Number Of Alleles Research Articles

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling of polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation (ABC) rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation.

The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.

Variability of Scots pine (<i>Pinus sylvestris</i> L.) plus trees in the Middle and Upper Volga Region with the use of ISSR markers

One of the serious issues in forest breeding is how to reduce the variability level in breeding populations of forest tree species that is a set of selected plus trees. The problem is that variability is jeopardized by the risk of losing the genetic diversity of future artificial forests, as well as emerging inbreeding depression in the seed plus trees progeny. DNA markers are an effective tool to study variability, identify features of the genetic structure and degree of plant differentiation. The research focuses on assessing the level of the genetic diversity and the degree of differentiation of plus trees of various geographic origin with the use of ISSR markers. We used six ISSR primers to study 270 plus trees grown in the Penza region, the Chuvash Republic, the Republic of Tatarstan and the Mari El Republic. The samples of plus trees under study were characterized by different levels of genetic diversity. Two hundred fifteen PCR fragments were identified for six ISSR primers in total, while the number of amplified fragments varied from 186 to 201 in different plus trees samples. The genetic variabil ity varied within the following limits: 95.7–96.9 %, polymorphic loci; 1.96–1.97, the number of alleles per locus; 1.31–1.48, the number of effective alleles per locus: finally, 0.291–0.429, Shannon’s index; 0.205–0.298, the expected heterozygosity. According to the analysis of molecular variance (AMOVA), 82 % of the variability of ISSR markers is typical for the plus tree samples, while only 18 % is variability among the compared groups of trees from different geographical zones. The dendrogram generated by UPGMA showed that the plus trees grown in the Penza region, the Chuvash Republic and the Republic of Tatarstan are similar in term of the genetic structure of plus trees, while the plus gene pool of Scots pine from the Mari El Republic stands alone. The results of the research prove that the level of genetic diversity, the structure of genetic variability, and the nature of differentiation of plus trees are consistent with those previously elicited for natural populations of Scots pine in the Middle and Upper Volga region.

Genetic epidemiology of alpha-1 antitrypsin deficiency in Macaronesia.

The prevalence of alpha-1 antitrypsin deficiency (AATD) in Macaronesia (i.e., Azores, Madeira, Canary Islands and Cape Verde archipelagos) is poorly known. Our goal is to update it by selecting the most reliable available articles. Literature search using Medline, EMBASE (via Ovid) and Google Scholar, until December 2023, for studies on prevalence of AATD in the general population and in screenings, published in peer-reviewed journals. Three studies carried out in the general population of Madeira, La Palma and Cape Verde, and three screenings carried out in La Palma (2) and Gran Canaria (1) were selected. The frequencies of PI*S in the general population showed an ascending gradient, from South to North, with values (per thousand) of 35 in Cape Verde, 82 in La Palma and 180 in Madeira. The PI*Z frequencies showed this same gradient, with values of 2 x1,000 in Cape Verde, 21 in La Palma and 25 in Madeira. Screenings detected high percentages of defective alleles, including several rare and null alleles, some unique to these islands. The frequencies of PI*S and PI*Z in Madeira are comparable to the highest in the world. Those of the Canary Islands are similar to those of the peninsular population of Spain, and contrast with the low rates of Cape Verde. Screenings detected high numbers of deficient alleles. These results support the systematic investigation of AATD in clinically suspected patients and in relatives of index cases, to reduce underdiagnosis and apply early preventive and therapeutic measures in those affected.

The genetic status and rescue measure for a geographically isolated population of Amur tigers

The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population’s genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.

Identification of superior and rare haplotypes to optimize branch number in soybean

Key messageUsing the integrated approach in the present study, we identified eleven significant SNPs, seven stable QTLs and 20 candidate genes associated with branch number in soybean.Branch number is a key yield-related quantitative trait that directly affects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs significantly associated with branch number across three environments using the five GWAS models. Based on the consistency of the SNP detection in multiple GWAS models and environments, seven genomic regions within the physical distance of ± 202.4 kb were delineated as stable QTLs. Of these QTLs, six QTLs were novel, viz., qBN7, qBN13, qBN16, qBN18, qBN19 and qBN20, whereas the remaining one, viz., qBN12, has been previously reported. Moreover, 11 haplotype blocks, viz., Hap4, Hap7, Hap12, Hap13A, Hap13B, Hap16, Hap17, Hap18, Hap19A, Hap19B and Hap20, were identified on nine different chromosomes. Haplotype allele number across the identified haplotype blocks varies from two to five, and different branch number phenotype is regulated by these alleles ranging from the lowest to highest through intermediate branching. Furthermore, 20 genes were identified underlying the genomic region of ± 202.4 kb of the identified SNPs as putative candidates; and six of them showed significant differential expression patterns among the soybean cultivars possessing contrasting branch number, which might be the potential candidates regulating branch number in soybean. The findings of this study can assist the soybean breeding programs for developing cultivars with desirable branch numbers.

Genetic diversity analysis of banana using SSR markers

Banana, a crucial fruit crop thriving in tropical and sub-tropical regions, facing a notable challenge of elevated sterility across various cultivated banana genotypes. This sterility issue hampers the cultivation of diverse banana varieties. Therefore, a focused endeavour is crucial to thoroughly investigate the richness of diversity within both wild and cultivated banana genotypes, aiming to preserve it for future utilization. In the present study, 21 Musa genotypes were collected from different places of North-Eastern Region, and conserved in the field gene bank at Department of Horticulture, College of Agriculture, Lembucherra, Tripura during 2015-2022. Molecular characterization and DNA fingerprinting of these banana accessions were performed by employing 16 banana SSR markers. The number of alleles per locus ranged from 15 to 24 with an average 20.375. The expected heterozygosity (He) ranged from 0.564-0.967 with a mean of 0.852, and the polymorphic information content (PIC) varies from 0.638–0.945 (mean = 0.859). Genetic diversity analysis showed dissimilar groups, indicating possibility of involvement of different accuminata and balbisiana types in evaluation of banana in NE region. The outcome of the current study will be useful for des igning banana crops against different stresses

Diversity of the Ghrelin Gene in Nigeria’s Fulani and Yoruba Ecotype Chickens

Ghrelin (GHRL) is a novel 28-amino acid gut-brain peptide linked to a gene associated with the regulation of growth hormones in birds. This study was carried out to investigate the polymorphism of the Ghrelin gene in Fulani and Yoruba ecotypes chickens in Nigeria. Blood samples were collected from seventy-eight (78) Nigerian indigenous chickens comprising of 41 Yoruba ecotype chickens and 37 Fulani ecotype chickens. Polymerase Chain Reaction-Restriction fragment length polymorphism (PCR-RFLP) method was used and the MboII restriction enzyme cut site 71 of the ghrelin and genetic structure were determined. Population structure was analyzed using allele and genotype frequencies, heterozygosity and genetic variation metrics. Two alleles (C and T) and three genotypes (CC, CT and TT) were observed. In the Yoruba Ecotype, the allele frequencies were C (0.34) and T (0.66) respectively while C (0.45) and T (0.55) were observed in the Fulani ecotype and the overall population was C (0.39) and T (0.61). The genotype frequencies obtained were; in the Yoruba ecotype, CC (0.10), CT (0.48), and TT (0.41) were observed. In the Fulani ecotype, CC (0.22), CT (0.45), and TT (0.32) were also observed, and in the overall population CC (0.15). CT (0.47) and TT (0.37) were observed. FIS values for the Yoruba ecotype (-0.0847) and Fulani ecotype (0.00702) reflects random mating and inbreeding respectively. The effective number of alleles indicates that the Fulani ecotype has more effective alleles compared to the Yoruba ecotype. These results suggest that the Yoruba ecotype may be at Hardy-Weinberg equilibrium, while Fulani ecotype deviates for the ghrelin locus. In summary, our results may open opportunities for genetic improvement in Nigerian indigenous chicken due to the polymorphic nature of the ghrelin gene.

Analysis of Genetic Variability of Potato Induced Mutants Using Simple Sequence Repeat (SSR) Markers

Aims: Potato (Solanum tuberosum L.) is ranked fourth amongst the world’s major stable food crop and second in Kenya after maize and thus plays a vital role in food and nutrition security and sustainable development. Despite its importance, potato production in Kenya is still low due to abiotic and biotic constraints. Traditional breeding and improvement have been difficult due to the narrow genetic diversity of the crop owed to the complex tetrasomic inheritance patterns. Induced mutation has been used to generate genetic variations in potato from which desired putative mutants are selected. In most cases the level of genetic variability is not known. The objective of this study was to determine the genetic variability of potato mutants using SSR markers. Study Design: The study involved three potato varieties; Asante, Kenya Mpya and Kenya Sherekea which are high yielding and commercially grown varieties in Kenya. Place and Duration of Study: Sample: They were irradiated at different dose rates of gamma rays at Co60 source at FAO/IAEA laboratories, Seiberdorf Austria in 2014. A total of 163 mutants were advanced to M1V4 generation at the University of Eldoret between 2015 and 2018. Methodology: Genomic DNA was extracted to assess the diversity with 20 SSRs markers. Results: All the 20 SSR primers were polymorphic with 6-19 bands amplified per primer and marker STM5127 showed the highest allele number (19) using PowerMarker software. The STRUCTURE analysis suggested that the potato mutants were clustered into six sub-populations based on the unweighted pair-group method of arithmetic averages (UPGMA) thus, the accessions were divided into three major clusters. Analysis of molecular variance (AMOVA) indicated that 8.6% of total molecular variance was attributed to diversity among sub-populations, while 91.4% of variance was associated with differences within sub-populations. Conclusion: This study highlights the most comprehensive investigation of the genetic diversity and population structure of potato mutants, and provides valuable information for genetic improvement, and systematic utilization.

Genetic Diversity in Katchaikatty Sheep based on Microsatellites Polymorphism

Background: Sheep is one of the important species of livestock in India contributing to meat production. India has 44 distinct breeds of sheep, out of which 10 are found in Tamil Nadu. The present study describes the molecular characterization of recently registered breed of sheep - Katchaikatty sheep, genetic variability and genetic structure of the population by microsatellite marker analyses. Methods: DNA from 50 unrelated Katchaikatty sheep was amplified with 25 FAO recommended fluorescent tagged ovine-specific microsatellite markers and genotyped on an automated Genetic Analyzer. In each locus, observed (no) and effective number of microsatellite alleles (ne), allele frequencies, observed (Ho) and expected (He) heterozygosity and heterozygosity deficit estimate (FIS), polymorphism information content (PIC) and Chi-square (χ2) test for Hardy-Weinberg equilibrium (HWE) were assessed. Mode-shift analyses were performed. Result: The study revealed a total of 144 alleles across all the loci. The number of alleles at each locus varied from one to 10 with a mean of 5.76 alleles. The PIC values in the microsatellite loci ranged from 0.34 (OarAE129) to 0.83 (OarFCB48) with an average of 0.59, which showed a high genetic polymorphism. Six out of 25 microsatellite loci studied were in Hardy-Weinberg equilibrium and 19/25 loci showed positive FIS values. The overall mean observed and expected heterozygosity were 0.50 and 0.65 respectively and the estimates elucidated a substantial genetic variability in Katchaikatty sheep population. Mode shift analysis revealed a normal L-shaped curve, describing that the Katchaikatty population had not experienced any genetic bottleneck and remained in mutation-drift equilibrium.

Investigating growth associated genomic short tandem repeats (STRs) in a resource population generated through molecular breeding of RIR chicken

The long-term selection based on phenotypes causes loss of variation in performance traits and slows down the genetic progress per generation in the population; genomic selection could restore the variability along with faster genetic progress. Genomic short tandem repeats (STRs) in a resource population of RIR chicken were explored investigating randomly selected 114 pedigreed chicks. Alleles separated through 3.4% MetaPhor agarose gel electrophoresis at ten STR loci, and data recorded on growth traits were analyzed. Twenty-six alleles were resolved with frequencies of 0.1140–0.7632 and > 38.60% for the most frequent alleles at ten STR loci. The most frequent genotypes appeared with frequency >21.93% at different loci. Polymorphic information contents ranged from 0.2961 (LEI0079) to 0.6716 (LEI0071). Effective number of alleles ranged from 1.5662 (LEI0079) to 3.5836 (LEI0071). Mean FIS statistics revealed overall 21.78% heterozygosity deficit. Average heterozygosity ranged from 0.3630 (LEI0079) to 0.7241 (LEI0071). Chi-square and G-square test showed the population in Hardy-Weinberg disequilibrium at nine loci. Chick weight was significantly influenced by the factor of sire, and body weight traits by sex and hatch factors of the birds coded with STR-genotypes. ADL0328-BB genotype had the highest chick weight. LEI0068-BC and LEI0071-CC genotypes showed maximum 28-weeks body weight. MCW0010-AA genotype had the potential bearing of the highest body weight records at 16, 32, 36 and 40 weeks of age. MCW0058-CC genotype revealed the same at 24 and 28 weeks of age. The study impacts on marker assisted selection program for genetic improvement of growth traits in poultry.

Molecular identification of Sinonovacula constricta, Sinonovacula rivularis and their interspecific hybrids using microsatellite markers

The razor clam Sinonovacula constricta, is one of the most commercially important cultured bivalves in China and Southeast Asia, while S. rivularis is its closer relatives discovered more than a decade ago. In order to obtain offspring with faster growth rate and stronger salt tolerance of S. constricta and S. rivularis, interspecific hybrids were produced, and the hybridity of the interspecific hybrids was confirmed by microsatellite markers. Microsatellite markers exhibit a high potential for transfer through cross-amplification in related species, and the transferability of 48 pairs of microsatellite marker primers from S. constricta were assessed in S. rivularis. Here, 24 universal microsatellite markers were successfully amplified in S. rivularis, of which 18 were polymorphic with the allele number from 2 to 5. The genetic diversity of two razor clams evaluated by 18 polymorphic microsatellite markers indicated that two species were both above the middle level, with a relatively higher genetic diversity, while S. constricta showed higher genetic diversity than S. rivularis according to the genetic parameters of Na, Ho, He and PIC. Furthermore, a total of two species-specific microsatellite markers were screened, which could be used for quick genetic identification of S. constricta, S. rivularis and their hybrids. The results suggest the induced interspecific hybrids are true hybrids between S. constricta and S. rivularis, which provide a basis for breeding, subsequent protection, and germplasm resources utilization of the razor clams.

Disentangling and quantifying the relative cognitive impact of concurrent mixed neurodegenerative pathologies

Neurodegenerative pathologies such as Alzheimer disease neuropathologic change (ADNC), Lewy body disease (LBD), limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC), and cerebrovascular disease (CVD) frequently coexist, but little is known about the exact contribution of each pathology to cognitive decline and dementia in subjects with mixed pathologies. We explored the relative cognitive impact of concurrent common and rare neurodegenerative pathologies employing multivariate logistic regression analysis adjusted for age, gender, and level of education. We analyzed a cohort of 6,262 subjects from the National Alzheimer’s Coordinating Center database, ranging from 0 to 6 comorbid neuropathologic findings per individual, where 95.7% of individuals had at least 1 neurodegenerative finding at autopsy and 75.5% had at least 2 neurodegenerative findings. We identified which neuropathologic entities correlate most frequently with one another and demonstrated that the total number of pathologies per individual was directly correlated with cognitive performance as assessed by Clinical Dementia Rating (CDR®) and Mini-Mental State Examination (MMSE). We show that ADNC, LBD, LATE-NC, CVD, hippocampal sclerosis, Pick disease, and FTLD-TDP significantly impact overall cognition as independent variables. More specifically, ADNC significantly affected all assessed cognitive domains, LBD affected attention, processing speed, and language, LATE-NC primarily affected tests related to logical memory and language, while CVD and other less common pathologies (including Pick disease, progressive supranuclear palsy, and corticobasal degeneration) had more variable neurocognitive effects. Additionally, ADNC, LBD, and higher numbers of comorbid neuropathologies were associated with the presence of at least one APOE ε4 allele, and ADNC and higher numbers of neuropathologies were inversely correlated with APOE ε2 alleles. Understanding the mechanisms by which individual and concomitant neuropathologies affect cognition and the degree to which each contributes is an imperative step in the development of biomarkers and disease-modifying therapeutics, particularly as these medical interventions become more targeted and personalized.

SSR Marker–Based Genetic Diversity and Relationship Analyses of Stephania tetrandra S. Moore

AbstractStephania tetrandra S. Moore (family: Menispermaceae), a dioecious herbaceous vine and the only species in the subgenus Botryodiscia of the genus Stephania of the family Menispermaceae, is mainly distributed in hilly areas south of the Huaihe River in China and found in many provinces of China, showing a high genetic diversity. This paper aimed to study genetic diversity of and genetic relationship among individuals of S. tetrandra within China to provide a basis for evaluation, exploitation, and utilization of S. tetrandra by using simple sequence repeat (SSR) molecular markers. Our results show that effective products were amplified from the 26 screened SSR gene loci, a total of 183 alleles amplified (2–16 alleles amplified by each pair of primers). Among the 26 loci, 16 had a PIC value higher than 0.5, indicating a high level of polymorphism. For most of the loci, the number of effective alleles was lower than that of the observed alleles, and the observed heterozygosity was lower than the expected heterozygosity. The genetic differentiation coefficient (0.021–0.547) was lower than 0.05 (low level of genetic differentiation) for 7 loci and higher than 0.25 (very high level of genetic differentiation) for 2 loci, and had a value representing a medium level of genetic differentiation for the remaining 17 loci. The intra-population inbreeding coefficient had a positive value for 21 loci, suggesting the presence of inbreeding and homozygous excess. The gene flow value was bigger than 1, indicating that genetic drift and natural selection played an unimportant role in population genetic differentiation of S. tetrandra. Based on discriminant analysis of principal components and Bayesian Information Criterion, K-means clustering was performed on 620 samples. These samples were divided into 9 genetic clusters, whose similarity coefficients and genetic distances were 0.755–0.918 and 0.067–0.280, respectively, indicating that these clusters were highly similar and short-distanced. The Bayesian clustering analysis was implemented in the STRUCTURE software to analyze the genetic structure of S. tetrandra and it was found that the 620 samples could be clustered into 5 ancestor groups; the 9 clusters and 40 natural populations inherited genes from the 5 groups to varying degrees, but the proportion of genes inherited from the 5 groups by each cluster and natural population differed. S. tetrandra was characterized by the presence of population structure and pronounced genetic subdivision, which, together with the presence of gene flow, may indicate a relatively stable recent state of these populations.

APOEε4 carriage associates with improved myocardial performance from adolescence to older age

BackgroundAlthough APOE ε4 allele carriage confers a risk for coronary artery disease, its persistence in humans might be explained by certain survival advantages (antagonistic pleiotropy).MethodsCombining data from ~ 37,000 persons from three older age British cohorts (1946 National Survey of Health and Development [NSHD], Southall and Brent Revised [SABRE], and UK Biobank) and one younger age cohort (Avon Longitudinal Study of Parents and Children [ALSPAC]), we explored whether APOE ε4 carriage associates with beneficial or unfavorable left ventricular (LV) structural and functional metrics by echocardiography and cardiovascular magnetic resonance (CMR).ResultsCompared to the non-APOE ε4 group, APOE ε4 carriers had similar cardiac phenotypes in terms of LV ejection fraction, E/e’, posterior wall and interventricular septal thickness, and LV mass. However, they had improved myocardial performance resulting in greater LV stroke volume generation per 1 mL of myocardium (higher myocardial contraction fraction). In NSHD (n = 1467) and SABRE (n = 1187), ε4 carriers had a 4% higher MCF (95% CI 1–7%, p = 0.016) using echocardiography. Using CMR data, in UK Biobank (n = 32,972), ε4 carriers had a 1% higher MCF 95% (CI 0–1%, p = 0.020) with a dose-response relationship based on the number of ε4 alleles. In addition, UK Biobank ε4 carriers also had more favorable radial and longitudinal strain rates compared to non APOE ε4 carriers. In ALSPAC (n = 1397), APOE ε4 carriers aged < 24 years had a 2% higher MCF (95% CI 0–5%, p = 0.059).ConclusionsBy triangulating results in four independent cohorts, across imaging modalities (echocardiography and CMR), and in ~ 37,000 individuals, our results point towards an association between ε4 carriage and improved cardiac performance in terms of LV MCF. This potentially favorable cardiac phenotype adds to the growing number of reported survival advantages attributed to the pleiotropic effects APOE ε4 carriage that might collectively explain its persistence in human populations.

Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq ™ DNA signature prep kit

Target and flanking region (FR) variation at 94 identity-informative SNPs (iSNPs) are investigated in 635 Northern Han Chinese using the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. The dataset presents the following performance characteristics (average values): ≥60% bases with a quality score of 20 or higher (%≥ Q20); >700 × of depth of coverage (DoC) from both Sample Details Reports and Flanking Region Reports; >80% of effective reads; ≥60% of allele coverage ratio (ACR); and ≥70% of inter-locus balance, while some stable low-performance characteristics are also observed: low DoC at rs1736442, rs1031825, rs7041158, rs338882, rs2920816, rs1493232, rs719366, and rs2342747; high noise at rs891700; and imbalanced ACR at rs6955448 and rs338882. The average amplicon length is 69 bp, suitable for detecting degraded samples. Bioinformatic concordance achieves 99.99% between the ForenSeq Universal Analysis Software (UAS) and the Integrative Genomic Viewer (IGV) inspection. Discordance results from flanking region deletions of rs10776839, rs8078417, rs2831700, and rs1454361. Due to FR variants within amplicons detected by massively parallel sequencing (MPS), the increases in the number of unique alleles, effective alleles (Ae), and observed heterozygosity (Hobs) are 46.81%, 4.51%, and 3.29%, respectively. Twelve FR variants are first reported to dbSNP, such as rs1252699848, rs1665500714, rs1771121532, rs2097285015, rs1851671415, rs2045669877, rs2046758811, rs2044248635, rs1251308240, rs1968822112, rs1981638299, and rs1341756746. All 94 iSNPs from target and amplicon data are in Hardy-Weinberg equilibrium (HWE) and independent within autosomes. As expected, forensic parameters from the amplicon data increase significantly on the combined power of discrimination (CPD = 1 – 3.9876 × 10−38) and the combined power of exclusion (CPE = 1 – 6.6690 × 10−8). Additionally, the power of the system effectiveness (CPD = 1 − 6.7054 × 10−72 and CPE = 1 − 4.4719 × 10−20) with sequence-based 27 autosomal STRs and 94 iSNP amplicons in combination is substantially improved compared to one type of marker alone. In conclusion, we have established a traditional length-based and current sequence-based reference database with 58 STRs and 94 iSNPs in the Northern Han Chinese population. We hope these data can serve as a solid reference and foundation for forensic practice.

The genetic diversity of Oncomelania hupensis robertsoni, intermediate hosts of Schistosoma japonicum in hilly regions of China, using microsatellite markers

BackgroundThe elimination of schistosomiasis remains a challenging task, with current measures primarily focused on the monitoring and control of Oncomelania hupensis (O. hupensis) snail, the sole intermediate host of Schistosome japonicum. Given the emerging, re-emerging, and persistent habitats of snails, understanding their genetic diversity might be essential for their successful monitoring and control. The aims of this study were to analyze the genetic diversity of Oncomelania hupensis robertsoni (O. h. robertsoni) using microsatellite DNA markers; and validate the applicability of previously identified microsatellite loci for O. hupensis in hilly regions.MethodsA total of 17 populations of O. h. robertsoni from Yunnan Province in China were selected for analysis of genetic diversity using six microsatellite DNA polymorphic loci (P82, P84, T4-22, T5-11, T5-13, and T6-27).ResultsThe number of alleles among populations ranged from 0 to 19, with an average of 5. The average ranges of expected (He) and observed (Ho) heterozygosity within populations were 0.506 to 0.761 and 0.443 to 0.792, respectively. The average fixation index within the population ranged from – 0.801 to 0.211. The average polymorphic information content (PIC) within the population ranged from 0.411 to 0.757, appearing to be polymorphic for all loci (all PIC > 0.5), except for P28 and P48. A total of 68 loci showed significant deviations from Hardy-Weinberg equilibrium (P < 0.05), and pairwise Fst values ranged from 0.051 to 0.379. The analysis of molecular variance indicated that 88% of the variation occurred within snail populations, whereas 12% occurred among snail populations. Phylogenetic trees and principal coordinate analysis revealed two distinct clusters within the snail population, corresponding to “Yunnan North” and “Yunnan South”.ConclusionsO. h. robertsoni exhibited a relatively high level of genetic differentiation, with variation chiefly existing within snail populations. All snail in this region could be separated into two clusters. The microsatellite loci P82 and P84 might not be suitable for classification studies of O. hupensis in hilly regions. These findings provided important information for the monitoring and control of snail, and for further genetic diversity studies on snail populations.Graphical

Assessing the Genetic Variation of Swarna rice (Oryza sativa L.) Cultivars using SSR marker

Swarna rice cultivars (Indian cultivar) are widely grown in the northern part of Bangladesh because of their higher yield, drought tolerance, higher quality of grain and good plant appearance. Therefore, a study was conducted to observe genetic diversity among eight Swarna cultivars grown in Bangladesh. The genetic diversity of the cultivars was assessed by one hundred SSR (simple sequence repeat) markers. Among these, forty-four primers were polymorphic. In total, 188 alleles from eight rice genotypes with an average of 4.27 alleles per locus were identified. Allele numbers varied from 2 to 11. The average polymorphism information content (PIC) was 0.533, with a range of 0.195 to 0.889. The most suitable markers found were RM149, RM232, and RM3421, which provided the highest PIC value of 0.889. Genetic dissimilarity coefficient values between pairs indicated that the Guti Swarna and Nepali Swarna cultivars along with the Guti Swarna and Deshi Guti Swarna cultivars were the most genetically distant (0.818) cultivars whereas the Nepali Swarna and Nironjon Swarna cultivars were the closest (0.091). A dendrogram constructed based on polymorphism indicated five major groups. It was observed that the Guti Swarna and Sumon Swarna cultivars formed two different solitary groups, I and II whereas the Nepali Swarna and Nironjon Swarna formed group III, the Lal Swarna and Swarna5 constructed group IV, and the Deshi Guti Swarna and Tiger Indian Swarna were in group V. Our findings may help in designing appropriate cross combinations for further improvement of Swarna cultivars.

High genetic diversity but limited gene flow in Flemish populations of the crested newt, Triturus cristatus

Habitat destruction and fragmentation are among the major causes of amphibian decline. We investigated to what extent geographic distance and barriers affect the genetic composition of the crested newt, Triturus cristatus in Flanders (North Belgium), causing inbreeding or loss of genetic diversity. Data from seven microsatellite loci and 170 individuals from seven metapopulations up to 180km apart revealed heterozygosities of 0.53 to 0.67 within populations and moderate levels of genetic divergence between populations (FST values from 0.074 to 0.141, harmonic means of Dest between 0.070 and 0.189). In all Flemish meta-populations, more than 90% of the individuals from a given geographic region were assigned to the same genetic cluster indicating&#x0D; little genetic exchange, even in De Panne where the two populations Oosthoek and Westhoek are only a few kilometres apart. Such sub-structuring on a micro-scale has also been described in other amphibians. Unique alleles in most populations further support the probability that genetic drift has already led to some isolation. With the exception of the Oosthoek population, however, we found no significant evidence for bottlenecks. Connectivity within pool clusters seems essential to the maintenance of genetic diversity in crested newts as is indicated by our findings from Tommelen, the population with the largest number of pools in close proximity, which also shows the highest levels of heterozygosity (He and Ho) and the second highest number and richness of alleles. In conclusion, our study indicates that dispersal and migration rates between the Flemish populations of Triturus cristatus are limited at the geographic scale studied here but that habitat fragmentation has not yet led to a significant loss of genetic diversity of the studied Flemish populations, possibly because crested newts are relatively long-lived, fragmentation of their habitat is relatively recent in Flanders, and most investigated pools are still connected at the local scale.

Biobank-scale inference of multi-individual identity by descent and gene conversion

We present a method for efficiently identifying clusters of identical-by-descent haplotypes in biobank-scale sequence data. Our multi-individual approach enables much more computationally efficient inference of identity by descent (IBD) than approaches that infer pairwise IBD segments and provides locus-specific IBD clusters rather than IBD segments. Our method's computation time, memory requirements, and output size scale linearly with the number of individuals in the dataset. We also present a method for using multi-individual IBD to detect alleles changed by gene conversion. Application of our methods to the autosomal sequence data for 125,361 White British individuals in the UK Biobank detects more than 9 million converted alleles. This is 2,900 times more alleles changed by gene conversion than were detected in a previous analysis of familial data. We estimate that more than 250,000 sequenced probands and a much larger number of additional genomes from multi-generational family members would be required to find a similar number of alleles changed by gene conversion using a family-based approach. Our IBD clustering method is implemented in the open-source ibd-cluster software package.