Levels Of Heterozygosity Research Articles

Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs.

Hundreds of genetic variants implicated in Mendelian disease have been characterized in dogs and commercial screening is being offered for most of them worldwide. There is typically limited information available regarding the broader population frequency of variants and uncertainty regarding their functional and clinical impact in ancestry backgrounds beyond the discovery breed. Genetic panel screening of disease-associated variants, commercially offered directly to the consumer or via a veterinary clinician, provides an opportunity to establish large-scale cohorts with phenotype data available to address open questions related to variant prevalence and relevance. We screened the largest canine cohort examined in a single study to date (1,054,293 representative dogs from our existing cohort of 3.5 million; a total of 811,628 mixed breed dogs and 242,665 purebreds from more than 150 countries) to examine the prevalence and distribution of a total of 250 genetic disease-associated variants in the general population. Electronic medical records from veterinary clinics were available for 43.5% of the genotyped dogs, enabling the clinical impact of variants to be investigated. We provide detailed frequencies for all tested variants across breeds and find that 57% of dogs carry at least one copy of a studied Mendelian disease-associated variant. Focusing on a subset of variants, we provide evidence of full penetrance for 10 variants, and plausible evidence for clinical significance of 22 variants, on diverse breed backgrounds. Specifically, we report that inherited hypocatalasia is a notable oral health condition, confirm that factor VII deficiency presents as subclinical bleeding propensity and verify two genetic causes of reduced leg length. We further assess genome-wide heterozygosity levels in over 100 breeds, and show that a reduction in genome-wide heterozygosity is associated with an increased Mendelian disease variant load. The accumulated knowledge represents a resource to guide discussions on genetic test relevance by breed.

Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes

BackgroundAmaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions.ResultsWe provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination.ConclusionsThe results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.

Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (Amaranthus hypochondriacus)

Grain Amaranth is the most promising C4 dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized orphan crop. The present study aimed to validate the genome-wide SSR to assess the genetic diversity among 94 Amaranthus hypochondriacus accessions using 57 genomic SSR (g-SSR) markers developed in-house. A total of 36 g-SSRs were recorded as polymorphic and amplified 138 alleles, with an average of 3.83 alleles per locus. Major allele frequency ranged from 0.29 to 0.98, with an average of 0.63 per marker. The expected heterozygosity ranged from 0.03 to 0.81, with an average of 0.46 per locus. Polymorphism information content (PIC) ranged from 0.03 to 0.79, with an average of 0.40, indicating a high level of polymorphism across amaranth accessions. Population structure analysis resulted into two major genetic clusters irrespective of their geographical origin, which suggests there may be sharing of common genomic regions across the accessions. High allelic frequency and heterozygosity levels indicate significant genetic variability in the germplasm, which can be further used in future breeding programs.

Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra

Genetic diversity plays a vital role in the adaptability of salmon to changing environmental conditions that can introduce new selective pressures on populations. Variability among local subpopulations may increase the chance that certain advantageous genes are passed down to future generations to mitigate susceptibility to novel diseases, warming oceans, loss of genetic stocks, and ocean acidification. Class I and II genes of the major histocompatibility complex (MHC) are crucial for the fitness of Chinook salmon due to the role they play in disease and pathogen resistance. The objective of this study was to assess the DNA sequence variability among wild and hatchery populations of Alaskan Chinook salmon at the class I α1 and class II β1 exons of the MHC. We hypothesized that the 96 wild samples taken from the Deshka River would display greater levels of observed heterozygosity (Ho) relative to expected heterozygosity (He) in suggesting that individuals with similar phenotypes mate with one another more frequently than would be expected under random mating patterns. Conversely, since no mate selection occurs in the William Jack Hernandez Sport Fish hatchery, we would not expect to see this discrepancy (He = Ho) in the 96 hatchery fish tested in this study. Alternatively, we hypothesized that post-mating selection is driving higher levels of observed heterozygosity as opposed to mate selection. If this is the case, we will observe higher than expected levels of heterozygosity among hatchery salmon. Both populations displayed higher levels of observed heterozygosity than expected heterozygosity at the Class I and II loci but genetic differentiation between the spatially distinct communities was minimal. Class I sequences showed evidence of balancing selection, despite high rates of non-synonymous substitutions observed, specifically at the peptide binding regions of both MHC genes.

Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo.

The iconic Cape buffalo has experienced several documented population declines in recent history. These declines have been largely attributed to the late 19th century rinderpest pandemic. However, the effect of the rinderpest pandemic on their genetic diversity remains contentious, and other factors that have potentially affected this diversity include environmental changes during the Pleistocene, range expansions and recent human activity. Motivated by this, we present analyses of whole genome sequencing data from 59 individuals from across the Cape buffalo range to assess present-day levels of genome-wide genetic diversity and what factors have influenced these levels. We found that the Cape buffalo has high average heterozygosity overall (0.40%), with the two southernmost populations having significantly lower heterozygosity levels (0.33% and 0.29%) on par with that of the domesticated water buffalo (0.29%). Interestingly, we found that these lower levels are probably due to recent inbreeding (average fraction of runs of homozygosity 23.7% and 19.9%) rather than factors further back in time during the Pleistocene. Moreover, detailed investigations of recent demographic history show that events across the past three centuries were the main drivers of the exceptional loss of genetic diversity in the southernmost populations, coincident with the onset of colonialism in the southern extreme of the Cape buffalo range. Hence, our results add to the growing body of studies suggesting that multiple recent human-mediated impacts during the colonial period caused massive losses of large mammal abundance in southern Africa.

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The crops variety growing in Armenia has not been fully explored yet, hence, their genetic potential has not been revealed. Therefore, study of gliadin (Gld) locus contained in cereals’ embryo will further clarify the process of allelofunds and genotypes, homozygocity and heterozigocity, genetic similarity, genetic formula and genomic analysis of studied cultivars and wild species. The research was carried out in 2021-2022 in the educational laboratory of Food Quality Control of the Armenian National Agrarian University. The samples of the studied plants were taken from the ex-situ seed collection of the National Genebank of Agricultural Crops and their Wild Relatives of the “Scientific Center of Agro-Biotechnology” branch of the Armenian National Agrarian University. From the electrophoretic spectrum of gliadin (Gld) for the study and identification of the genetic diversity of the inventory samples of cereals diversity protein formulas were deciphered, allelotypes and genotypes, homozygosity and heterozygosity levels were determined, and genomic analysis was performed. According to the genomic analysis of the studied cereals varieties and wild relatives using protein markers, gliadin is spread into four zones: α, β, γ and ω. The genes regulating the synthesis of different parts of gliadin of α, β, γ, ω zones, are polymorphic located in chromosomes 6B(S), 1A(S), 1B(S), 1D(S), and in the case of Alti aghaj, Voskehask and Gjulgian also in 6A chromosome. There are no genes regulating the synthesis of gliadin segments in chromosome 6D(α). Research results, as genetic markers, can be used in identification and selection of studied varieties and wild species.

GENETIC CHARACTERISTICS OF PADDLEFISH (POLYODON SPATHULA (WALBAUM, 1792)) BROOD STOCKS

GENETIC CHARACTERISTICS OF PADDLEFISH (POLYODON SPATHULA (WALBAUM, 1792)) BROOD STOCKS

PREVALENCE OF ARTERIAL HYPERTENSION CANDIDATE GENES IN THE NEWLY ARRIVED POPULATION OF THE NORTH-EAST RUSSIA

Arterial hypertension (AH) is one of the most serious problems of modern health care. In the northern regions it has become a catastrophe, being the most common cause of early disability and mortality among the employable newly-arrived population. At high latitudes, AH is characterized by a more severe course; it is accompanied by early damage to target organs; and it is more often in young people. AH occurs as a result of a combined interaction of polymorphism in genes, which are involved in blood pressure regulation. It is also provoked by the environmental factors. 
 The aim of the study is to assess the prevalence of polymorphisms in four AH candidate genes (AGT (rs4762), AGTR1 (rs5186), ADD1 (rs4961), NOS3 (rs2070744)) in the newly arrived population of the North-East Russia.
 Materials and methods. The cross-sectional study involved practically healthy unrelated men, mostly Europeans, living or born on the territory of the Magadan region (n=101). The average age of the subjects was 46.12±1.5 (20–77 years old). PCR was used to perform molecular genetic testing of genes directly involved in the work of the main blood pressure regulation systems: AGT, AGTR1, ADD1, NOS3. The author calculated phenotypic and gene frequencies, observed and expected heterozygosity levels, Wright's fixation index (D) and population genetic distance (according to Nei). Clustering methods and multidimensional scaling were used to visualize the genetic relationship of different populations.
 Results. In the newly arrived population of the North-East Russia, genotype distribution corresponds to the Hardy – Weinberg equilibrium (p>0.05). Allelic diversity for the studied loci varies from Ho=0.25 (AGT locus) to Ho=0.44 (eNOS locus).
 Conclusion. The result of the study is the revealed characteristics of AH candidate gene frequency in the newly arrived population of the North-East Russia. It is found that allelic variants that increase the risk of AH developing are minor. Their frequency varies from 13.37 % (AGT*T allele, AGT locus) to 35.64 % (eNOS*C allele, eNOS locus).

S-alleles and mating system in natural populations of Capsella grandiflora (Brassicaceae) and its congeneric relatives

Population-level estimates and studies on geographical distribution of S-alleles (SRK-alleles) are missing for most self-incompatible species. We screened natural populations of the self-incompatible diploid Capsella grandiflora for SRK-alleles and identified 63 alleles altogether across its whole distribution area. The native range in Greece had 61 alleles whereas in the introduced range in northern Italy only 20 alleles could be detected. Allozyme studies confirmed outbreeding in natural populations of C. grandiflora in general, but observed heterozygosity levels were low in some loci. Moreover, lower multi-locus outcrossing rates were recorded for the mainland Greece populations. In contrast to the SRK-allele profiles, we found no differences in allozyme profiles between native and introduced ranges. We detected five SRK-alleles in the diploid self-compatible C. orientalis while four SRK-alleles were discovered in the allotetraploid C. bursa-pastoris. Capsella bursa-pastoris shares SRK-alleles with both of its parent species, C. grandiflora and C. orientalis.

Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus).

Conservation genetic theory suggests that small and isolated populations should be subject to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12-171), the population maintains high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest are underpinning the maintenance of the population's high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

Experimental Outcrossing in Agaricus bisporus Revealed a Major and Unexpected Involvement of Airborne Mycelium Fragments.

Agaricus bisporus var. bisporus, the button mushroom, has a predominantly pseudohomothallic life cycle. Most of its spores are heterokaryotic and give rise to fertile heterokaryons. However, previous studies have suggested that outcrossing should not be rare in wild populations. In order to discover how outcrossing occurs, we experimentally favored it between aerial propagules of a fruiting donor mycelium and a delayed receiver mycelium that only invaded culture trays. Two donor/receiver pairs were studied, and potentially hybrid basidiomata collected on the receiver trays were analyzed with a mitochondrial marker, two unlinked nuclear CAPS markers, then haplotype markers based on DNA sequences obtained after PCR cloning of the rDNA ITS region and the fruk gene. For one of the two pairs, most basidiomata were hybrids between the donor and the receiver. Genotyping of the hybrids revealed only two genotypes consistent with outcrossing involving airborne mycelium fragments rather than basidiospores. The resident receiver heterokaryon that provided its mitochondria to the hybrid basidiomata is suspected to have had a trophic contribution to their growth and successful fruiting. The high level of heterozygosity and the cultivar introgression previously revealed in wild populations of this pseudohomothallic species may result from outcrossing involving airborne pieces of mycelium.

Migratory behaviour is positively associated with genetic diversity in butterflies.

Migration is typically associated with risk and uncertainty at the population level, but little is known about its cost-benefit trade-offs at the species level. Migratory insects in particular often exhibit strong demographic fluctuations due to local bottlenecks and outbreaks. Here, we use genomic data to investigate levels of heterozygosity and long-term population size dynamics in migratory insects, as an alternative to classical local and short-term approaches such as regional field monitoring. We analyse whole-genome sequences from 97 Lepidoptera species and show that individuals of migratory species have significantly higher levels of genome-wide heterozygosity, a proxy for effective population size, than do nonmigratory species. Also, we contribute whole-genome data for one of the most emblematic insect migratory species, the painted lady butterfly (Vanessa cardui), sampled across its worldwide distributional range. This species exhibits one of the highest levels of genomic heterozygosity described in Lepidoptera (2.95 ± 0.15%). Coalescent modelling (PSMC) shows historical demographic stability in V. cardui, and high effective population size estimates of 2-20 million individuals 10,000 years ago. The study reveals that the high risks associated with migration and local environmental fluctuations do not seem to decrease overall genetic diversity and demographic stability in migratory Lepidoptera. We propose a "compensatory" demographic model for migratory r-strategist organisms in which local bottlenecks are counterbalanced by reproductive success elsewhere within their typically large distributional ranges. Our findings highlight that the boundaries of populations are substantially different for sedentary and migratory insects, and that, in the latter, local and even regional field monitoring results may not reflect whole population dynamics. Genomic diversity patterns may elucidate key aspects of an insect's migratory nature and population dynamics at large spatiotemporal scales.

Association of Klotho Protein Levels and KL-VS Heterozygosity With Alzheimer Disease and Amyloid and Tau Burden

Identification of proteins and genetic factors that reduce Alzheimer disease (AD) pathology is of importance when searching for novel AD treatments. Heterozygosity of the KL-VS haplotype has been associated with reduced amyloid and tau burden. Whether this association is mediated by the Klotho protein remains unclear. To assess concentrations of Klotho in cerebrospinal fluid (CSF) and plasma among cognitively healthy controls and patients with AD and to correlate these findings with KL-VS heterozygosity status and amyloid and tau burden. This case-control study combined 2 independent case-control AD cohorts consisting of 243 referred patients with AD and volunteer controls recruited from January 1, 2009, to December 31, 2018. Klotho levels were measured in CSF and plasma and correlated with KL-VS heterozygosity status and levels of CSF amyloid-β 42 (Aβ42), total tau, and phosphorylated tau. Statistical analysis was performed from January 1, 2021, to March 1, 2022. Associations of Klotho levels in CSF and plasma with levels of CSF biomarkers were analyzed using linear regression. Association analyses were stratified separately by clinical groups, APOE4 status, and KL-VS heterozygosity. Pearson correlation was used to assess the correlation between CSF and plasma Klotho levels. A total of 243 participants were included: 117 controls (45 men [38.5%]; median age, 65 years [range, 41-84 years]), 102 patients with mild cognitive impairment due to AD (AD-MCI; 59 men [57.8%]; median age, 66 years [range, 46-80 years]), and 24 patients with dementia due to AD (AD-dementia; 12 men [50.0%]; median age, 64.5 years [range, 54-75 years]). Median CSF Klotho levels were higher in controls (1236.4 pg/mL [range, 20.4-1726.3 pg/mL]; β = 0.103; 95% CI, 0.023-0.183; P = .01) and patients with AD-MCI (1188.1 pg/mL [range, 756.3-1810.3 pg/mL]; β = 0.095; 95% CI, 0.018-0.172; P = .02) compared with patients with AD-dementia (1073.3 pg/mL [range, 698.2-1661.4 pg/mL]). Higher levels of CSF Klotho were associated with lower CSF Aβ42 burden (β = 0.519; 95% CI, 0.201-0.836; P < .001) and tau burden (CSF total tau levels: β = -0.884; 95% CI, 0.223 to -0.395; P < .001; CSF phosphorylated tau levels: β = -0.672; 95% CI, -1.022 to -0.321; P < .001) independent of clinical, KL-VS heterozygosity, or APOE4 status. There was a weak correlation between Klotho CSF and plasma levels among the entire cohort (Pearson correlation r = 0.377; P < .001). The findings of this case-control study suggest that Klotho protein levels were associated with clinical stages of AD, cognitive decline, and amyloid and tau burden and that these outcomes were more clearly mediated by the protein directly rather than the KL-VS heterozygosity variant. When selecting individuals at risk for clinical trials, the Klotho protein level and not only the genetic profile should be considered.

Genetic variation of LEI0258 locus at major histocompatibility complex (MHC) region in Ethiopian indigenous village chicken

&#x0D; Indigenous chickens are locally adapted to environmental challenges and provide subsistence to millions of farmers in Africa. However, their productivity remains low compared to exotic strains. Efforts are being made to combine the local adaptation of indigenous chicken with productive traits of exotic chicken. Understanding the link between genetic diversity and environmental challenges leads to marker-assisted breed improvement programs for sustainable chicken production at smallholder level. Genetic variation at LEI0258 VNTR locus located within the MHC region has been linked to infectious disease resistance/susceptibility in commercial breeds. The aim of this study was to investigate allelic variability, genetic diversity and genetic relationships of 24 chicken populations in Ethiopia. Here, the diversity at LEI0258 in 236 chickens from 24 Ethiopian indigenous chicken populations using the major Histo-compatibility Complex linked LEI0258 marker is reported. A total of 236 DNA samples were genotyped by capillary electrophoresis from 24 chicken populations. The number of alleles, allele frequency, and heterozygosity levels were used to measure genetic variation at LEI0258 locus in Ethiopian indigenous village chicken. Twenty-nine LEI0258 alleles were observed using capillary electrophoresis that ranged from 185 to 569 bp with no significant difference in allele frequencies between populations. The number of alleles ranged from 179 (Meseret) to 569 (Batambie), with an average of 9.6 alleles per population. Allelic polymorphism was further evaluated through genotyping by Sanger sequencing. Twenty-three DNA samples with different fragment sizes were re-amplified and their alleles sequenced to depict polympormisms based on the combination of two repeat regions at 12 bp and 13 bp, respectively, and flanking regions with SNP and indels. The repeat region at 12 bp appeared 2 to 18 times, whereas the region at 13 bp appeared invariant in all populations. Sequence relationships revealed two distinct groups of alleles. The number of indels and mutations were 33 and 17, respectively. From capillary electrophoresis, the fixation coefficient of the sub-population within the total population (FST), inbreeding/fixation/ coefficient of an individual in a sub population (FIS) and total inbreeding /heterozygosity deficit/ coefficient of an individual within the total population (FIT) in the locus was 0.03, 0.08 and 0.11, respectively. Three percent of the genetic diversity was due to differences among populations, where as 8% and 89% were variations among individuals and variations within individuals, respectively. Despite the overall low genetic differentiation, both fragment and sequencing analysis revealed high allelic and genetic variability across the 24 populations. The high diversity at LEI0258 in Ethiopian indigenous village chicken populations supports the importance of the MHC region in relation to the disease challenges faced by smallholder poultry farmers across Ethiopia. We recommend that breed improvement programs ensure the maintenance of this diversity by selecting breeding stock as diverse as possible at the LEI0258 locus.

Multilocus genetic analysis of two-breed chicken hybrids

Abstract. Background. Due to the fact that now many new forms of poultry are created by crossing existing breeds and populations, a comprehensive genetic analysis of hybrid chickens as a ground for further breeding work is of particular importance. Aim. To study the features of the population and genetic organization of the genomes of inter-breed chicken hybrids. Materials and methodology. The experimental work was based on the use of an oligonucleotide probe (GTG)5, which was labeled with digoxygenin. The probe was hybridized with genomic DNA on a nylon filter, and then labeled DNA fragments were visualized using a streptavidin-alkaline phosphatase conjugate chemistry. The number and distribution of DNA fragments was highly specific for each individual. These parameters under study include similarity coefficient (BS), genetic distances between groups (D) and average heterozygosity levels (H). Scientific novelty. For the first time, marker DNA fragments characterizing individual groups of birds have been identified; these fragments can be used in the certification of populations. The novelty of the work also lies in the determination of the main genetic characteristics in new groups of hybrid chickens, which will be used to consolidate the desired breeding traits. Results. Based on the data obtained, it can be concluded that there are relatively small genetic differences between various hybrid forms, which is the result of using the same source breeds. Brahma × Sussex Light and Uzbek Game × Amrock hybrids were relatively distant from each other (D = 0.070). Sussex Light× Amrock hybrids were the most genetically diverse according to the criterion of average heterozygosity (P = 0.66).

Blood donor biobank and HLA imputation as a resource for HLA homozygous cells for therapeutic and research use

BackgroundAllogeneic therapeutic cells may be rejected if they express HLA alleles not found in the recipient. As finding cell donors with a full HLA match to a recipient requires vast donor pools, the use of HLA homozygous cells has been suggested as an alternative. HLA homozygous cells should be well tolerated by those who carry at least one copy of donor HLA alleles. HLA-A-B homozygotes could be valuable for HLA-matched thrombocyte products. We evaluated the feasibility of blood donor biobank and HLA imputation for the identification of potential cell donors homozygous for HLA alleles.MethodsWe imputed HLA-A, -B, -C, -DRB1, -DQA1, -DQB1 and -DPB1 alleles from genotypes of 20,737 Finnish blood donors in the Blood Service Biobank. We confirmed homozygosity by sequencing HLA alleles in 30 samples and by examining 36,161 MHC-located polymorphic DNA markers.ResultsThree hundred and seventeen individuals (1.5%), representing 41 different haplotypes, were found to be homozygous for HLA-A, -B, -C, -DRB1, -DQA1 and -DQB1 alleles. Ten most frequent haplotypes homozygous for HLA-A to -DQB1 were HLA-compatible with 49.5%, and three most frequent homozygotes to 30.4% of the Finnish population. Ten most frequent HLA-A-B homozygotes were compatible with 75.3%, and three most frequent haplotypes to 42.6% of the Finnish population. HLA homozygotes had a low level of heterozygosity in MHC-located DNA markers, in particular in HLA haplotypes enriched in Finland.ConclusionsThe present study shows that HLA imputation in a blood donor biobank of reasonable size can be used to identify HLA homozygous blood donors suitable for cell therapy, HLA-typed thrombocytes and research. The homozygotes were HLA-compatible with a large fraction of the Finnish population. Regular blood donors reported to have positive attitude to research donation appear a good option for these purposes. Differences in population frequencies of HLA haplotypes emphasize the need for population-specific collections of HLA homozygous samples.

Assessing Leaf Morphometric Symmetry of Four Chinese Quercus Species in a Mixed Forest

(1) Background: Oaks have achieved notoriety for sufficient levels of sympatric species richness allowing hybridization, thus generating substantial phenotypic variation. Leaf fluctuation asymmetry is an important attribute, as it reflects not only genetic variability but also species buffering capacity. (2) Methods: We investigated the phenotypic diversity of four-oak species (Quercus acutissima, Q. variabilis, Q. fabri, and Q. serrata var. brevipetiolata) using leaf geometric morphometric analysis. Eight leaf morphological indicators (length, width, perimeter, area, left and right areas, areal ratio, and normalized symmetry index) were used to determine the hybridization level, whereas bilateral symmetry indicators were used to assess species environmental adaptation; (3) Results: Phenotypic variation ranged from 1.54 to 29.35 folds and significantly diverged among the studied species. Taxonomically species in Section Quercus (Q. fabri and Q. serrata var. brevipetiolata) are lower than those in Section Cerris (Q. acutissima and Q. variabilis) with good bilateral symmetry. The bilateral symmetry index of Q. variabilis had a larger range of variation, indicating better environmental adaptability; (4) Conclusions: We presume that species in Section Quercus with less leaf fluctuation asymmetry have a high level of genetic heterozygosity; however, this assumption requires further verification. The observed phenotypic diversity reflects a combination of environmental and genetic factors.

Genetic diversity analysis of Eggplant Germplasm from Iran: assessments by morphological and SSR markers.

Eggplant is an important vegetable that has long been cultivated in different parts of Iran. The major objectives of the eggplant breeding program are to improve fruit quality, increase yield performance through heterosis breeding, and introduce abilities of pest and disease resistance from wild relatives. In order to select suitable parents for breeding purposes, with respect to the genetic and morphological diversity of eggplant cultivars, it is necessary to have sufficient knowledge of genetic diversity and classification of germplasms. This experiment was conducted in a randomized block design at the Seed and Plant Improvement Institute (SPII) in Karaj, Iran. Here, morphological diversity was assessed among a collection of eggplants which comprised four Iranian lines and 13 non-Iranian genotypes. For this purpose, 16 morphological traits were analyzed in the plants. Given the weakness of morphological analysis in providing precise characterizations of genetic divergence, a molecular study was also carried out by using five Simple Sequence Repeat (SSR) markers. In addition to the univariate analysis, the multi-descriptor variation was studied among the genotypes using two methods of multivariate analyses. The genotypes differed significantly in terms of the morphological traits. The multivariate analyses of morphological data indicated that eggplants from two different origins were clearly differentiated. Three main clusters were distinguished by a morphological UPGMA dendrogram in which non-Iranian genotypes, with the exception of 11,212, constituted cluster I and required the maximum number of days to flower, days to fruit set, and days to first harvest. Cluster II was identified with two Iranian lines BJ30, Y60, and one non-Iranian genotype (11,212) which showed the highest values of stem diameter, fruit diameter, fruit length, fruit length-to-width ratio, number of fruits per plant, and yield. Cluster III comprised two Iranian lines, D1 and D7, and showed the maximum plant height, number of internodes, number of nodes, number of leaves, number of stems, fruit weight, and fruits weight per plant. The highest and lowest intra-cluster genetic distances were observed in cluster I and cluster II, respectively. Based on SSR analysis, high levels of similarity were detected between several genotypes, namely, Y60 and 13,411; BJ30 and 1111; D7 and 13,521; 21,881 and 13,421. High levels of heterozygosity and polymorphism information content (PIC) were observed in this study. This not only indicated high levels of polymorphism and an equal distribution of the evaluated loci but also suggested that these genotypes can be considered for the development of diverse parental lines which are of interest in breeding programs.

Differences and changes: an evaluation of the genetic diversity of Arabian mares from Polish state studs born between 1996 and 2013

Abstract The goal of our study was to estimate genetic diversity of Arabian horses from Polish state studs which could have changed due to the extensive use of foreign sires in Polish breeding after 1989. The analysis focused on 1,388 Arabian mares born from 1996 to 2013 in the Białka, Janów Podlaski and Michałów studs. Basic parameters of pedigree, mitochondrial DNA and microsatellite analyses were considered in the study. In the pedigree analysis, changes in the gene pool over the years were noted through the considerable increase of contribution of new founders’ genes and the considerable decrease of inbreeding level. The microsatellite analysis confirmed progressive changes in the gene pool but, contrary to expectations, only three new microsatellite alleles were detected, and a decreased level of heterozygosity was observed. In turn, mtDNA analysis showed a stable genetic situation in the studs throughout the period analysed. The results of the analyses present a diverse picture of the population, which is clearly divided into the three subpopulations of Białka, Janów Podlaski and Michałów, although the pictures presented differed depending on the analytical methods used. Genetic differences among the studs should be considered a positive feature of the Polish population. In order to preserve the present level of population genetic diversity, changes in breeding policy are needed that aim to stop the loss of genes of the historical ancestors of Polish Arabian horses.

ABCL-371 STR Loci Allele Imbalance at 9p24.1 in Primary Mediastinal B-Cell Lymphoma

Molecular factors that determine the prognosis of immunotherapy response in primary mediastinal B-cell lymphoma (PMBCL) are not yet described. PD-L1/L2 expression levels in tumor samples have demonstrated clinical utility for many solid tumors. PD-L1/L2 expression levels could be affected by chromosomal lesions on 9p24.1 (losses or gains). Short tandem repeat (STR) analysis of appropriate markers is the simplest way to detect these lesions. To analyze possible associations between STR loci allele imbalance (AI) on 9p24.1 and PD-L1 expression levels in tumor cells from PMBCL patients. Two STR Loci (gt) n and (ttat)m on 9p24.1 in tumor cells were analyzed for a cohort of 36 PMBCL patients admitted to the National Medical Research Center for Hematology (Moscow, Russia) from 2013 to 2022. For six patients, STR data were compared with PD-L1 expression assessed by immunohistochemistry. DNA was isolated from tumor biopsy samples taken at diagnosis. Control DNA samples were taken from the blood of patients in complete remission or from the buccal epithelium. STR analysis for AI was performed by PCR with original primers. The fragment analysis was performed on an ABI3130 Genetic Analyzer. Inclusion criteria: de novo diagnosed PMBCL patients. pretreatment. The heterozygosity level for the (gt)n locus was 31 of 36 patients (86%), and AI was found in 16 of 31 (51.6%). The heterozygosity level for the (ttat)m locus was 20 of 36 patients (56%), and AI was found in 9 of 20 (45%). One patient was homozygous for both loci. No patients were found with AI at one locus and a normal heterozygous variant at the second locus. PD-L1 expression in tumor cells was evaluated for six patients. In two patients with aberrant STR loci, PD-L1 expression was found in 75%-100% of tumor cells. None of the four patients with normal 9p24.1 STR markers had PD-L1-positive cells. The high incidence of AI in the 9p24.1 locus indicates its possible involvement in the pathogenesis of PMBCL. The association between AI and PD-L1 expression in tumor cells requires confirmation in an extended cohort of patients. This study was supported by Rakfond grant 2/2020.