Levels Of Heterozygosity Research Articles

Genetic Characterization of Procambarus clarkii Cultured in Sichuan Province Based on Microsatellite Markers

The Procambarus clarkii production sector in Sichuan Province, China, is experiencing rapid growth. However, the industry faces significant challenges, including on-farm breeding and the widespread “Catch Big, Keep Small” farming practice, which have led to substantial genetic degradation within P. clarkii populations. Moreover, the uncertainty surrounding the origins of breeding stocks poses an additional obstacle to the local selection and cultivation of high-quality juvenile P. clarkii. With the objective of inferring the genetic lineage of cultivated P. clarkii in Sichuan, twelve microsatellite loci were employed to investigate the genetic characters of six P. clarkii populations from Sichuan and two from Hubei Province, China. The results revealed that the Sichuan populations exhibited higher levels of heterozygosity (Ho = 0.549~0.699, He = 0.547~0.607) and genetic diversity than the Hubei populations (Na = 4.00~5.250, PIC = 0.467~0.535). Notably, the DY population located in northeastern Sichuan showed the highest heterozygosity (Ho = 0.699, He = 0.607) and genetic diversity (Na = 5.250, PIC = 0.535) among the eight populations. Population structure, principal coordinate analysis and clustering analysis illuminated a close genetic relationship between the Qionglai population in Sichuan and the Jianli population in Hubei. Additionally, the remaining five Sichuan populations (Luxian, Nanxi, Xingwen, Neijiang and Daying) exhibited strong genetic affinity with the QianJiang population in Hubei, and particularly high genetic exchange may have occurred between Daying and Qianjiang (Fst = 0.001, Nm = 217.141). These results suggest that the primary cultivated P. clarkii populations in Sichuan likely originated from Qianjiang and Jianli counties in Hubei, with Qianjiang contributing a more substantial proportion. The genetic diversity of Sichuan populations was higher than those of some other Chinese P. clarkii farming provinces and even some native populations. Specifically, the Daying population emerges as a potential breeding germplasm source for crayfish in Sichuan. In contrast, the Qionglai population exhibits relatively low genetic diversity, highlighting the need for strategic enhancement through interactions with other populations to promote diversity and resilience. Furthermore, fostering genetic exchange among locally cultivated populations within the southern Sichuan basin is strategic to elevate the quality of P. clarkii germplasm resources.

Genetic structure of cattle of the siberian branch by microsatellite loci

Molecular-genetic methods are essential tools for the utilization and conservation of animal genetic resources. These methods facilitate more efficient management and control of breeding programs within livestock production systems. For studying the genetic diversity of a population, the use of STR markers is relevant due to the high variability of repeats. This study presents a genetic characterization of a Holstein and Black Pied cattle population (n = 10233) in Western Siberia using 12 microsatellite loci (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53). A total of 145 alleles were identified across all loci, with frequencies ranging from 0.00005 to 0.68961. The highest level of genetic diversity was observed at the TGLA122 locus (25 alleles) with an average number of effective alleles (Ne) of 4.5. The least polymorphic locus was BM1824 (7 alleles) with an average Ne of 3.27. The average observed (Ho) and expected (He) heterozygosity across all loci was 0.6. The highest variability was observed at the TGLA53 locus, with a Wright’s fixation index (Fis) of 0.161, indicating a heterozygote deficiency. A similar deficiency was observed at the BM1818 locus. All other loci exhibited a positive Fis, with the highest value observed at the ETH3 locus (-0.074), indicating an excess of heterozygotes. The average Fis across all loci was -0.02, suggesting a sufficient level of heterozygosity within the studied population. These findings provide valuable information for population studies and practical breeding programs aiming to manage genetic diversity and improve selection efficiency in this cattle population.

Identification of the genetic background of laboratory rats through amplicon-based next-generation sequencing for single-nucleotide polymorphism genotyping

BackgroundLaboratory rats, as model animals, have been extensively used in the fields of life science and medicine. It is crucial to routinely monitor the genetic background of laboratory rats. The conventional approach relies on gel electrophoresis and capillary electrophoresis (CE) technologies. However, the experimental and data analysis procedures for both of these methods are time consuming and costly.ResultsWe established a single-nucleotide polymorphism (SNP) typing scheme using multiplex polymerase chain reaction (PCR) and next-generation sequencing (NGS) to address the genetic background ambiguity in laboratory rats. This methodology involved three rounds of PCR and two rounds of magnetic bead selection to improve the quality of the sequencing data. We simultaneously analysed 100 laboratory rats (including rats of 5 inbred strains and 2 in-house closed colonies), and the sequencing depth varied from an average of 108.25 to 5189.89, with sample uniformity ranging from 82.5 to 97.5%. A total of 98.9% of the amplicons were successfully genotyped (≥ 30 reads). Genetic background analysis revealed that all 38 experimental rats from the 5 inbred strains were successfully identified (without a heterozygous allele). For the 2 in-house closed colonies, the average heterozygosity (0.162 and 0.169) deviated from the typical range of 0.5–0.7, indicating a departure from the ideal heterozygosity level. Additionally, we employed multiplex PCR-CE to validate the NGS-based method, which yielded consistent results for all the rat strains. These results demonstrated that this approach significantly improves efficiency, saves time, reduces costs and ensures accuracy.ConclusionBy utilizing NGS technology, our developed method leverages SNP genotyping for genetic background identification in laboratory rats, demonstrating advantages in terms of labour efficiency and cost-effectiveness, thereby rendering it well suited for projects involving extensive sample cohorts.

Взаимосвязь геномного и расчетного инбридинга в популяции крупного рогатого скота голштинской породы Свердловской области

Abstract. The purpose of this paper is to study the inbreeding change of Holstein cattle in Sverdlovsk region and to show the correlation between genomic and estimated inbreeding. Methods. The study was conducted in six farms of the Sverdlovsk region and included 512 cows and heifers with date of birth from 2007 to 2022 and 12 breeding bulls. Chips GGP Bovine 150K (Neogen, USA) and Bovine 50K (Illumina, USA) were used for genotyping. Genome inbreeding estimates F were conducted with --het function in PLINK v1.9. Homozygosity inbreeding coefficient FROH was calculated with “sliding window” package of detectRUNS; FPED was taken from SELEX database, where it was calculated by pedigrees with Wright-Kislovsky formula. Scientific novelty. The comparison of genomic inbreeding for different age groups and estimation of correlations with pedigree inbreeding was conducted in Sverdlovsk region for the first time. Results. Our studies show that inbreeding coefficients increase radically from younger to older age groups. Holstein breed bulls show the highest value of inbreeding. At the same time heterozygosity level, estimated with sMLH tends to decrease with age. In addition, a strong correlation between estimated by pedegree inbreeding FPED and date of birth, as well as weak correlations between FPED and genomic coefficients (which have strong correlations with each other) were established.

Genetic Diversity, Kinship, and Polychromatism in the Spotted Eagle Ray Aetobatus ocellatus of Fiji

The spotted eagle ray Aetobatus ocellatus (Kuhl, 1923) has a widespread Indo-West Pacific distribution and displays substantial population genetic structuring. Genetic data are crucial for understanding the species’ diversity, connectivity, and adaptation. However, molecular genetic information on A. ocellatus from Melanesia is lacking, which impedes our understanding of gene flow among geographic regions. In this study, we sampled 45 A. ocellatus, primarily from Fiji’s largest fish market in the capital, Suva. Mitochondrial DNA Cytochrome C Oxidase subunit I (COI) barcoding was used for species identification, and DArT-seqTM technology was applied to assess the nuclear genetic diversity. Barcoding of the COI gene showed a 98.6% to 99.8% similarity to A. ocellatus reference sequences in the Barcode of Life Data System, and the 45 individuals were represented by three major evolutionary haplotype clusters. Genotyping resulted in 24,313 Single-Nucleotide Polymorphisms (SNPs) which were quality-filtered to 7094 SNPs per individual. The observed heterozygosity level was 0.310. The inbreeding coefficient was positive, and genotyping identified one full-sibling pair and one half-sibling pair from the 45 individuals. Additionally, eagle rays exhibit polychromatic patterns, and at least three ventral pattern variations were recorded in specimens from the market. Collectively, our main findings characterize the genetic profile of A. ocellatus in Fiji and can help to understand the diversification of this species within the region.

Analysis of inbreeding depression in five S1 Cassava families of elite varieties at the seedling nursery and clonal evaluation trial stages.

Background Cassava is an outcrossing, highly heterozygous plant that is reported to suffer from inbreeding depression. However, unraveling recessive traits and exploring additive genes would require a limited level of inbreeding for the genetic improvement of cassava. Method The impact of inbreeding depression (ID) on agronomic and biotic tolerance of cassava was evaluated using the S1 progenies of five African cassava varieties (TMS 30572, TME 419, TMS 98/0505, TMS 01/1371, and TMS 98/0002) at the seedling and clonal evaluation stages. Results At both trial stages, the effects of ID were severe on average performance of fresh root yield and fresh foliage yield; moderate on harvest index, dry matter content, vigor, and tolerance to cassava mosaic disease, cassava bacterial blight, and cassava anthracnose diseases; and less severe on plant height. Further examination of S1 families using molecular markers showed varying levels of heterozygosity at several loci across the genome. In addition, the degree of heterozygosity and ID varied by the S1 family. The TMS 01/1371 family showed the lowest degree of heterozygosity and ID on the average performance of different agronomic attributes, indicating that inbreeding may be strategically explored in this family to increase genetic gain and identify useful recessive traits. Lastly, the observed depression from inbreeding was higher in seedling evaluation than in clonal evaluation trials for fresh root yield, fresh foliage yield, harvest index, and dry matter content. Conclusion S1 individuals showing relatively low heterozygosity based on SNP data were selected as parents to advance genetic gain in cassava. Generally, reduced heterozygosity was prominent in traits with severe ID impacts on average phenotypic performance. Our results highlight the relative importance of exploring non-additive genetic effects and transgressive segregations for favorable allele combinations in cassava improvement.

Assessment of genetic diversity and population structure of U.S. Polypay sheep from breed origins to future genomic selection.

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic diversity and population structure of U.S. Polypay sheep using both pedigree- and genomic-based methods. Pedigree data from 193 Polypay flocks participating in the National Sheep Improvement Program (NSIP) were combined with pedigree records from USSES (n = 162,997), tracing back to the breed's origin. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip containing 51,867 single nucleotide polymorphisms (SNPs). Four subgroups were used for the pedigree-based analyses: 1) the current generation of animals born in 2020-2022 (n = 20,701), 2) the current generation with a minimum of four generations of known ancestors (n = 12,685), 3) only genotyped animals (n = 1,856), and 4) the sires of the current generation (n = 509). Pedigree-based inbreeding for the full population was 2.2%, with a rate of inbreeding of 0.22% per generation. Pedigree-based inbreeding, Wright's inbreeding, and genomic inbreeding based on runs of homozygosity were 2.9%, 1.3%, and 5.1%, respectively, for the genotyped population. The effective population size ranged from 41 to 249 for the pedigree-based methods and 118 for the genomic-based estimate. Expected and observed heterozygosity levels were 0.409 and 0.403, respectively. Population substructure was evident based on the fixation index (FST), principal component analysis, and model-based population structure. These analyses provided evidence of differentiation from the foundation flock (USSES). Overall, the Polypay breed exhibited substantial genetic diversity and the presence of a population substructure that provides a basis for the implementation of genomic selection in the breed.

High conservation importance of range-edge populations of Hooded Vultures (Necrosyrtes monachus)

Critically endangered Hooded Vultures (Necrosyrtes monachus Temminck, 1823), like many vulture species globally, are experiencing rapid population declines due to anthropogenic factors such as poisonings, human persecution, trading for belief-based use, and habitat loss/degradation. The Hooded Vulture is widespread across sub-Saharan Africa. Although it is considered one of the most abundant vultures in West Africa, this vulture species is less common in East and southern Africa, with the population at the southern-most edge of the distribution (in South Africa and Eswatini) estimated at only 100–200 mature individuals. The distribution of Hooded Vultures has contracted dramatically in southern Africa, with breeding populations largely confined to protected areas such as the Greater Kruger National Park. This study aimed to investigate the genetic diversity of the southern African range-edge population and assess if the recent contraction in the distribution has resulted in the population experiencing a genetic bottleneck. Sixteen microsatellite loci were amplified for samples collected along the Olifants River in the Greater Kruger National Park (n = 30). The genetic diversity in the South African population was compared to samples (n = 30) collected in Ghana, where Hooded Vultures are more abundant. Contrary to expectations, the South African peripheral Hooded Vulture population showed higher levels of heterozygosity (HO = 0.495) than the Ghanaian population (HO = 0.315). Neither population showed signs of recent bottleneck events when tested using demographic modelling and Approximate Bayesian computation (ABC). However, both populations showed high levels of inbreeding and relatedness. Our results suggest that despite being a small peripheral population, the South African Hooded Vulture population showed a similar level of genetic diversity as individuals sampled from a core population within the species distribution (in Ghana). This study supports the need for Hooded Vulture conservation efforts in the southern African region and highlights the evolutionary importance of range-edge populations.

Comprehensive genetic analysis reveals the genetic structure and diversity of Calanthe hoshii (Orchidaceae), an endemic species of the Ogasawara Islands: Implications for appropriate conservation of a critically endangered species

AbstractThe Ogasawara Islands, isolated from the continent throughout their geological history, harbor abundant endemic species. However, 32% of the native plant species are on the Japanese Red List, signaling their endangered status. Among these endangered species, Calanthe hoshii stands out as highly susceptible to extinction. Two wild and 89 ex situ individuals were alive in 2020, but the last known wild individual died in October 2021, indicating this species may have become extinct in the wild. Despite the conservation efforts under the Act for the Conservation of Endangered Species of Wild Fauna and Flora, the lack of essential information regarding genetic diversity and population structure among the remaining individuals poses a significant obstacle to developing effective conservation measures. In this research, we conducted a genetic analysis of the wild and ex situ individuals, which revealed notably reduced genetic diversity between individuals, with individual heterozygosity levels (1.0 × 10−5) measuring one‐ninth of those observed within a closely related species Calanthe triplicata (1.5 × 10−4). Comprehensive genetic analysis revealed that C. hoshii consisted of three genetic clusters of different sizes: cluster 1 comprised 95% of the total population, while clusters 2 and 3, with few individuals, were only found in the ex situ populations at Koishikawa Botanical Garden. Since extant C. hoshii maintains a remarkably low genetic diversity at both individual and population levels, it is necessary to consider future management strategies, such as artificial breeding among different clades identified in this study, to safeguard the stability and resilience of this species.

Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia.

Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north-central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic-environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post-introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.

Evidence for human-caused founder effect in populations of Solanum jamesii at archaeological sites: II. Genetic sequencing establishes ancient transport across the Southwest USA.

The domestication of wild plant species can begin with gathering and transport of propagules by Indigenous peoples. The effect on genomic composition, especially in clonal, self-incompatible perennials would be instantaneous and drastic with respect to new, anthropogenic populations subsequently established. Reductions in genetic diversity and mating capability would be symptomatic and the presence of unique alleles and genetic sequences would reveal the origins and ancestry of populations associated with archaeological sites. The current distribution of the Four Corners potato, Solanum jamesii Torr. in the Southwestern USA, may thus reflect the early stages of a domestication process that began with tuber transport. Herein genetic sequencing (GBS) data are used to further examine the hypothesis of domestication in this culturally significant species by sampling 25 archaeological and non-archaeological populations. Archaeological populations from Utah, Colorado and northern Arizona have lower levels of polymorphic loci, unique alleles, and heterozygosity than non-archaeological populations from the Mogollon region of central Arizona and New Mexico. Principle components analysis, Fst values, and structure analysis revealed that genetic relationships among archaeological populations did not correspond to geographic proximity. Populations in Escalante, Utah were related to those on the Mogollon Rim (400 km south) and had multiple origins and significant disjunctions with those populations in Bears Ears, Chaco Canyon, and Mesa Verde sites. Movement of tubers from the Mogollon region may have occurred many times and in multiple directions during the past, resulting in the complex genetic patterns seen in populations from across the Four Corners region.

Genetic prospective of a local invader: the strange pattern of Pontastacus leptodactylus population structure in Greece and Turkey based on microsatellite DNA.

The combination of the increasing demand of freshwater crayfish exports, the reduced population sizes due to overfishing, the crayfish plague epidemics and the habitat degradation, have led to unrecorded translocations of Pontastacus leptodactylus in Greek lakes. In the present study, the genetics of five narrow clawed crayfish (P. leptodactylus) populations were studied, namely three translocated populations inhabiting in Northern Greece, one native Greek population from Evros river and one potential progeny source population from Turkey. Nine microsatellite loci previously designed for the specific species were investigated, in order to assess the levels of genetic diversity and further to confirm the origin of these translocated populations some decades after the translocation events. Our results confirmed that the source population for the translocated Greek population is the Turkish lake Eğirdir. Further, despite the low values of the number of alleles, heterozygosity, and FST the populations were generally diverse, providing evidence for local adaptation. The low values of FIS for the translocated populations in combination with the high values of gene flow, possibly indicate the existence of re-introducing events. Apart from the translocated populations, high levels of genetic diversity and heterozygosity were observed in Evros population, suggesting it as a possible unit for future conservation purposes both as a donor population for reintroduction purposes as well as a unique gene pool protection source. To the best of our knowledge this is the first study dealing with the genetic composition of Greek P. leptodactylus populations from Nothern Greece, operating as a first step towards the development of proper management practices for restocking events and monitoring of translocated populations.

Microsatellite polymorphism based genetic variation in two sympatric species of Drosophila: D.bipectinata and D. malerkotliana

Drosophila bipectinata and D. malerkotliana are found to be distributed all along the Oriental-Australian continents and have common phylogenetic descent. The genetic divergence of these two species have been studied by using genetic markers like chromosome inversions and allozyme variants to establish the extent of variation they have experienced since their speciation. In this study, microsatellite variations have been considered to observe the genetic differentiation among the seven natural populations of D. bipectinata and six populations of D. malerkotliana. Results pertaining to both the species indicate that the level of average heterozygosity increases from north to south. Distinct genetic differentiation has been observed between north and south populations of both the species giving an indication that north and south populations have undergone genetic structuring due to absence of gene flow between them and varying environmental conditions. Based on the frequencies of microsatellite variants of the two species, we have computed the level of variation between these two species. The analysis in this regard shows an almost similar trend of genetic variation being experienced by these two species which could be a kind of parallel evolution occurring due to similar ecological niches occupied by them and similar impact of evolutionary forces.

Use of ISSR markers for genotyping an experimental group of largemouth bass Micropterus salmoides (LACEPEDE, 1802), reared in ponds of Polissia of Ukraine

The aim of this study was to investigate the genetic structure of the experimental group of largemouth bass reared in the ponds of Polissia of Ukraine using ISSR markers. To accomplish these tasks, ISSR genotyping of the genetic structure of largemouth bass was performed using four fragments of trinucleotide loci. The genetic structure of the experimental group of largemouth bass of the pond fsh farm "Nyvka" was characterised using 4 primers B – (GAG)6C; C – (AGC)6G; D – (ACC)6G and E – (AGC)6C. Fins fragments were used for the study. In the course of the work, the optimal conditions for ISSR-PCR analysis were selected. The study revealed a number of factors that affect the efciency of these markers: DNA concentration, number of amplifcation cycles. For 4 markers, 80 alleles with a molecular weight of 160–1320 bp were identifed. The ranges of amplicons for the selected markers were determined: marker B – from 150 to 1186 bp; marker C – from 640 to 200 bp; D – from 1320 to 225 bp; and E – within 630–160 bp. The most polymorphic marker is marker B – 26 alleles, the least polymorphic marker is marker E – 15 alleles. In the studied experimental group of largemouth bass, the effective number of alleles varied from 10.2 for marker E to 12.2 for marker C, D. The indicators of genetic variability were determined by calculating allelic frequencies, the maximum level of available heterozygosity is 0.918 for marker C, D, and the lowest for marker E is up to 0.902. A method has been proposed that makes it possible to analyse the genetic structure of the experimental group of largemouth bass using these primers and to implement genetic information at different stages of the selection process. Keywords: ISSR-PCR, genetic structure, largemouth bass, DNA– markers, genotype, amplicons, genetic polymorphism, molecular genetic marker.

A comprehensive genome survey study unveils the genomic characteristics and phylogenetic evolution of fishes in the Uranoscopidae family

The construction of high-quality genomes is fundamental for molecular studies of species. Currently, there are no published genome sequences within the Uranoscopidae family, and research on the genomic characteristics of this family is lacking. In this study, genomic analyses of seven species from the Uranoscopidae family which captured from the southeastern coast of China were conducted using next-generation sequencing technology. The results revealed that the genomic characteristics of the seven species are relatively similar. The genome sizes of the seven Uranoscopidae species ranged from 536.00 Mb to 652.49 Mb, with repeat sequence proportions between 20.09% and 36.64%, and heterozygosity levels ranging from 0.41% to 0.88%. The assembled draft genomes exhibited GC contents of these species ranging from approximately 42.14% to 43.53%. Furthermore, the mitochondrial sequences for the seven species were assembled, with sizes ranging from 14,966 to 18,446 bp. The evolutionary relationships between different species were depicted through the mapping of conserved genes, whole-genome variances and mitochondrial genome sequences. Besides, the historical effective population sizes of all species experienced rapid expansion after the Last Interglacial Period, with three species undergoing bottleneck effects. In conclusion, this study provides a reference for the subsequent construction of high-quality genomes for species within the Uranoscopidae family and offers a rich data resource for further evolutionary research.

Genomic variability of the MHC region: Empirical evidence from five horse breeds

The purpose of this study was to analyse the level of variability in the autosomal genome, especially in the equine major histocompatibility complex region, in five horse breeds and identify heterozygosity-rich regions and potential footprints of balancing selection. Depending on data quality control, the dataset consisted of 51,168 or 53,874 single nucleotide polymorphism markers, available for 514 individuals (89 Lipizzan, 238 Old Kladruber, 47 Shagya Arabian, 61 Czech Warmblood and 81 Slovak Warmblood horses). Genomic variability within and between breeds was examined based on levels of heterozygosity (observed and expected), genomic inbreeding, Wright's FIS index and linkage disequilibrium. Subsequently, the screening of heterozygosity-rich regions and balancing selection signals derived from Tajima's D positive values was performed. As expected, due to the polymorphic nature of the major histocompatibility complex, the genomic variability level was generally higher when analysing only markers located in this area (mainly around genes belonging to class I). The Slovak and Czech Warmblood horses, as breeds with open herdbook, showed higher average values of heterozygosity indices than Lipizzan, Old Kladruber or Shagya Arabian breeds. Concerning only markers in the major histocompatibility complex region in complete or very high linkage disequilibrium, common patterns were found close to EQMHCB2, MHCB3 and EQMHCC1 genes belonging to class I and DQA1, DRB2, DRB3 and HLA-DOB genes from class II. Genome-wide, the number of heterozygosity-rich regions per animal ranged from 345.25 (Old Kladruber) to 603.33 (Czech Warmblood). Across all breeds, 254 heterozygosity-rich regions were detected directly in the major histocompatibility complex region (194 in class I and 60 in class II). Among them, the highest overlap showed regions found in the genomes of historically connected Czech and Slovak Warmblood breeds. The results suggested that the frequency of markers in heterozygosity-rich regions increased in Lipizzan, Old Kladruber and Shagya Arabian breeds in the genomic region of EQMCE1 gene (class I) and in Czech and Slovak Warmblood horses in DQB1, DQA2, DQB2, DQA3 and DRB2 genes (class II). Although the identified heterozygosity-rich regions formed 330 islands across the genomes of tested breeds, these islands were outside the major histocompatibility complex region. On the other hand, four of 425 balancing selection signals detected across breeds were located directly in the major histocompatibility complex region, close to DRA, DRB1, DQA1, DQB1 and DQB2 genes (class II). Shared islands and balancing selection footprints among breeds were found mainly on chromosomes 7 and 11.

Genetic Variability and Genetic Differentiation of Populations in the Grooved Carpet Shell Clam (Ruditapes decussatus) Based on Intron Polymorphisms

Genetic Variability and Genetic Differentiation of Populations in the Grooved Carpet Shell Clam (Ruditapes decussatus) Based on Intron Polymorphisms

Assessing the gut microbiome and the influence of host genetics on a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus)

AbstractThe Northern muriqui (Brachyteles hypoxanthus) is one of the world's most critically endangered primates, with only ~1000 mature individuals remaining in the wild. Habitat loss and hunting have led to its sharp decline, making conservation efforts crucial. Analyses of gut microbiomes in wild populations can provide valuable information on host health and vulnerability, and ultimately, contribute to baseline knowledge toward improving conservation programs and reintroduction efforts. In this study, we analyzed the microbiome (16S rRNA metabarcoding) of fecal samples belonging to 53 uniquely genotyped individuals from three social groups from the Caparaó National Park, aiming to provide the first assessment of the microbiome diversity and composition for this species. Our results showed the muriqui gut microbiome was predominantly composed of the phyla Bacteroidetes and Firmicutes, with the dominant classes represented by Bacteroidia and Clostridia. High similarity in bacterial diversity and composition was found for individuals from distinct groups, suggesting a negligible geographical effect at the fine spatial scale analyzed. No significant effect of host genotype heterozygosity levels on microbiota diversity was recovered, but a significant influence of genetic distance on microbiota community structure and composition was demonstrated. Our findings stress the importance of considering associations between host genetics and the microbiome and suggest that the analyzed populations host a similar microbiome composition. This detailed microbiome assessment can aid conservation actions, including future anthropogenic impact assessments and animal reintroductions.

Boom-bust population dynamics drive rapid genetic change

Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype-by-sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone. The sandy inland mouse (Pseudomys hermannsburgensis) experiences marked boom-bust population dynamics in response to the highly variable desert environment. We show that heterozygosity levels declined, and population differentiation (FST) increased, during bust periods when populations became small and isolated, but that heterozygosity was rapidly restored during episodic population booms. In contrast, the lesser hairy-footed dunnart (Sminthopsis youngsoni), a desert marsupial that maintains relatively stable population sizes, showed no linear declines in heterozygosity. These results reveal two contrasting ways in which genetic diversity is maintained in highly variable environments. In one species, diversity is conserved through the maintenance of stable population sizes across time. In the other species, diversity is conserved through rapid genetic mixing during population booms that restores heterozygosity lost during population busts.

A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants.

The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here, we present a phased assembly of genome of the almond cv. Texas. This new assembly has 13% more assembled sequence than the previous version of the Texas genome and has an increased contiguity, in particular in repetitive regions such as the centromeres. Our analysis shows that the 'Texas' genome has a high degree of heterozygosity, both at SNPs, short indels, and structural variants level. Many of the SVs are the result of heterozygous transposable element insertions, and in many cases, they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes are often associated with allele-specific gene expression, which highlights the importance of heterozygous SVs in almond.