Levels Of Inbreeding Research Articles

Performance evaluation of Marwari lambs for growth traits and impact of inbreeding

This study aimed at the performance evaluation of a closed flock of Marwari sheep and also to study the effect of accumulated inbreeding on the growth traits using a linear mixed model methodology. The data generated for 39 years (1981 to 2020) on Marwari sheep maintained at ICAR-Central Sheep & Wool Research Institute, Arid Region Campus (CSWRI, ARC), Bikaner, Rajasthan, India were used for analysis on growth traits. The overall least-squares means (LSM) of live weights at birth (BWT), weaning (3MWT), 6 months (6MWT), 9 months (9MWT) and 12 months (12MWT) were observed to be 3.02 ± 0.01, 14.30 ± 0.04, 20.12 ± 0.05, 23.68 ± 0.06 and 26.39 ± 0.07 kg, respectively. Overall LSM for average daily gain from birth to 3 months (ADG1), 3 to 6 months (ADG2) and 6 to 12 months (ADG3) were 125.44 ± 0.40, 67.37 ± 0.40 and 35.83 ± 0.29 g/day, respectively. Kleiber ratio (KR) from birth to 3 months (KR1), 3 to 6 months (KR2), and 6 to 12 months (KR3) were 16.78 ± 0.02, 6.58 ± 0.04 and 3.05 ± 0.02, respectively. Results revealed a 4.36, 25.83, 36.33, 31.50 and 28.99% improvement in the live weights since the inception of the improvement programme. This is also reflected by a significant effect of sire on all the growth traits. The estimate of inbreeding in the flock was 1.55%. Highly inbred animals were 5.13% (>5% Fi). The study revealed the non-significant effect of inbreeding level on all growth traits except for BWT and KR3. For BWT, inbreeding classes had variation; however, a negative effect was not seen. The inbreeding class (>5% Fi) was reduced by 0.05 units for KR3 as against its preceding class. Dam's age at lambing and weight influenced the birth weight and subsequent weights. The study concluded that the selection programme of Marwari sheep is in the right direction; however, regular monitoring of inbreeding is necessary and factors affecting growth must be monitored to attain better growth rates in the nucleus.

Deciphering the genetic structure of the Quebec founder population using genealogies

Using genealogy to study the demographic history of a population makes it possible to overcome the models and assumptions often used in population genetics. The Quebec founder population is one of the few populations in the world having access to the complete genealogy of the last 400 years. The goal of this study is to follow the evolution of the Quebec population structure over time from the beginning of European colonization until the present day. To do so, we calculated the kinship coefficients of all ancestors’ pairs in the ascending genealogy of 665 subjects from eight regional and ethnocultural groups per 25-year period. We show that the Quebec population structure appeared progressively in the St. Lawrence valley as early as 1750 with the distinction of the Saguenay and Gaspesian groups. At that time, the ancestors of two groups, the Sagueneans and the Acadians from the Gaspé Peninsula, experienced a marked increase in kinship and inbreeding levels which have shaped the structure and led to the contemporary population structure. Interestingly, this structure arose before the colonization of the Saguenay region and at the very beginning of the Gaspé Peninsula settlement. The resulting regional founder effects in these groups led to differences in the present-day identity-by-descent sharing, the Gaspé and North Shore groups sharing more large segments and the Sagueneans more short segments. This is also reflected by the distribution of the number of most recent common ancestors at different generations and their genetic contribution to the studied subjects.

Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep.

The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.

Post-glacial colonization of the Fennoscandian coast by a plant parasitic insect with an unusual life history.

Species that exhibit very peculiar ecological traits combined with limited dispersal ability pose a challenge to our understanding of ecological and evolutionary mechanisms. This is especially true when they have managed to spread over long distances, overcome physical barriers, and colonize large areas. Climate and landscape changes, trophic web relations, as well as life history all interact to shape migration routes and present-day species distributions and their population genetic structures. Here we analyzed the post-glacial colonization of northern Europe by the gall midge Contarinia vincetoxici, which is a monophagous parasite on the perennial herb White swallowwort (Vincetoxicum hirundinaria). This insect not only has a narrow feeding niche but also limited dispersal ability and an exceptionally long dormancy. Gall midge larvae (n = 329) were collected from 16 sites along its distribution range in Denmark, Sweden, and Finland. Using microsatellite loci and knowledge of the species and the regions' history, we investigated the role of landscape change, host plant distribution, insect population dynamics, and life history in shaping the population genetic structure of the insect. We devoted particular interest to the role of the insect's presumed poor dispersal capacity in combination with its exceptionally extended diapause. We found significant levels of local inbreeding (95% highest posterior density interval = 0.42-0.47), low-level within-population heterozygosity (mean H E = 0.45, range 0.20-0.61) with private alleles in all populations except two. We also found significant (p < .001) regional isolation-by-distance patterns, suggesting regularly recurring mainly short-distance dispersal. According to approximate Bayesian computations, C. vincetoxici appears to have colonized the study area via wind-aided flights from remote areas approximately 4600-700 years before present when the land has gradually risen above the sea level. Extremely long dormancy periods have allowed the species to "disperse in time", thereby aiding population persistence despite generally low census population sizes.

Estimation of inbreeding, between-breed genomic relatedness and definition of sub-populations in red-pied cattle breeds

Currently, enhancing the collaboration between related breeds is of main importance to increase the competitivity and the sustainability of local breeds. One type of collaboration is the development of an across-breed reference population that will allow a better management of local breeds. For this purpose, the genomic relatedness between the local target breed and possible breeds to be included in the reference population should be estimated. In Europe, there are several local red-pied cattle breeds that would benefit from this kind of collaboration. However, how different red-pied cattle breeds from the Benelux are related to each other and can collaborate is still unclear. The objectives of this study were therefore: (1) to estimate the level of inbreeding of the East Belgian Red and White (EBRW), the Red-Pied of the Ösling (RPO) and Dutch red-pied cattle breeds; (2) to determine the genomic relatedness of several red-pied cattle breeds, with a special focus on two endangered breeds: the EBRW and the RPO, and (3) based on the second objective, to detect animals from other breeds that were genomically close enough to be considered as advantageous in the creation of an across-breed reference population of EBRW or RPO. The estimated inbreeding levels based on runs of homozygosity were relatively low for almost all the studied breeds and especially for the EBRW and RPO. This would imply that inbreeding is currently not an issue in these two endangered breeds and that their sustainability is not threatened by their level of inbreeding. The results from the principal component analysis, the phylogenetic tree and the clustering all highlighted that the EBRW and RPO breeds were included in the genomic continuum of the studied red-pied cattle breeds and can be therefore considered as genomically close to Dutch red-pied cattle breeds, highlighting the possibility of a collaboration between these breeds. Especially, EBRW animals were closely related to Deep Red and Improved Red animals while, to a lesser extent, the RPO animals were closely related to the Meuse-Rhine-Yssel breed. Based on these results, we could use distance measures, based either on the principal component analysis or clustering, to detect animals from Dutch breeds that were genomically closest to the EBRW or RPO breeds. This will finally allow the building of an across-breed reference population for EBRW or RPO for further genomic evaluations, considering these genomically closest animals from other breeds.

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei.

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

"Type D" killer whale genomes reveal long-term small population size and low genetic diversity.

Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations.

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds.

The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH <4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.

Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data

Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.

The Relationship between Inbreeding and Fitness Is Different between Two Genetic Lines of European Bison

The pedigree data for European bison are published in the European Bison Pedigree Book, established one hundred years ago. The species passed a serious bottleneck and was kept in captivity for more than 30 years. After reintroduction, some individuals were captured and moved to enclosures, which caused gaps in pedigree data. To prevent the underestimation of inbreeding value, only animals with a fully known pedigree were used in the analysis. European bison were divided into two genetic lines, Lowland-Caucasian (LC) and Lowland (LB), with different numbers of founders (all 12 vs. 7 of them). The relation between inbreeding and survival up to one month of age, calculated using logistic regression, gave different results for every genetic line. In the LC line (N = 5441), the average inbreeding level was equal to 0.253 and the influence into survival was negative (exp(B) = 0.190), but in the LB line (N = 1227), the inbreeding level was much higher (0.410) but the influence into survival was positive (exp(B) = 6.596). It could be assumed that the difference between lines is a result of purging in the first period of species restitution.

Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs

Bernese mountain dogs are a large dog breed formed in the early 1900s in Switzerland. While originally farm dogs that were used for pulling carts, guarding, and driving cattle, today they are considered multi-purpose companion and family dogs. The breed is predisposed to several complex diseases, such as histiocytic sarcoma, degenerative myelopathy, or hip dysplasia. Using whole-genome sequencing (WGS) data, we assessed the genomic architecture of 33 unrelated dogs from four countries: France, Sweden, Switzerland, and the United States. Analysis of runs of homozygosity (ROH) identified 12,643 ROH with an average length of 2.29 Mb and an average inbreeding coefficient of 0.395. Multidimensional scaling analysis of the genetic relatedness revealed limited clustering of European versus USA dogs, suggesting exchanges of breeding stock between continents. Furthermore, only two mtDNA haplotypes were detected in the 33 studied dogs, both of which are widespread throughout multiple dog breeds. WGS-based ROH analyses revealed several fixed or nearly fixed regions harboring discreet morphological trait-associated as well as disease-associated genetic variants. Several genes involved in the regulation of immune cells were found in the ROH shared by all dogs, which is notable in the context of the breed's strong predisposition to hematopoietic cancers. High levels of inbreeding and relatedness, strongly exaggerated in the last 30 years, have likely led to the high prevalence of specific genetic disorders in this breed.

Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations

Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.

Assessing the Genomics Structure of Dorper and White Dorper Variants, and Dorper Populations in South Africa and Hungary.

Dorper sheep was developed for meat production in arid and semi-arid regions under extensive production systems in South Africa. Two variants with distinct head and neck colors were bred during their development process. White Dorper have a white coat while Dorper have a black head and neck. Both variants have grown in popularity around the world. Therefore, understanding the genomic architecture between South African Dorpers and Dorper populations adapted to other climatic regions, as well as genomic differences between Dorper and White Dorper variants is vital for their molecular management. Using the ovine 50K SNP chip, this study compared the genetic architecture of Dorper variants between populations from South Africa and Hungary. The Dorper populations in both countries had high genetic diversity levels, although Dorper in Hungary showed high levels of inbreeding. White Dorpers from both countries were genetically closely related, while Dorpers were distantly related according to principal component analysis and neighbor-joining tree. Additionally, whereas all groups displayed unique selection signatures for local adaptation, Dorpers from Hungary had a similar linkage disequilibrium decay. Environmental differences and color may have influenced the genetic differentiation between the Dorpers. For their molecular management and prospective genomic selection, it is crucial to understand the Dorper sheep's genomic architecture, and the results of this study can be interpreted as a step in this direction.

Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia.

Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n= 24) and landlocked (Arctic Superior; n= 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.

Evidence of an Absence of Inbreeding Depression in a Wild Population of Weddell Seals (Leptonychotes weddellii).

Inbreeding depression can reduce the viability of wild populations. Detecting inbreeding depression in the wild is difficult; developing accurate estimates of inbreeding can be time and labor intensive. In this study, we used a two-step modeling procedure to incorporate uncertainty inherent in estimating individual inbreeding coefficients from multilocus genotypes into estimates of inbreeding depression in a population of Weddell seals (Leptonychotes weddellii). The two-step modeling procedure presented in this paper provides a method for estimating the magnitude of a known source of error, which is assumed absent in classic regression models, and incorporating this error into inferences about inbreeding depression. The method is essentially an errors-in-variables regression with non-normal errors in both the dependent and independent variables. These models, therefore, allow for a better evaluation of the uncertainty surrounding the biological importance of inbreeding depression in non-pedigreed wild populations. For this study we genotyped 154 adult female seals from the population in Erebus Bay, Antarctica, at 29 microsatellite loci, 12 of which are novel. We used a statistical evidence approach to inference rather than hypothesis testing because the discovery of both low and high levels of inbreeding are of scientific interest. We found evidence for an absence of inbreeding depression in lifetime reproductive success, adult survival, age at maturity, and the reproductive interval of female seals in this population.

Time is running out: Microsatellite data predict the imminent extinction of the boreal lynx (Lynx lynx) in France

The Eurasian lynx reappeared in the French Jura Mountains, in the late 1970s, as the result of the dispersion of lynxes from the Carpathian region reintroduced in Switzerland in the early 1970s. Since then, the state of this population has remained poorly known. One estimate gives the number of individuals between 120 and 150. Opportunistic observation and monitoring suggest poor connectivity with the populations in Germany or in other parts of Switzerland. Forty years after its comeback in France, we could expect a higher number of individuals, but possible inbreeding depression as well as threats such as poaching and collisions with cars may explain the limitation of number of individuals observed and may lead to a new extinction of the specie in this region. We used 23 microsatellite markers and 78 DNA samples, collected between 2008 and 2020, to establish the genetic state of the French Jura Mountain lynx population. Our results show extremely low genetic diversity with an observed heterozygosity (Ho) of 0.36 and an effective population size (Ne) of 38.2. When comparing the source population (Carpathian), the inbreeding level is very worrying (Fe = 0.41). These results are among the lowest recorded for the Eurasian lynx. To avoid extinction, which we estimate will occur in approximately 30 years, we recommend the introduction of new genetic material. Although reintroduction is controversial, solutions such as the replacement of poached lynxes and the exchange of orphan lynxes between care centers are good initial actions for population strengthening. This offers a rapid intervention while studying solutions for more sustainable conservation

Population dynamics of a long-term selection experiment in White Plymouth Rock chickens selected for low or high body weight

The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selection horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 individuals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was available. Inbreeding (F) and average relatedness (AR) coefficients were computed. Average F per generation and AR coefficients were 1.3 (SD 0.8) % and 0.53 (SD 0.001) for LWS, and 1.5 (SD 1.1) % and 0.66 (SD 0.001) for HWS. Mean F for the entire pedigree was 0.26 (0.16) and 0.33 (0.19), and maximum F was 0.64 and 0.63, in LWS and HWS, respectively. Based on Wright's fixation index, at generation 59, substantial genetic differences were established between lines. The effective population size was 39 in LWS and 33 in HWS. The effective number of founders was 17 and 15, effective number of ancestors were 12 and 8, and genome equivalents were 2.5 and 1.9 in LWS and HWS, respectively. About 30 founders explained the marginal contribution to both lines. By generation 59, only 7 male and 6 female founders contributed to both lines. Moderately high levels of inbreeding and low effective population sizes were inevitable, as this was a closed population. However, effects on the fitness of the population were expected to be less substantial because founders were a combination of 7 lines. The effective numbers of founders and ancestors were relatively low compared to the actual number of founders, as few ancestors contributed to descendants. Based on these evaluations, it can be inferred that LWS and HWS had similar population structures. Comparisons of selection responses in the 2 lines therefore should be reliable.

Analysis of the genomic landscape of inbreeding in two divergent groups of Spanish Florida goats.

The analysis of the genomic landscape of inbreeding using runs of homozygosity (ROH) patterns is becoming an interesting tool to partially understand phenotypic differences among individuals. In this study, we analysed genome-wide ROH patterns in two groups of Florida goats. We first determined the inbreeding levels of each individual by calculating ROH-based inbreeding coefficients (FROH ). Then, the individuals were divided into two groups based on FROH : high inbreeding (HI, FROH >0.1) and low inbreeding (LI, FROH <0.03). Finally, we performed an extensive in-depth analysis of ROH distribution in each group separately. We found a higher abundance of short ROH in LI, whereas long ROH was more frequent in HI. Furthermore, ROH abundance was not evenly distributed among chromosomes within groups, with some chromosomes showing larger numbers of ROH, like CHI6, CHI7 and CHI27. A different landscape was observed in recent inbreeding (ROH >8Mb), with significant increases in CHI6, CHI11 and CHI28. Determination of genomic regions with significantly increased ROH (ROH islands-ROHi) showed 13 ROHi related to whole inbreeding and five ROHi associated with recent inbreeding analysis. Within these genomic regions, 123 and 101 genes were identified in HI and LI, respectively, including 10 and seven candidate genes previously related to production, fertility and heat resistance in goats and livestock species.

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 Mātangi 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.

Analysis of exterior indices of Russian sturgeon juveniles grown at sturgeon fish factories of the Astrakhan region

The aim of our work was to assess the exterior features of Russian sturgeon juveniles grown at sturgeon fish factories (SFF) of the Astrakhan region. In the process of research, samples of juveniles, obtained from six factories, which are conditionally divided into six groups, were studied: group I - Zhitninsky SFF, group II - Aleksandrovsky SFF, group III - Sergievsky SFF, group IV - Bertyulsky SFF, group V - Kizansky SFF and group VI - Lebyazhy SFF. Assessment of Russian sturgeon juveniles was carried out postmortally on 360 individuals with 60 instances from each factory. According to the data obtained, the following exterior indices were calculated: fatness index, runability index, high back index, long head index and caudal peduncle index. In the process of our research, it was found that the index of long-headedness showed the least variability in all the studied samples. The coefficient of variation of indicators in all six groups did not exceed 10%. The highest coefficient of variation was observed in terms of the average weight (in the studied samples it ranged from 30.0% to 67.0%) and the caudal peduncle index (from 15.0% to 20.0%). Besides, it is worth noting that the sample from group VI had the lowest level of variability among the studied groups, that indicates the uniformity of the obtained juveniles and the high quality of the fish breeding indicators of the released juveniles. In the sample of group IV, on the contrary, the highest level of variability was observed, as evidenced by the maximum values of the coefficient of variation and standard deviation for 4 of the studied indicators out of 7. At the same time, during the study, it was noted that on the quality of the released Russian sturgeon juvenile, and later on the percentage of commercial return, was influenced not only by the hydrochemical regime and the state of the natural food supply in nursery ponds, but also by the high level of inbreeding of the brood stock on sturgeon fish factories.