Rate Of Inbreeding Research Articles

Biases in quantitative genetic parameters estimations caused by self-fertilization in the Caribbean pectinid Argopecten nucleus (Mollusca: Bivalvia)

Inbreeding can cause an important bias in the estimates of quantitative genetic parameters, which in turn can affect the estimated potential for a selection response in species that are simultaneous hermaphrodite with partial self-fertilization. In the present study, the biases caused by self-fertilization on heritability (h2) estimates for productive traits were assessed at different ages in the tropical hermaphrodite pectinid Argopecten nucleus. Self-fertilization rates were estimated in both oocytes and adults, as the percentage of zygotes formed from unfertilized oocytes and by paternity analysis using microsatellite genetic markers, respectively. Fifty sexually mature individuals were individually spawned and genotyped using microsatellite markers. The sperm of one individual used as a male was used to fertilize the oocytes of 4 other individuals, generating 10 half-sibling families (HS) and 40 full-siblings families (FS). At the age of 3.5 months, the total weight, and the length, height, and width of the shell of 60 animals per FS family were individually measured. At the age of 9 months, the same measurements were repeated in the same individuals, which were then euthanized to weigh the soft tissues. In addition, the fecundity was estimated in each individual (number of oocytes produced), and a paternity analysis was performed. No significant differences were found in the average inbreeding rates estimated in oocytes and adults. However, no significant correlation was observed in the estimates of family self-fertilization rates when using both methods. The individuals derived from crossbreeding showed higher average values for productive traits than those produced by selfing, although interactions between the genotype and the depth of culture were observed in both groups. The h2 estimates using statistical models that consider self-fertilization in adults (models II and III) were lower than those observed when self-fertilization rates were estimated in oocytes, or not included in the model. However, the genetic correlations between the traits were similar using both methods for estimating self-fertilization rates. The present results suggest that self-fertilization results in inbreeding depression and induces an overestimation of the h2 for productive traits, but it does not affect estimates of genetic correlations or genotype by environment interactions.

Analysis of genetic variability and population structure of the Mangalica pig breed using pedigree data

The maintenance of genetic diversity (GD) and low rate of inbreeding are two main goals for any conservation programs, especially in a small, closed population which is likely to violate these conservation targets in a long run. Among the conservation programs in Hungary probably the most characterizing is that of the Mangalica pigs, which is an autochthonous Hungarian pig breed group that has been preserved for biological diversity since 1973. The current study aimed to expose the evolution of population structure, GD and inbreeding coefficient with different approaches by analysing the pedigree of these breeds in the context of the conservation program. Genealogy analysis used the data of 12,808, 2393 and 3963 Blonde, Swallow-Belly and Red breeding animals born between 1980 and 2021, respectively. The reference populations (REF2021) were defined as breeding animals born between 2016 and 2021. Pedigree completeness was more than 90% in the fifth generation and the complete generation equivalent ranged from 4.29 to 7.08 and from 6.87 to 9.73 for the whole and the reference populations (REF2021), respectively. Generation interval on average was vary from 3.06 to 3.45 years with the longer pathways to the son. Most of different estimated inbreeding coefficient showed increased trends through pedigrees except for the Kalinowski new inbreeding coefficient (FNew) which decreased in all breeds in the last decade. The mean Wright inbreeding coefficient (Fw) was low, being 5.50%, 4.30% and 7.54% for the Blonde, Swallow-Belly, and Red reference populations (REF2021), respectively. Fw showed strong correlation with FNew but low correlation with FBal while the two types of ancestral inbreeding coefficients (FBal and FKal) were ranging from moderate strong to strong correlation in every breed. Effective population size of the reference populations (REF2021) was 85.57, 76.91, and 57.56, respectively. Based on the predicted future inbreeding for the next 25 years only the Red Mangalica breed was predicted to be “Transitional” in the endangerment categories. The GD loss in these three breeds was 5.6%, 5.7% and 8.7%, respectively, in which the loss due to genetic drift was decisive compared to the unequal founder contributions. In conclusion, the three populations at the present and in the next few generations are having optimistic perspective in terms of GD. These populations should be focused on reducing new inbreeding in mating plans and the Red population need to be monitored more carefully because of its current highest GD loss, smallest effective population size and highest inbreeding coefficient.

Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study.

Nucleus-based breeding programs are characterized by intense selection that results in high genetic gain, which inevitably means reduction of genetic variation in the breeding population. Therefore, genetic variation in such breeding systems is typically managed systematically, for example, by avoiding mating the closest relatives to limit progeny inbreeding. However, intense selection requires maximum effort to make such breeding programs sustainable in the long-term. The objective of this study was to use simulation to evaluate the long-term impact of genomic selection on genetic mean and variance in an intense layer chicken breeding program. We developed a large-scale stochastic simulation of an intense layer chicken breeding program to compare conventional truncation selection to genomic truncation selection optimized with either minimization of progeny inbreeding or full-scale optimal contribution selection. We compared the programs in terms of genetic mean, genic variance, conversion efficiency, rate of inbreeding, effective population size, and accuracy of selection. Our results confirmed that genomic truncation selection has immediate benefits compared to conventional truncation selection in all specified metrics. A simple minimization of progeny inbreeding after genomic truncation selection did not provide any significant improvements. Optimal contribution selection was successful in having better conversion efficiency and effective population size compared to genomic truncation selection, but it must be fine-tuned for balance between loss of genetic variance and genetic gain. In our simulation, we measured this balance using trigonometric penalty degrees between truncation selection and a balanced solution and concluded that the best results were between 45° and 65°. This balance is specific to the breeding program and depends on how much immediate genetic gain a breeding program may risk vs. save for the future. Furthermore, our results show that the persistence of accuracy is better with optimal contribution selection compared to truncation selection. In general, our results show that optimal contribution selection can ensure long-term success in intensive breeding programs using genomic selection.

Is now the time? Review of genetic rescue as a conservation tool for brook trout.

Brook trout populations have been declining throughout their native range in the east coast of the United States. Many populations are now distributed in small, isolated habitat patches where low genetic diversity and high rates of inbreeding reduce contemporary viability and long-term adaptive potential. Although human-assisted gene flow could theoretically improve conservation outcomes through genetic rescue, there is widespread hesitancy to use this tool to support brook trout conservation. Here, we review the major uncertainties that have limited genetic rescue from being considered as a viable conservation tool for isolated brook trout populations and compare the risks of genetic rescue with other management alternatives. Drawing on theoretical and empirical studies, we discuss methods for implementing genetic rescue in brook trout that could yield long-term evolutionary benefits while avoiding negative fitness effects associated with outbreeding depression and the spread of maladapted alleles. We also highlight the potential for future collaborative efforts to accelerate our understanding of genetic rescue as a viable tool for conservation. Ultimately, while we acknowledge that genetic rescue is not without risk, we emphasize the merits that this tool offers for protecting and propagating adaptive potential and improving species' resilience to rapid environmental change.

MDSi: Multi-omics Database for Setaria italica

BackgroundFoxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows the high inbreeding rate and close relationship to several major foods, feed, fuel and bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cycle. The de novo assembled genome data with high-quality and an efficient Agrobacterium-mediated genetic transformation system made xiaomi an ideal C4 model system. The mini foxtail millet has been widely shared in the research community and as a result there is a growing need for a user-friendly portal and intuitive interface to perform exploratory analysis of the data.ResultsHere, we built a Multi-omics Database for Setaria italica (MDSi, http://sky.sxau.edu.cn/MDSi.htm), that contains xiaomi genome of 161,844 annotations, 34,436 protein-coding genes and their expression information in 29 different tissues of xiaomi (6) and JG21 (23) samples that can be showed as an Electronic Fluorescent Pictograph (xEFP) in-situ. Moreover, the whole-genome resequencing (WGS) data of 398 germplasms, including 360 foxtail millets and 38 green foxtails and the corresponding metabolic data were available in MDSi. The SNPs and Indels of these germplasms were called in advance and can be searched and compared in an interactive manner. Common tools including BLAST, GBrowse, JBrowse, map viewer, and data downloads were implemented in MDSi.ConclusionThe MDSi constructed in this study integrated and visualized data from three levels of genomics, transcriptomics and metabolomics, and also provides information on the variation of hundreds of germplasm resources that can satisfies the mainstream requirements and supports the corresponding research community.

Uncovering inbreeding, small populations, and strong genetic isolation in an Australian threatened frog, Litoria littlejohni

AbstractThe status of many amphibian populations remains unclear due to undetected declines driven by disease and difficulties in obtaining accurate population estimates. Here, we used genome complexity reduction-based sequencing technology to study the poorly understood Littlejohn’s treefrog, Litoria littlejohni across its fragmented distribution in eastern Australia. We detected five identifiable genetic clusters, with moderate to strong genetic isolation. At a regional scale, population isolation was likely driven by population crashes, resulting in small populations impacted by founder effects. Moderate genetic isolation was detected among populations on the Woronora Plateau despite short distances between population clusters. Evidence of recent declines was apparent in three populations that had very small effective population size, reduced genetic diversity and high inbreeding values. The rates of inbreeding detected in these populations combined with their small size leave these populations at elevated risk of extinction. The Cordeaux Cluster was identified as the most robust population as it was the largest and most genetically diverse. This study exemplifies the value of employing genetic methods to study rare, cryptic species. Despite low recapture rates using traditional capture-recapture demographic methods, we were able to derive population estimates, describe patterns of gene flow, and demonstrate the need for urgent conservation management.

The persistence of the critically endangered Asiatic cheetah relies upon urgent connectivity protection: a landscape genetics perspective

Decreasing genetic diversity, gene flow rates and population connectivity can increase inbreeding rates and extinction risks. Asiatic cheetah is a critically endangered mammal with large home range that suffered from extreme range reduction and population decline. Their population is now fragmented into two subpopulations. We used genetic markers to estimate genetic diversity, relatedness, minimum effective population size and gene flow, and to assess population structure. Putative corridors connecting subpopulations were inferred using connectivity models based on topography, land cover and human footprints resistance variables. Individual pairwise genetic relatedness was compared with resistance values obtained from these models and with Euclidean distances between samples to assess the most important factors shaping the current genetic structure. The estimated effective population size was extremely low (Ne = 11 to 17). Both Northern and Southern Subpopulations exhibited low genetic diversity and high relatedness. Several signatures of gene flow and movement of individuals between subpopulations were observed suggesting that inferred corridors potentially connecting subpopulations are functional. However, no traces of gene flow were observed for the latest generations, maybe due to a decrease of functional connectivity in recent years. The resistance model including all variables was best related to genetic relatedness, whereas population differentiation is mostly driven by isolation by distance. The very low estimated effective population size, decreased genetic diversity, and high relatedness of Asiatic cheetah suggests that population reinforcement, removing obstacles to connectivity and boosting prey population conservation in stepping stones are urgently needed to prevent the imminent extinction of iconic biodiversity.

POPULATION DOCUMENTATION OF PELUNG CHICKENS IN FIVE SUB-DISTRICTS IN BANDUNG REGENCY

Pelung chicken is animal-genetic-resources which has a relatively larger physical appearance compared to other local chickens and has a long, melodious and rhythmic sound. Bandung Regency that has a fairly high population of Pelung chickens, but the number and structure of the population have not been documented. This research aims to determine the number and structure of the population, effective population size and inbreeding rate of Pelung chickens. The data collection technique was carried out by means of a survey, namely direct interviews with respondents in sub-districts including Ciparay, Kutawaringin, Katapang, Cicalengka and Cikancung. The variables observed in this research were male and female Pelung chickens grouped based on age, effective population size and inbreeding rate. The population data was then analyzed by quantitative descriptive method. The results showed that total population of Pelung chickens was 1,133 birds. The effective population size of Pelung chickens is 397 birds. The population structure of male Pelung 0-3 months was 228 birds, >3-6 months was 169 birds and >6 months was 201 birds, then for female Pelung chickens 0-3 months was 219 birds, >3-6 months was 119 birds and >6 months was 197 birds. The inbreeding rate of Pelung chickens is 0.13%.

Genetic diversity and IUCN Red List status.

The International Union for Conservation of Nature (IUCN) Red List is an important and widely used tool for conservation assessment. The IUCN uses information about a species' range, population size, habitat quality and fragmentation levels, and trends in abundance to assess extinction risk. Genetic diversity is not considered, although it affects extinction risk. Declining populations are more strongly affected by genetic drift and higher rates of inbreeding, which can reduce the efficiency of selection, lead to fitness declines, and hinder species' capacities to adapt to environmental change. Given the importance of conserving genetic diversity, attempts have been made to find relationships between red-list status and genetic diversity. Yet, there is still no consensus on whether genetic diversity is captured by the current IUCN Red List categories in a way that is informative for conservation. To assess the predictive power of correlations between genetic diversity and IUCN Red List status in vertebrates, we synthesized previous work and reanalyzed data sets based on 3types of genetic data: mitochondrial DNA, microsatellites, and whole genomes. Consistent with previous work, species with higher extinction risk status tended to have lower genetic diversity for all marker types, but these relationships were weak and varied across taxa. Regardless of marker type, genetic diversity did not accurately identify threatened species for any taxonomic group. Our results indicate that red-list status is not a useful metric for informing species-specific decisions about the protection of genetic diversity and that genetic data cannot be used to identify threat status in the absence of demographic data. Thus, there is a need to develop and assess metrics specifically designed to assess genetic diversity and inform conservation policy, including policies recently adopted by the UN's Convention on Biological Diversity Kunming-Montreal Global Biodiversity Framework.

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.

Genetic diversity and within-breed variation in three indigenous Ethiopian sheep based on whole-genome analysis

The objective of this work was to study genetic diversity by comparing whole genome sequence data of Rutana, Gumuz and Washera sheep found in Amhara and Benishanguel gumuz regional states of Ethiopia. We employed variant calling format tools version 0.1.15 to calculate some genetic diversity indices such as observed heterozygosity, expected heterozygosity, inbreeding coefficient, and nucleotide diversity. The results revealed that, observed heterozygosity ranged from 0.33 in Gumuz to 0.34 in Rutana and Washera sheep. Expected heterozygosity ranged from 0.37 in Rutana to 0.38 in Gumuz and Washera sheep. Expected heterozygosity was found to be higher than observed heterozygosity. Higher inbreeding coefficient (0.12) was recorded for Gumuz sheep compared to 0.09 of Rutana and Washera sheep. Mean nucleotide diversity values were 0.0029, 0.0030 and 0.0028 for Gumuz, Rutana and Washera sheep, respectively. Higher values of nucleotide diversity were recorded. Population structure analysis using principal component analysis revealed no clear separation between Gumuz, Rutana and Washera sheep populations with possibility of gene flow attributed to geographical location proximity. The smaller population size, closed breeding system, genetic drift and uncontrolled (non-random) mating might lead to higher rate of inbreeding in Gumuz, Rutana and Washera sheep, requiring timely intervention. This intervention helps to prevent inbreeding depression and extinction of these valuable breeds of sheep, which helps in sustaining the livelihood of sheep keepers in lowlands and highlands. Nevertheless, the whole-genome analysis revealed high within-breed variation. Uncovered areas of studies like mapping quantitative trait loci, identifying genes underpinning productivity traits such as carcass quantity and meat quality could be carried out on diversified sheep resources identified by the current study. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. Designing conservation-based within-breed sheep selective breeding programs are recommended considering economically important traits into account.

Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India

The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (n = 19), Tharparkar (n = 17), and Gir (n = 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (FROH) revealed that Gir had the highest FROH (0.099) proposing more inbreeding rate in this population. Effective population size (Ne) decreased slowly over the last 60 generations and at 13 generations ago; Ne was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (r = 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.

Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of Seriola lalandi.

Developing sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as well as a 90 K SNP genotyping array based on different populations of yellowtail kingfish (Seriola lalandi). The minimum and maximum distance between adjacent marker pairs were 0.7 Mb and 13 Mb, respectively, with an average marker spacing of 2 Mb. Weak evidence of the linkage disequilibrium between adjacent marker pairs was found. The results showed high panel performance for parental assignment, with probability exclusion values equaling 1. The rate of false positives when using cross-population data was null. A skewed distribution of genetic contributions by dominant females was observed, thus increasing the risk of higher rates of inbreeding in subsequent captive generations when no parentage data are used. All these results are discussed in the context of breeding program design, using this marker panel to increase the sustainability of this aquaculture resource.

Estimating inbreeding rate and effective population size in the Finnish Ayrshire population in the era of genomic selection.

Genomic selection has been applied in dairy cattle breeding over the last decade. Using genomic information may speed up genetic gain as breeding values can be predicted reasonably accurately directly after birth. However, genetic diversity may decrease if the inbreeding rate per generation increases and the effective population size decreases. Despite many positive qualities of the Finnish Ayrshire, for example, high average protein yield and fertility, over time the breed has lost its place as the most common dairy breed in Finland. Thus, maintaining the genetic variability of the breed is becoming more important. The aim of our research was to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data. The genomic data included 46,914 imputed single nucleotide polymorphism (SNP) variants from 75,038 individuals, and the pedigree data included 2,770,025 individuals. All animals in the data were born between 2000 and 2020. Genomic inbreeding coefficients were estimated as the proportion of SNPs in runs of homozygosity (ROH) out of the total number of SNPs. The inbreeding rate was estimated by regressing the mean genomic inbreeding coefficients on birth years. Effective population size was then estimated based on the inbreeding rate. Additionally, effective population size was estimated from the mean increase in individual inbreeding using pedigree data. Introduction of genomic selection was assumed to have taken place gradually; years 2012-2014 were treated as a transition period from the traditional phenotype-based breeding value estimation to genomic-based estimation. The median length of the identified homozygous segments was 5.5Mbp, and a slight increase in the proportion of segments over 10Mbp was observed after 2010. The inbreeding rate decreased from 2000 to 2011 and subsequently increased slightly. The pedigree- and genomic-based estimates of inbreeding rate were similar to each other. The estimates of effective population size based on the regression method were very sensitive to the number of years considered; thus, the estimates were not very reliable. The effective population size estimated from the mean increase in individual inbreeding reached its highest value of 160 in 2011 and decreased to 150 after that. In addition, the generation interval in the sire path has decreased from 5.5 years to 3.5 years after genomic selection was implemented. Based on our results, after the implementation of genomic selection, the proportion of long ROH stretches has increased, the generation interval in the sire path has decreased, the inbreeding rate has increased and the effective population size has decreased. However, the effective population size is still at a good level, allowing for an efficient selection scheme in the Finnish Ayrshire breed.

Exploring island syndromes: Variable matrix permeability in Phalaenopsis pulcherrima (Orchidaceae), a specialist lithophyte of tropical Asian inselbergs.

Plants confined to island-like habitats are hypothesised to possess a suite of functional traits that promote on-spot persistence and recruitment, but this may come at the cost of broad-based colonising potential. Ecological functions that define this island syndrome are expected to generate a characteristic genetic signature. Here we examine genetic structuring in the orchid Phalaenopsis pulcherrima, a specialist lithophyte of tropical Asian inselbergs, both at the scale of individual outcrops and across much of its range in Indochina and on Hainan Island, to infer patterns of gene flow in the context of an exploration of island syndrome traits. We sampled 323 individuals occurring in 20 populations on 15 widely scattered inselbergs, and quantified genetic diversity, isolation-by-distance and genetic structuring using 14 microsatellite markers. To incorporate a temporal dimension, we inferred historical demography and estimated direction of gene flow using Bayesian approaches. We uncovered high genotypic diversity, high heterozygosity and low rates of inbreeding, as well as strong evidence for the occurrence of two genetic clusters, one comprising the populations of Hainan Island and the other those of mainland Indochina. Connectivity was greater within, rather than between the two clusters, with the former unequivocally supported as ancestral. Despite a strong capacity for on-spot persistence conferred by clonality, incomplete self-sterility and an ability to utilize multiple magnet species for pollination, our data reveal that P. pulcherrima also possesses traits that promote landscape-scale gene flow, including deceptive pollination and wind-borne seed dispersal, generating an ecological profile that neither fully conforms to, nor fully contradicts, a putative island syndrome. A terrestrial matrix is shown to be significantly more permeable than open water, with the direction of historic gene flow indicating that island populations can serve as refugia for postglacial colonisation of continental landmasses by effective dispersers.

Genetic Diversity and Trends of Ancestral and New Inbreeding in German Sheep Breeds by Pedigree Data.

In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of rams may risk losing genetic diversity and increasing rates of inbreeding. On the other hand, breeds with a low number of founder animals and only regional popularity may not leave their endangered status, as the number of breeders interested in the breed is limited. The objective of the present study was to determine demographic measures of genetic diversity and recent as well as ancestral trends of inbreeding in all autochthonous German sheep breeds and sheep of all breeding directions, including wool, meat, and milk. We used pedigree data from 1,435,562 sheep of 35 different breeds and a reference population of 981,093 sheep, born from 2010 to 2020. The mean number of equivalent generations, founders, effective founders, effective ancestors, and effective founder genomes were 5.77, 1669, 123.2, 63.5, and 33.0, respectively. Genetic drift accounted for 69% of the loss of genetic diversity, while loss due to unequal founder contributions was 31%. The mean inbreeding coefficient, individual rate of inbreeding (∆Fi), and realized effective population size across breeds were 0.031, 0.0074, and 91.4, respectively, with a significantly decreasing trend in ∆Fi in 11/35 breeds. New inbreeding, according to Kalinowski, contributed to 71.8% of individual inbreeding, but ancestral inbreeding coefficients showed an increasing trend in all breeds. In conclusion, in our study, all but one of the mountain-stone sheep breeds and the country sheep breed Wald were the most vulnerable populations, with Ne < 50. The next most endangered breeds are exotic, country, and heath breeds, with average Ne of 66, 83, and 89, respectively. The wool, meat, and milk breeds showed the highest genetic diversity, with average Ne of 158, 120, and 111, respectively. The results of our study should help strengthen conservation program efforts for the most endangered sheep breeds and maintain a high genetic diversity in all sheep breeds.

Pedigree Data from Six Rhesus Macaque (Macaca mulatta) Matrilines at the California National Primate Research Center Indicate Inbreeding and Loss of Genetic Variation.

Relatedness and kinship structure in matrilines are a potential source of social stability. The current study aimed to analyze the extant pedigrees of 6 living matrilines in different field cages to assess rates of cross-generational inbreeding and loss of genetic variation over time. All 6 matrilines showed increasing levels of inbreeding over generation time, although the rates of increase were different. The female-to-male-adult sex ratio was correlated with average matriline inbreeding levels, while the number of adult males was positively correlated with average matriline genetic diversity. Over five times more paternal half-sibs than maternal half-sibs were present because paternity had been restricted to a few males yearly. Therefore, the relatedness through the paternal lines was over five times greater than that of the maternal lines. Overall, each matriline lost low to moderate levels of genetic variation with time. The current rates of gene flow between field cages by cross-fostered infants have not stopped inbreeding within these matrilines or loss of diversity due to genetic drift. This situation probably developed because translocated animals, especially males, may not breed successfully. Only 4 of the 22 translocated individuals, all females, eventually reproduced, resulting in 13 offspring and generating an overall breeding success of 0.59 across all 6 study matrilines. However, even this low rate of reproduction by the translocated animals reduced inbreeding and kinship among matrilines and increased genetic heterogeneity in the matrilines. Based on this study, we propose several colony management strategies, including equalizing adult sex ratios to increase the effective population size in the field cages, increasing the number of cross-fostered infants, and relying more on multigenerational pedigree data to aid the alignment of genetic and behavioral management techniques.

Популяционно-генетическая структура степного орла: есть ли надежда на сохранение вида?

For centuries, Steppe Eagle (Aquila nipalensis) had been the most numerous Palearctic Aquila species, but nowadays it has been decreasing in numbers progressively, so in 2015 the IUCN changed the species status to “endangered”. The decrease is evidently related to Steppe Eagles’ electrocution at nesting areas and during migration, poisoning by veterinarian drugs when feeding on agricultural animal carcasses at wintering grounds, steppe fires and total habitat loss combined with loss of prey like susliks. To the contrary, the sister Aquila species, the Imperial Eagle (Aquila heliaca), which exhibits similar biological traits and lives simpatrically to the Steppe Eagle at some parts of areas, shows local increase in numbers and even substitutes the decreasing Steppe Eagle in steppe biomes. In the 1960s, many Palearctic birds of prey came through population decline due to so-called “DDT crisis” – massive pesticide poisoning. To restore the species numbers, specific conservation actions were initiated in Europe to support population numbers and genetic diversity of raptors. Regarding the Steppe Eagle with its nesting area located mostly at Kazakhstan, Russian, Mongolian and Chinese territories, the implications of DDT and electrocution impacts on the population numbers stayed poorly investigated. Meanwhile, loss of genetic stability can be a reason for lasting population decline. Genetic threats like population fragmentation, genetic erosion, and inbreeding depression are believed more prolonged in comparison to anthropogenic impacts and more rarely come under increasing scrutiny of conservation practitioners. However, if exist, they can lead to species extinction regardless of removal of all other threats. The Steppe Eagle population structure stays poorly investigated. In 2018, during the 1st Steppe Eagle conservation international workshop, this problem was highlighted with recommendations for filling this gap. Our presented study was conducted following this recommendation and focused on genetic structure, fragmentation, and effective number comparison of the Steppe Eagle population at the individual samples) and sympatric populations of the Imperial Eagle (over 100 samples). For conservation criteria estimation, we used widespread genetic markers like nuclear microsatellites (9 loci) and mitochondrial control region (D-loop). Also we performed molecular individual tagging and parentage analysis to study the population structure using samples from the numerous Western Kazakhstan population. We also used GIS methods to study geographic fragmentation of populations. The genetic analysis showed that the Steppe Eagle population structure is highly similar to that of the Imperial Eagle but with less genetic diversity and has traces of repeated survival of “population bottlenecks” with huge decline in the number and genetic diversity. Fragmentation analysis showed no genetic isolation of geographically fragmented nesting groups despite the presumed natal phylopatry in accordance with our Steppe Eagle parentage data. Preliminary estimation of the Steppe Eagle population effective numbers by linkage disequilibrium method showed rather high values inspite of the lasting population decline. The molecular coancestry estimation showed more serious decline during the latest bottleneck which was also far below the ancestral Imperial Eagle population at the studied areas. The inbreeding rate for the Steppe Eagle population at the most part of the species areas turned out to outnumber one for the local population of the Imperial Eagle. Our data showed no immediate genetic threats for the Steppe Eagle population restoration and also demonstrated traces of multiple bottlenecks in the species evolution. Still the genetic structure of the species population keeps some traits of modern decline and should be monitored permanently according to the species numbers. Unique population structure patterns of the Steppe Eagle between other Aquilinae species and their conservation aspects are directions for future Aquila nipalensis genetic research.

Monitoring of recessive defects associated with low reproductive performance in dairy cattle in Uruguay.

Most dairy cattle breeds originate show an average generational inbreeding rate of 1%, which favors the occurrence of recessive defects associated with low reproductive performance. The objective of this study was to monitor recessive defects associated with low reproductive performance in dairy cattle. To monitor bulls carrying the Holstein Friesian haplotype (HH) 1, HH3, and HH4 haplotypes, we analyzed the records of 3,028 national and imported Holstein Friesian bulls from the 2021 updated sires' catalog published by "Evaluaciones Genéticas Lecheras"; and to determine the presence of these mentioned haplotypes, as well as Jersey haplotype (JH) 1 and complex vertebral malformation (CVM), were genotype with the GeneTitan® 2,500 single nucleotide polymorphism (SNP) bovine chip, estimate their frequencies and evaluate their impact on the fertility of 100 Holstein Friesian cows and 70 Holstein Friesian-Jersey crosses belonging to an experimental dairy. From a total of 1,468 (48.5%) bulls with genetic information from the sires' catalog for HH1 and 1,471 (48.6%) for HH3 and HH4, we found 90 (6.1%) carriers for HH1, 60 (4.1%) for HH3, and 6 (0.4%) for HH4, respectively. By genotyping with the chip, we calculated the herd frequency of the mutant alleles and herd prevalence of carriers for HH1 and CVM as q = 0.003 and 0.022; 0.59% and 4.3% (call rate >0.99), respectively. No mutant alleles were found for HH3, HH4, and JH1 in the analyzed population. We examined reproductive data by observing the presence of CVM and HH1 mutant alleles in repeat cows with an average of four services to achieve pregnancy. This study demonstrated the presence of recessive defects associated with low reproductive performance in the analyzed population, which can affect the health and productivity of dairy cattle. Therefore, cows and bulls should be closely monitored through genetic testing to lower the incidence of recessive defects in dairy cattle.

Identifying influential sires and distinct clusters of selection candidates based on genomic relationships to reduce inbreeding in the US Holstein.

High relatedness in the US Holstein breed can be attributed to the increased rate of inbreeding that resulted from strong selection and the extensive use of a few bulls via reproductive biotechnology. The objectives of this study were to determine whether clustering could separate selected candidates into genetically different groups and whether such clustering could reduce the expected inbreeding of the next generation. A genomic relationship matrix composed of 1,145 sires with the most registered progeny in the breed born after 1985 was used for principal component analysis and k-means clustering. The 5 clusters reduced the variance by 25% and contained 171 (C1), 252 (C2), 200 (C3), 244 (C4), and 278 (C5) animals, respectively. The 2 most predominant families were C1 and C2, while C4 contained the most international animals. On average, C1 and C5 contained older animals; the average birth year per cluster was 1988 (C1), 1996 (C2 and C3), 1999 (C4), and 1990 (C5). Increasing to 10 clusters allowed the separation of the predominant sons. Statistically significant differences were observed for indices (net merit index, cheese merit index, and fluid merit index), daughter pregnancy rate, and production traits (milk, fat, and protein), with older clusters having lower merit for production but higher for reproduction. K-means clustering was also used for 20,099 animals considered as selection candidates. Based on the reduction in variance achieved by clustering, 5 to 7 clusters were appropriate. The number of animals in each cluster was 3,577 (C1), 3,073 (C2), 3,302 (C3), 5,931 (C4), and 4,216 (C5). The expected inbreeding from within or across cluster mating was calculated using the complete pedigree, assuming the mean inbreeding of animals born in the same year when parents are unknown. Generally, inbreeding was highest within cluster mating and lowest across cluster mating. Even when 10 clusters were used, one cluster always gave low inbreeding in all scenarios. This suggests that this cluster contains animals that differ from all other groups but still contains enough diversity within itself. Based on lower across cluster inbreeding, up to 7 clusters were appropriate. Statistically significant differences in genomic estimated breeding values were found between clusters. The rankings of clusters for different traits were mostly the same except for reproduction and fat. Results show that diversity within the population exists and clustering of selection candidates can reduce the expected inbreeding of the next generations.