Levels Of Inbreeding Research Articles

Development and optimization of expected cross value for mate selection problems

In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.

When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine.

The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.

Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population.

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

Elucidating population structure and genetic diversity of intercross sheep through pedigree analysis

The aim of this study was to assess the population structure and genetic diversity along with determining the accuracy of ongoing selection program in a closed flock of Intercross sheep through pedigree analysis. The pedigree records of 2245 animals maintained at CSWRI-NTRS, Garsa, Kullu during the period from 2012 to 2023 were utilized to calculate the genealogical information, genetic conservation index and other parameters based on gene origin probabilities. Lambs born during 2020 and 2023 were considered as reference population. ENDOG version 4.8 software package was used for pedigree analysis. Analysis revealed that the mean generation interval for the reference population was 3.20 years with a longer interval in dam-offspring pathways relative to sire-offspring pathways. Average inbreeding coefficients for whole and reference population were 0.21 and 0.49 % and corresponding average relatedness was 1.24 and 1.72 %, respectively. The average maximum, equivalent and completed generations were 2.50, 1.96 and 1.63 with 0.12 %, 0.17 % and 0.20 % increase in inbreeding coefficient, respectively. This resultant effective population size estimated using individual increase in inbreeding was 156.52. Effective numbers of founders (fe) and ancestors (fa) was 68 and 61, respectively for reference population with a ratio of 1.11, indicating occurrence of minor effects of bottleneck in the flock. The genetic contribution of most influent ancestors contributing 50 % of the gene pool was only 23. The estimated founder genome (fg) and non-founder genome (fng) were 35.87 and 75.91, respectively in the present population. The estimate for fg/fa ratio was 0.59 which explained that 59 % of the original genetic diversity is exit in the reference population. Genetic conservation index (GCI) ranged from 1 % to 20.28 % with a mean value of 4.91 %. Overall, males recorded a slightly higher GCI than females, i.e., 5.23 vs 4.65 %, respectively. The results revealed that, the population has augmented genetic diversity and low level of inbreeding. Small fraction of genetic diversity was vanished due to unequal contribution of founders and minor bottleneck effects occurred due to disproportionate contribution of breeding animals to gene pool of population. Use of a sufficient number of breeding rams and optimum contribution selection (OCS) is recommended to maintain the genetic diversity as well as enhancing production potential in this population.

Exploring influential factors in Chinese engineering professors' industrial experience: A big data and CV analysis approach

There is a long-standing criticism in academic circles about the inadequacy of engineering industrial experience for professors in Chinese research universities, but there is a lack of analysis of the manifestations and root causes of the problem. The research aims to contribute meaningful insights into the factors influencing the industrial experience of engineering professors in Chinese research universities, facilitating informed policymaking and fostering collaborative efforts between academia and industry. This paper examines Chinese engineering professors' industrial experience using big data mining, computing, modeling, and image rendering. The data was collected from the publicly available CVs from the websites of various Chinese universities which contains data on colleges and universities across China and analyzed engineering professors' professional trajectories and industrial experience using the method of resume analysis. A nonlinear logistic regression model is fitted to determine the impact of multiple independent variables on the probability of engineering industrial experience among professors, with logit transformation and maximum likelihood estimation. The results show that a low percentage of engineering university professors in Chinese research universities have had industry employment after obtaining their Ph.D. degrees. The regression model indicates that gender, level of inbreeding, overseas study experience, university level, and birth age significantly affect the engineering experience of professors. This study proposes several policy recommendations based on comparative analysis and its research. The study's findings are critical for policymakers to create policies that promote industrial partnerships as a fundamental aspect of the professional development of engineering faculty and for further research in the field.

Genomic predictions under different genetic architectures are impacted by mating designs

Mating in animal communities must be managed in a way that assures the performance increase in the progenies without increasing the rate of inbreeding. It has currently become possible to identify millions of single nucleotide polymorphisms (SNPs), and it is feasible to select animals based on genome-wide marker profiles. This study aimed to evaluate the impact of five mating designs among individuals (random, positive and negative assortative, minimized and maximized inbreeding) on genomic prediction accuracy. The choice of these five particular mating designs provides a thorough analysis of the way genetic diversity, relatedness, inbreeding, and biological conditions influence the accuracy of genomic predictions. Utilizing a stochastic simulation technique, various marker and quantitative trait loci (QTL) densities were taken into account. The heritabilities of a simulated trait were 0.05, 0.30, and 0.60. A validation population that only had genotypic records was taken into consideration, and a reference population that had both genotypic and phenotypic records was considered for every simulation scenario. By measuring the correlation between estimated and true breeding values, the prediction accuracy was calculated. Computing the regression of true genomic breeding value on estimated genomic breeding value allowed for the examination of prediction bias. The scenario with a positive assortative mating design had the highest accuracy of genomic prediction (0.733 ± 0.003 to 0.966 ± 0.001). In a case of negative assortative mating, the genomic evaluation's accuracy was lowest (0.680 ± 0.011 to 0.899 ± 0.003). Applying the positive assortative mating design resulted in the unbiased regression coefficients of true genomic breeding value on estimated genomic breeding value. Based on the current results, it is suggested to implement positive assortative mating in genomic evaluation programs to obtain unbiased genomic predictions with greater accuracy. This study implies that animal breeding programs can improve offspring performance without compromising genetic health by carefully managing mating strategies based on genetic diversity, relatedness, and inbreeding levels. To maximize breeding results and ensure long-term genetic improvement in animal populations, this study highlights the importance of considering different mating designs when evaluating genomic information. When incorporating positive assortative mating or other mating schemes into genomic evaluation programs, it is critical to consider the complex relationship between gene interactions, environmental influences, and genetic drift to ensure the stability and effectiveness of breeding efforts. Further research and comprehensive analyzes are needed to fully understand the impact of these factors and their possible complex interactions on the accuracy of genomic prediction and to develop strategies that optimize breeding outcomes in animal populations.

Evolution history and the importance of genomic diversity facing climate change. The case of Agave marmorata Roezl., a microendemic agave used for mezcal production

Social Impact StatementFor hundreds of years, Agave marmorata plants have been used in the production of alcoholic beverages in Mexico. This species is very important in small‐scale rural economies because it is a large plant, yielding five liters of mezcal. However, the production of these beverages takes place when it reaches its reproductive stage, which takes up to 35 years. Due to its slow maturation and high demand, it is considered an endangered species. Therefore, as a conservation strategy, this study proposes the creation of nurseries, genetic breeding programs, and demographic monitoring of wild populations to counteract the extraction of wild plants and, the conservation of the genetic diversity.Summary Agave marmorata Roezl., is an endemic species distributed in the states of Oaxaca and Puebla, Mexico, and locally is widely used to produce mezcal. We assessed the genomic diversity and differentiation using the RADseq method and 29,101 high‐quality single nucleotide polymorphisms (SNPs) in wild plants and grown under three different management types (cultivated, plants used as live fences, and young plants growing in nurseries). We examined the demographic history and used species distribution modeling to understand the future of A. marmorata under scenarios of climate change. We found high levels of genomic diversity (HS = 0.229) and moderate levels of inbreeding (FIS = 0.106 and Fhat3 = 0.190). The cultivated samples harbored less genetic diversity than the wild plants. Furthermore, we estimated low differentiation between cultivated and wild localities (FST = 0.037). In the wild samples, we identified two main genetic groups, one in the East and another in the West of its distribution area. This genetic structure possibly derived from a population contraction during the Pleistocene (~216,879.75 BP) and the formation of two refugia in small areas with climatic stability. Furthermore, the demographic reconstruction indicated that A. marmorata went through a recent population expansion event, with a large current Ne (Ne = 8,009). The future climate change models indicated contrasting possible changes in its distribution range, from an increase to the reduction of its suitable habitat, differences related to model parametrization, and future levels of CO2 production. We propose conservation measures for the different management types of the species while also considering the biotic and abiotic interactions of Agave marmorata.

Genomic Reconstruction of the Successful Establishment of a Feralized Bovine Population on the Subantarctic Island of Amsterdam.

The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean Zebu in the founder ancestry. Comparative analysis of whole-genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants. Interestingly, the population's success in the harsh environment can be attributed to preadaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts.

Together inbreeding and reproductive compensation favor lethal t-haplotypes.

Male mice who are heterozygous for distorting and non-distorting alleles at the t-haplotype transmit the driving t-haplotype around 90% of the time-a drastic departure from Mendelian expectations. This selfish act comes at a cost. The mechanism underlying transmission distortion in this system causes severe sterility in males homozygous for the drive alleles, ultimately preventing its fixation. Curiously, many driving t-haplotypes also induce embryonic lethality in both sexes when homozygous; however, this is neither universal nor a necessity for this distortion mechanism. Charlesworth provided an adaptive explanation for the evolution of lethal t-haplotypes in a population segregating for distorting and non-distorting t alleles-if mothers compensate by replacing dead embryos with new offspring (or by transferring energy to surviving offspring), a recessive lethal can be favored because it effectively allows mothers the opportunity to trade in infertile males for potentially fertile offspring. This model, however, requires near complete reproductive compensation for the invasion of the lethal t-haplotype and produces an equilibrium frequency of lethal drivers well below what is observed in nature. We show that low levels of systemic inbreeding, which we model as brother-sister mating, allow lethal t-haplotypes to invade with much lower levels of reproductive compensation. Furthermore, inbreeding allows these lethal haplotypes to largely displace the ancestral male-sterile haplotypes. Our results show that together inbreeding and reproductive compensation move expected equilibria closer to observed haplotype frequencies in natural populations and occur under lower, potentially more reasonable, parameters.

Evaluation of selection strategies in dual-purpose and specialized breeding of indigenous chicken

This study aimed to evaluate various selection strategies for adoption in dual-purpose (ICD), meat (ICM) and layer (ICL) breeding goals in indigenous chicken breeding programs. The ICM goal aimed to improve live weight (LW12), daily gain (ADG) and egg weight (EW12) or together with feed efficiency and antibody response. For the ICL goal, age at first egg (AFE) and egg number (EN12) or together with feed efficiency and antibody response were targeted. In the ICD goal, the objective was to improve LW12, ADG, AFE and EN12 or together with feed efficiency and antibody response. Highest total index responses of US$ 49.83, US$ 65.71, and US$ 37.90 were estimated in indices targeting only production traits in the ICD, ICM and ICL goals, respectively. Highest index accuracy estimates of 0.77 and 0.70 were observed in indices that considered production and feed-related traits in the ICD and ICL goals, respectively, while in the ICM goal, the highest estimate of 0.96 was observed in an index targeting only production traits. Inbreeding levels ranged from 0.60 to 1.14% across the various indices considered in the breeding goals. Targeting only production traits in the ICD, ICM and ICL goals required the least number of generations of selection of 7.46, 5.50, and 8.52, respectively, to achieve predefined gains. Generally, a strategy targeting only production traits in a goal was the most optimal but resulted to unfavorable correlated responses in feed efficiency and antibody response. Addition of feed efficiency or/and antibody response in a goal was, however, not attractive due to the decline in total index response and accuracy and increase in inbreeding levels and number of generations of selection. Considering the feed availability and disease challenges in the tropics, choice of including feed efficiency or/and antibody response in the ICD, ICM and ICL goals should depend on targeted production system, resource availability to support breeding activities and magnitude of correlated responses on these traits when not included in the goals.

Island demographics and trait associations in white-tailed deer.

When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.

Population genomics of the invasive Northern Giant Hornet Vespa mandarinia in North America and across its native range

The northern giant hornet Vespa mandarinia (NGH) is a voracious predator of other insect species, including honey bees. NGH’s native range spans subtropical and temperate regions across much of east and southeast Asia and, in 2019, exotic populations of the species were discovered in North America. Despite this broad range and invasive potential, investigation of the population genomic structure of NGH across its native and introduced ranges has thus far been limited to a small number of mitochondrial samples. Here, we present analyses of genomic data from NGH individuals collected across the species’ native range and from exotic individuals collected in North America. We provide the first survey of whole-genome population variation for any hornet species, covering this species’ native and invasive ranges, and in doing so confirm likely origins in Japan and South Korea for the two introductions. We additionally show that, while this introduced population exhibited strongly elevated levels of inbreeding, these signatures of inbreeding are also present in some long-standing native populations, which may indicate that inbreeding depression alone is insufficient to prevent the persistence of NGH populations. As well as highlighting the importance of ongoing monitoring and eradication efforts to limit the spread of this species outside of its natural range, our data will serve as a foundational database for future genomic studies into introduced hornet populations.

Analysis of genetic diversity and structure of endangered Dengchuan cattle population using a single-nucleotide polymorphism chip

This study aimed to evaluate the genetic diversity and structure within the Dengchuan cattle population and effectively protect and utilize their germplasm resources. Herein, the single-nucleotide polymorphisms (SNPs) of 100 Dengchuan cattle (46 bulls and 54 cows) were determined using the GGP Bovine 100K SNP Beadchip. The results showed that among the Dengchuan cattle, a total of 101,220 SNPs were detected, and there were 83,534 SNPs that passed quality control, of which 85.7% were polymorphic. The average genetic distance based on identity-by-state (IBS) within the conservation population of Dengchuan cattle was 0.26 ± 0.02. A total of 3,999 genome-length runs of homozygosity (ROHs) were detected in the Dengchuan cattle, with ROH lengths primarily concentrated in the range of 1–5 Mb, accounting for 87.02% of the total. The average inbreeding coefficient based on ROHs was 4.6%, within the conservation population of Dengchuan cattle, whereas it was 4.9% for bulls, and the Wright inbreeding coefficient (FIS) value was 2.4%, demonstrating a low level of inbreeding within the Dengchuan cattle population. Based on neighbor-joining tree analysis, the Dengchuan cattle could be divided into 16 families. In summary, the conservation population of Dengchuan cattle displays relatively abundant diversity and a moderate genetic relationship. Inbreeding was observed among a few individuals, but the overall inbreeding level of the population remained low. It is important to maintain this low level of inbreeding when introducing purebred bloodlines to expand the core group. This approach will ensure the long-term conservation of Dengchuan cattle germplasm resources and prevent loss of genetic diversity.

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

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

Development and Validation of a Resistance Management Model for the Soybean Cyst Nematode, Heterodera glycines.

Plant-parasitic nematodes are a key yield-limiting pest of crops around the world. Deployment of plant resistance genes are an important management tactic for many economically important plant-parasitic nematodes. The selection for virulence in nematode populations is a major threat to the effectiveness of resistance gene-based management. Little research has gone into resistance management modelling despite the importance of both plant-parasitic nematodes and resistance genes for their management. In this paper, we report on a cyst nematode resistance management model created to explore the factors which are most important for determining the durability of resistance genes to this important family of plant-parasitic nematodes. The relative dominance of virulence expression, the level of inbreeding, and the number of generations per cropping season were the most important factors in predicting resistance gene durability. Aspects of cyst nematode biology that reduce the number of generations per season for a portion of the population had a much smaller effect on the durability of resistance genes. These factors included delayed hatching within a season and early dormancy. The accuracy and utility of the model was tested using the soybean cyst nematode (SCN) rhg1-mediated resistance system. The model accurately predicted the rate at which virulence to the rhg1b resistance gene developed in Iowa over a two-decade period. The model suggested resistance gene pyramids as the most durable management solution for SCN with multiple possible avenues to obtain acceptable efficacy and durability.

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America.

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

225 Genomic diversity of Katahdin sheep and impacts on genomic prediction

Abstract In the late 1950s, Katahdin hair sheep were developed as a composite breed of medium size and moderate prolificacy, with potential to express resistance to gastrointestinal nematodes. With its increasing popularity and the recent adoption of genomic prediction in the Katahdin breeding program, evaluating the genetic diversity in this breed is necessary. Prediction accuracies rely on the strength of genetic relationships. That strength often increases with selection using genomically-enhanced estimated breeding values; however, it carries the risk of decreasing diversity. We aim to characterize the genetic diversity present in the breed and the subsequent impact on the accuracies of genomic predictions. Genotypes on Katahdin sheep from member flocks in the National Sheep Improvement Program were used. Data from two medium density 50k bead chips and one high density 600k bead chip were merged and limited to shared autosomal single nucleotide polymorphisms (SNP). After quality control, there were 9,705 animals and 31,984 SNP remaining. Only for analyses of inbreeding and heterozygosity, linkage disequilibrium (LD) pruning was performed; variants with an LD score exceeding 0.8 were removed with 29,904 SNP remaining. To determine the extent of population structure, principal component (PC) analysis was conducted with PC one and PC two explaining 4.9% and 3.8% of the variation in the population, respectively. When examining subpopulations, a single ancestral population explained 99.9% of the genetic variation among animals. When clustered by identity-by-state, all animals were placed in a single cluster. Inbreeding coefficients were estimated with four methods: method of moments, variance-standardized relationship minus one, excess homozygosity, and correlation between uniting gametes. Across methods, average inbreeding coefficients ranged from 1.14% to 1.20% with Pearson and Spearman correlations ranging from -0.51 to 0.91 (Table 1). Historical effective population sizes (Ne) were estimated for earlier generations, and a linear regression fit to predict more recent Ne. At the founding of the breed, historical Ne was estimated to be 310, and the current Ne was estimated to be 150. Effects of Ne on the accuracy of genomic predictions were examined for reference population sizes ranging from 1k to 25k for traits of low (0.1), moderate (0.3), and high (0.5) heritabilities. The corresponding number of effective chromosomal segments were 2NeL, where L was the length of the genome in morgans (26M). Accuracies of genomic predictions increased as the reference population size grew, with only marginal gains once the population exceeded 15k. Overall, there were no detectable genetic subpopulations in the Katahdin breed. Current levels of inbreeding were low. With a small Ne the breed can achieve high accuracy for genomic predictions by aiming for a reference population of 15k animals. Negative impacts on genetic diversity due to genomic selection are not of immediate concern.

Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics

BackgroundRendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs.ResultsGenetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample.ConclusionsThe Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.

Demographic and conservation genomic assessment of the threatened marbled teal (Marmaronetta angustirostris).

Genetic assessment of species that have experienced dramatic population declines provides critical information that is instrumental for the design of conservation recovery programs. Here, we use different sources of molecular data (mtDNA and ddRAD-seq) to evaluate the genetic status of wild and captive populations of marbled teal (Marmaronetta angustirostris), a duck species classified as critically endangered in Spain and near threatened at a global scale. First, we determined the evolutionary and demographic trajectories of the wild population from Spain and the currently much larger population from Iraq, which is also the documented source of European zoo stocks. Second, we evaluated the suitability of the different captive populations for ongoing restocking programs in Spain and assessed their potential impact on the genetic composition of wild populations. Populations from Spain and Iraq were assigned to distinct genetic clusters, albeit with an overall low level of genetic differentiation, in line with their recent divergence (<8000 years ago) and lack of phylogeographic structure in the species. Demogenomic inferences revealed that the two populations have experienced parallel demographic trajectories, with a marked bottleneck during the last glacial period followed by a sudden demographic expansion and stability since the onset of the Holocene. The wild population from Spain presented high levels of inbreeding, but we found no evidence of recent genetic bottlenecks compatible with the human-driven decline of the species during the past century. The captive populations from the two Spanish centers involved in restocking programs showed genetic introgression from European zoos; however, we found limited evidence of introgression from the zoo genetic stock into the wild population from Spain, suggesting captive-bred birds have limited breeding success in the wild. Our study illustrates how ex situ conservation programs should consider the genetic distinctiveness of populations when establishing breeding stocks and highlights the importance of genetically assessing captive populations prior to reinforcement actions.

Genomic diversity of the locally developed Latvian Darkheaded sheep breed

The Latvian Darkheaded is the only locally developed sheep breed. The breed was formed at the beginning of the 20th century by crossing local coarse-wooled sheep with the British Shropshire and Oxfordshire breeds. The breed was later improved by adding Ile-de-France, Texel, German blackheads, and Finnsheep to achieve higher prolificacy and better meat quality. Previous studies have reported the Latvian Darkheaded sheep to be closely related to Estonian and Lithuanian Blackface breeds, according to microsatellite data. To expand our knowledge of the genetic resources of the Latvian Darkheaded breed, we conducted a whole-genome resequencing analysis on 40 native sheep. The investigation showed that local sheep harbor genetic diversity levels similar to those observed among other improved breeds of European origin, including Charollais and Suffolk. Genome-wide nucleotide diversity (π) in Latvian Darkheaded sheep was 3.91 × 10−3, whereas the average observed heterozygosity among the 40 animals was 0.267 and 0.438 within the subsample of unrelated individuals. The Ne has rapidly decreased to 200 ten generations ago with a recent drop to Ne 73 four generations ago. However, inbreeding levels based on runs of homozygosity were, on average, low, with FROH ranging between 0.016 and 0.059. The analysis of the genomic composition of the breed confirmed shared ancestry with sheep of British origin, reflecting the history of the breed. Nevertheless, Latvian Darkheaded sheep were genetically separable. The contemporary Latvian Darkheaded sheep population is genetically diverse with a low inbreeding rate. However, further development of breed management programs is necessary to prevent an increase in inbreeding, loss of genetic diversity, and depletion of breed-specific genetic resources, ensuring the preservation of the native Latvian Darkheaded sheep.