Genomic Characterization of Local Croatian Sheep Breeds-Effective Population Size, Inbreeding & Signatures of Selection.

The Istrian (IS) and the Pag sheep (PS) are local Croatian breeds which provide significant income for the regional economy and have a cultural and traditional importance for the inhabitants. The aim of this study was to estimate some important population specific genetic parameters in IS (N = 1293) and PS (N = 2637) based on genome wide SNPs. Estimates of linkage disequilibrium effective population size (Ne) evidenced more genetic variability in PS (Ne = 838) compared to IS (Ne = 197), regardless of historical time (both recent and ancient genetic variability). The discrepancy in the recent genetic variability between these breeds was additionally confirmed by the estimates of genomic inbreeding (FROH), which was estimated to be notably higher in IS (FROH>2 = 0.062) than in PS (FROH>2 = 0.029). The average FROH2-4, FROH4-8, FROH8-16, and FROH>16 were 0.26, 1.65, 2.14, and 3.72 for IS and 0.22, 0.61, 0.75, and 1.58 for PS, thus evidencing a high contribution of recent inbreeding in the overall inbreeding. One ROH island with > 30% of SNP incidence in ROHs was detected in IS (OAR6; 34,253,440-38,238,124 bp) while there was no ROH islands detected in PS. Seven genes (CCSER1, HERC3, LCORL, NAP1L5, PKD2, PYURF, and SPP1) involved in growth, feed intake, milk production, immune responses, and resistance were associated with the found autozygosity. The results of this study represent the first comprehensive insight into genomic variability of these two Croatian local sheep breeds and will serve as a baseline for setting up the most promising strategy of genomic Optimum Contribution Selection.

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.

Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population.

BACKGROUND: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. RESULTS: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. CONCLUSIONS: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

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.

Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data.

The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017-2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5-37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires.

Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus).

Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species' genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum (LGM), possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.

Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity.

Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wgResidual) and ssGREML (gResidual) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree-based (Fped) and ROH-based genomic (FROH) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when Fped was used. However, all traits were negatively affected by the increase in genomic inbreeding, and FROH was found to capture more inbreeding depression than Fped. Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.

Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle.

Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.

Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance.

This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (F NEJ), Li and Horvitz (F L&H), Van Raden method 1 (F VR1) and method 2 (F VR2), and Yang (F YAN). Inbreeding based on runs of homozygosity (F ROH) and pedigree inbreeding (F PED) were also computed. F ROH, F NEJ, and F L&H were also adjusted for their average values in the first generation of selection and named F ROH0, F NEJ0, and F L&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆F PEDt) and individual increases in inbreeding (∆F PEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆F NEJ0, ∆F L&H, ∆F L&H0, ∆F VR1, ∆F VR2, ∆F YAN, and ∆F ROH0). The Ne was obtained from different ∆F, such as Ne PEDt, Ne PEDi, Ne NEJ0, Ne L&H, Ne L&H0, Ne VR1, Ne VR2, Ne YAN, and Ne ROH0. Comparing with F PED , F ROH , F NEJ and F VR2 overestimated inbreeding while F NEJ0 , F L&H , F L&H0 , F VR1 and F YAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. F ROH had the highest correlation with F PED (0.89); F YAN had correlations >0.95 with all the other molecular inbreeding coefficients. Ne PEDi was more reliable than Ne PEDt and presented similar behaviour to Ne L&H0 and Ne NEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation Ne PEDi was 42.20, Ne L&H0 was 45.04 and Ne NEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively F ROH presented the highest correlation with F PED, which addresses the identity by descent probability (IBD). The evolution of Ne L&H0 and Ne NEJ0 was the most similar to that of Ne PEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.

A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond.

Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1-5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.

Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle.

BACKGROUND: Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and depression. Recently, many measures have been used for genome-based inbreeding coefficients; however, with no consensus on which is the most appropriate. Therefore, we compared the pedigree- ([Formula: see text]) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ([Formula: see text]), correlation between uniting gametes ([Formula: see text]), the observed vs expected number of homozygous genotypes ([Formula: see text]), runs of homozygosity (ROH) segments ([Formula: see text]) and heterozygosity by descent segments ([Formula: see text]). We quantified inbreeding depression from estimating regression coefficients of inbreeding coefficients on three reproductive traits: age at first calving (AFC), calving difficulty (CD) and gestation length (GL) in Japanese Black cattle. RESULTS: The highest correlations with [Formula: see text] were for [Formula: see text] (0.86) and [Formula: see text] (0.85) whereas [Formula: see text] and [Formula: see text] provided weak correlations with [Formula: see text], with range 0.33-0.55. Except for [Formula: see text] and [Formula: see text], there were strong correlations among genome-based inbreeding coefficients ([Formula: see text] 0.94). The estimates of regression coefficients of inbreeding depression for [Formula: see text] was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but [Formula: see text] had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than [Formula: see text]. In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for [Formula: see text] had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, [Formula: see text] provided significant effects at chromosomal level in four chromosomes for AFC, three chromosomes for CD, and two chromosomes for GL. In addition, similar results were obtained for [Formula: see text]. CONCLUSIONS: Genome-based inbreeding coefficients can capture more phenotypic variation than [Formula: see text]. In particular, [Formula: see text] and [Formula: see text] can be considered good estimators for quantifying inbreeding level and identifying inbreeding depression at the chromosome level. These findings might improve the quantification of inbreeding and breeding programs using genome-based inbreeding coefficients.

Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation.

BACKGROUND: Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. RESULTS: In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. CONCLUSIONS: The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.

The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India.

BACKGROUND: Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE: The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS: For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS: A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS: This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.

Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine.

For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Matangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome-wide association approach to test the locus-specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern.

Estimates of genomic inbreeding and identification of candidate regions in Beijing-You chicken populations.

Runs of homozygosity (ROHs) has become an effective method for analysing inbreeding in livestock populations. Moreover, ROHs is well-suited to detect signatures of selection via ROH islands. This study aimed to investigate the occurrence and distribution of ROHs, compare the genomic inbreeding coefficients and identify the genomic regions with high ROH frequencies in different Beijing-You chicken (BY) populations, including a random conservation population (BY_R), a pedigree conservation population (BY_P), and a commercial population obtained from the market (BY_C). Among them, BY_R in 2010 and 2019 were BY_R1 and BY_R2 respectively. A total of 27 916 ROHs were identified. The average number of ROHs per individual across the three BY populations ranged from 213 (BY_P) to 161 (BY_C), and the average length of ROHs ranged from 0.432 Mb (BY_R2) to 0.451 Mb (BY_P). The highest inbreeding coefficient calculated based on ROHs (FROH ) was 0.1 in BY_P, whereas the lowest FROH was 0.0743 in BY_C. In addition, the inbreeding coefficient of BY_R2 (FROH  = 0.0798) was higher than that of BY_R1 (FROH  = 0.0579). Furthermore, the highest proportion of long ROH fragments (>4 Mb) was observed in BY_P and BY_C. This study showed the top 10 ROH islands of each population, and these ROH islands harboured 53 genes, some of which were related to limb development, body size and immune response. These findings contribute to the understanding of genetic diversity and population demography, and might help improve breeding and conservation strategies for BY populations.

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse.

BACKGROUND: Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability. RESULTS: The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. CONCLUSIONS: Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

Using Pedigree and Genomic Data toward Better Management of Inbreeding in Italian Dairy Sheep and Goat Breeds.

The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds. Pedigree and genomic data (medium-density SNPchip) were obtained for 3107 goats and 2511 sheep. We estimated pedigree depth (number of fully traced generations, FullGen) and inbreeding (FPED), as well as two genomic inbreeding indexes, using runs of the homozygosity (FROH) and genomic relationship matrix (FGRM). The correlation between the inbreeding coefficients was assessed. A linear regression model (LRM) was fitted for estimating FPED from FROH. After quality control on genomic data, we retained 5085 animals. Mean inbreeding values were low, with higher FROH than FPED and FGRM. Breed differences can partially depend on different managements. The correlation between FPED and FROH was the highest and directly related to pedigree depth. The best LRM was chosen for FullGen ≥4 and ≥6 for goats and sheep, respectively; after excluding animals with extreme residuals, a new refined regression equation was calculated. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of calculating genomic-based inbreeding coefficients. A better estimation of animals' relatedness contributes to improve animal breeding and conservation.

Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data.

Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.

Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker.

Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (N e ), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current N e of Gauteng was the lowest at 371 animals, while the historical N e across populations suggests that the ancestor N e has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (F ROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high N e and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.

Genome-wide run of homozygosity analysis reveals candidate genomic regions associated with environmental adaptations of Tibetan native chickens.

BACKGROUND: In Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau. These breeds are partly included in the conservation plans because they represent important chicken genetic resources. However, the genetic diversity of these chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 populations of Tibetan chicken including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken breed, we investigated the genetic diversity of these chicken breeds by genetic differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses. RESULTS: Our results revealed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, while subtle genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (FROH) of 0.11 was observed in LZ. In other populations, the FROH ranged from 0.04 to 0.06. In total, 74, 111, 62, 42 and 54 ROH islands containing SNPs ranked top 1% for concurrency were identified in SH, NM, DZ, LZ and LW, respectively. Genes common to the ROH islands in the five populations included BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4. This suggested their essential roles in adaptation of the chickens. We also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes in all populations. These genes had been implicated in digestion, neurite growth and high-altitude adaptation. CONCLUSIONS: High genetic diversity is observed in Tibetan native chickens. Inbreeding is more intense in the Nyingchi population which is also genetically distant from other chicken populations. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity offer valuable insights for the genetic mechanism of adaptation, and provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens.