Project database for ACKR1 gene data and mined long haplotypes. These haplotypes are useful for high throughput analysis with next generation sequencing. Our approach is scalable, using automated bioinformatics tools, and can be applied to any gene.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04169-6.

Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Simple Summary

In the local populations, the increase in inbreeding is a relevant problem for the reduction in production, reproduction, and adaptive traits. The application of genomic technologies has facilitated the assessment of inbreeding in these populations. The current study aims to investigate the patterns of homozygosity in five Italian local goat populations. The results showed the different selection histories and breeding schemes of these goat populations. The analysis also indicated the importance of this information to avoid future loss of diversity and to produce information for designing optimal breeding and conservation programs.

Abstract

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal

Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analyzed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of the lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome 5. The release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterization of genes of interest and genetic modification of this economically important species.

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Laiwu pigs, distinguished by their high intramuscular fat of 7-9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1-5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.

Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs

Objective

Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency.

Methods

In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies.

Results

In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (F_ROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits.

Conclusion

This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (F_ROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.

Genetic Testing in Neurodevelopmental Disorders

Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.

Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds

Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and F_ST, to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and F_ST methods, respectively. We found several candidate genes (e.g., NCR3, ARID5A, HIST1H2BN, DEFB4, DEFB7, HSPA1L, HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping.

Genetic ancestry plays a central role in population pharmacogenomics

Recent studies have pointed out the essential role of genetic ancestry in population pharmacogenetics. In this study, we analyzed the whole-genome sequencing data from The 1000 Genomes Project (Phase 3) and the pharmacogenetic information from Drug Bank, PharmGKB, PharmaADME, and Biotransformation. Here we show that ancestry-informative markers are enriched in pharmacogenetic loci, suggesting that trans-ancestry differentiation must be carefully considered in population pharmacogenetics studies. Ancestry-informative pharmacogenetic loci are located in both protein-coding and non-protein-coding regions, illustrating that a whole-genome analysis is necessary for an unbiased examination over pharmacogenetic loci. Finally, those ancestry-informative pharmacogenetic loci that target multiple drugs are often a functional variant, which reflects their importance in biological functions and pathways. In summary, we develop an efficient algorithm for an ultrahigh-dimensional principal component analysis. We create genetic catalogs of ancestry-informative markers and genes. We explore pharmacogenetic patterns and establish a high-accuracy prediction panel of genetic ancestry. Moreover, we construct a genetic ancestry pharmacogenomic database Genetic Ancestry PhD (http://hcyang.stat.sinica.edu.tw/databases/genetic_ancestry_phd/).

Hsin-Chou Yang et al. examine population structure in several genomic databases and identify that pharmacogenetic loci are enriched for markers of genetic ancestry. Their results suggest that genetic ancestry must be carefully considered in population pharmacogenetics studies.

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Absence of heterozygosity detected by single-nucleotide polymorphism array in prenatal diagnosis

OBJECTIVES

To investigate the general occurrence and clinical significance of absence of heterozygosity (AOH), detected by single-nucleotide polymorphism (SNP) array on prenatal diagnosis.

METHODS

We recruited pregnancies undergoing invasive prenatal diagnosis at our fetal medicine center over a 6-year period. All fetuses underwent SNP array using the Affymetrix CytoScan HD array platform. AOH was defined as a chromosomal homozygosity segment with neutral copy number. Cases with AOH over 10 Mb in size or with suspected pathogenicity were further analyzed, and the clinical features and outcome were reviewed.

RESULTS

Of 10 294 recruited fetuses, 100 (0.97%) with AOH were identified; in 81 (81.0%) of these, AOH occurred in a single chromosome, while 19 (19.0%) patients had multiple AOHs in different chromosomes. AOH was observed in all chromosomes, chromosomes X, 2 and 16 being the most frequently involved. The length of AOH ranged from partial chromosome (9.002-80.222 Mb) to the entire chromosome. Similar AOH regions displayed varied clinical manifestations. In total, 55 patients presented with concomitant ultrasound abnormalities, the most common being multiple abnormalities (14/55 (25.5%)), genitourinary malformations (8/55 (14.5%)), skeletal malformations (5/55 (9.1%)) and small-for-gestational age (5/55 (9.1%)). Notably, the rate of adverse perinatal outcome (including termination of pregnancy, neonatal death, fetal death, selective reduction and miscarriage) in fetuses with AOH and ultrasound abnormalities (30/48 (62.5%)) was higher than in those without ultrasound abnormalities (6/40 (15.0%)) (P < 0.001). Further non-invasive prenatal testing using cell-free fetal DNA from maternal blood indicated chromosomal copy number abnormalities in 11 patients; however, they were confirmed as AOH by SNP array of the amniotic fluid.

CONCLUSIONS

Genetic counseling regarding a prenatal diagnosis of AOH remains challenging. To evaluate comprehensively its significance, we propose a management strategy involving further serial ultrasound examinations, parental verification, whole-exome sequencing, placental study and effective follow-up. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Simple Summary

The objective of this study was to evaluate the genetic background and inbreeding depression in the Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH). Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals; 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. A 1% increase in inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to sustainable breeding programs for the Mexican Romosinuano cattle breed.

Abstract

The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.

Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data

Anqing six-end-white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore underlying genetic mechanisms. A relative extended haplotype homozygosity (REHH) test was performed in the population of 79 AQ pigs to seek evidence demonstrating that selective actions have left an imprint on the whole genome. In total, 430 500 REHH tests were performed on 53 067 core regions with average REHH tests of 8.11, average lengths of 11.50 kb and an overall length of 610.38 Mb which accounted for 26.94% of the whole genome. Finally, a total of 1819 core haplotypes (P < 0.01) and 586 candidate genes were obtained. These genes were mainly related to meat quality (MYOG, SNX19), resistance to disease (CRISPLD2, CD14) and reproduction traits (ERBB2, NRP2). A panel of genes within the 30 top significant REHH tests was mainly categorized to traits of meat quality and disease resistance. Among 13 KEGG pathways, MAPK, GnRH and Oxytocin signaling pathways, associated with the biological processes of crucial economic traits, were noteworthy. The excellent characteristics of the AQ pig benefited from the combination of natural and human factors. We provide a sketch map that shows the distribution of selection footprints on the whole genome of AQ pig and found potential genes for future studies.

Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear (Pyrus spp.)

Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application in self-incompatible plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European pears (109), and interspecific hybrids (45) were investigated using genotyping-by-sequencing in this study. Fruit phenotypes including fruit weight, firmness, Brix, titratable acidity, and flavor volatiles were measured for genotype-phenotype analyses. The average number of ROH and the average total genomic length of ROH were 6 and 11 Mb, respectively, in Asian accessions, and 13 and 30 Mb, respectively, in European accessions. Significant associations between genomic inbreeding coefficients (F_ROH) and phenotypes were observed for 23 out of 32 traits analyzed. An overlap between ROH islands and significant markers from genome-wide association analyses was observed. Previously published quantitative trait loci for fruit traits and disease resistances also overlapped with some of the ROH islands. A prominent ROH island at the bottom of linkage group 17 overlapped with a recombination-supressed genomic region harboring the self-incompatibility locus. The observed ROH patterns suggested that systematic breeding of European pears would have started earlier than of Asian pears. Our research suggest that F_ROH would serve as a novel tool for managing inbreeding in gene-banks of self-incompatible plant species. ROH mapping provides a complementary strategy to unravel the genetic architecture of complex traits, and to evaluate differential selection in outbred plants. This seminal work would provide foundation for the ROH research in self-incompatible plants.

A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species

BACKGROUND

Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available.

RESULTS

The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep).

CONCLUSIONS

We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.

Genomic and pedigree estimation of inbreeding depression for semen traits in the Basco-Béarnaise dairy sheep breed

Inbreeding depression is associated with a decrease in performance and fitness of the animals. The goal of this study was to evaluate pedigree-based and genomic methods to estimate the level of inbreeding and inbreeding depression for 3 semen traits (volume, concentration, and motility score) in the Basco-Béarnaise sheep breed. Data comprised 16,196 (or 15,071) phenotypic records from 620 rams (of which 533 rams had genotypes of 36,464 SNPs). The pedigree included 8,266 animals, composed of the 620 rams and their ancestors. The number of equivalent complete generations for the 620 rams was 7.04. Inbreeding coefficients were estimated using genomic and pedigree-based information. Genomic inbreeding coefficients were estimated from individual SNP and using segments of homozygous SNP (runs of homozygosity, ROH). Short ROH are of old origin, whereas long ROH are due to recent inbreeding. Considering that the equivalent number of generations in Basco-Béarnaise was 6, inbreeding coefficients for ROH with a length >4 Mb refer to all (recent + old) inbreeding, those with a length >17 Mb correspond to recent inbreeding, and the difference between them indicates old inbreeding. Pedigree-based inbreeding coefficients were also estimated classically, or accounting for nonzero relationships for unknown parents, or including metafounder relationships (estimated using markers) to account for missing pedigree information. Finally, inbreeding coefficients combining genotyped and nongenotyped animal information were computed from matrix H of the single-step approach, also including metafounders. Inbreeding depression was estimated differently depending on the approach used to compute inbreeding coefficients. These 8 estimators of inbreeding coefficients were included as covariates in different animal models. No inbreeding depression was detected for sperm volume or sperm concentration. Inbreeding depression was significant for the motility of spermatozoa. The effect of old and recent inbreeding on motility was null and negative, respectively, demonstrating the existence of purging by selection of deleterious recessive alleles affecting motility. A 10% increase in inbreeding would result in a reduction in mean motility ranging between 0.09 and 0.22 points in the score (from 0 to 5). Motility is unfavorably affected by increasing recent inbreeding but the impact is very small. Runs of homozygosity and metafounders allow us to accurately estimate inbreeding depression and detect recent inbreeding.