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Background: Chloroquine (CQ) resistance is conferred by mutations in the Plasmodium falciparum CQ resistance transporter (pfcrt). Following CQ withdrawal for anti-malarial treatment, studies across malaria-endemic countries have shown a range of responses. In some areas, CQ sensitive parasites re-emerge, and in others, mutant haplotypes persist. Active surveillance of resistance mutations in clinical parasites is essential to inform treatment regimens; this effort requires fast, reliable, and cost-effective methods that work on a variety of sample types with reagents accessible in malaria-endemic countries. Methods: Quantitative PCR followed by High-Resolution Melt (HRM) analysis was performed in a field setting to assess pfcrt mutations in two groups of clinical samples from Southwestern Uganda. Group 1 samples (119 in total) were collected in 2010 as predominantly Giemsa-stained slides; Group 2 samples (125 in total) were collected in 2015 as blood spots on filter paper. The Rotor-Gene Q instrument was utilized to assess the impact of different PCR-HRM reagent mixes and the detection of mixed haplotypes present in the clinical samples. Finally, the prevalence of the wild type (CVMNK) and resistant pfcrt haplotypes (CVIET and SVMNT) was evaluated in this understudied Southwestern region of Uganda. Results: The sample source (i.e. Giemsa-stained slides or blood spots) and type of LCGreen-based reagent mixes did not impact the success of PCR-HRM. The detection limit of 10− 5 ng and the ability to identify mixed haplotypes as low as 10 % was similar to other HRM platforms. The CVIET haplotype predominated in the clinical samples (66 %, 162/244); however, there was a large regional variation between the sample groups (94 % CVIET in Group 1 and 44 % CVIET in Group 2). Conclusions: The HRM-based method exhibits the flexibility required to conduct reliable assessment of resistance alleles from various sample types generated during the clinical management of malaria. Large regional variations in CQ resistance haplotypes across Southwestern Uganda emphasizes the need for continued local parasite genotype assessment to inform anti-malarial treatment policies. [ABSTRACT FROM AUTHOR]

Objectives: The study evaluated sub-microscopic malaria infections in pregnancy using two malaria Rapid Diagnostic Tests (mRDTs), microscopy and RT-PCR and characterized Plasmodium falciparum dihydrofolate reductase (Pfdhfr) and Plasmodium falciparum dihydropteroate synthase (Pfdhps) drug resistant markers in positive samples. Methods: This was a cross sectional survey of 121 pregnant women. Participants were finger pricked, blood drops were collected for rapid diagnosis with P. falciparum histidine-rich protein 11 rapid diagnostic test kit and the ultra-sensitive Alere Pf malaria RDT, Blood smears for microscopy and dried blood spots on Whatman filter paper for molecular analysis were made. Real time PCR targeting the var acidic terminal sequence (varATS) gene of P. falciparum was carried out on a CFX 96 real time system thermocycler (BioRad) in discriminating malaria infections. For each run, laboratory strain of P. falciparum 3D7 and nuclease free water were used as positive and negative controls respectively. Additionally, High resolution melt analyses was employed for genotyping of the different drug resistance markers. Results: Out of one hundred and twenty-one pregnant women sampled, the SD Bioline™ Malaria Ag P.f HRP2-based malaria rapid diagnostic test (mRDT) detected eight (0.06%) cases, the ultra-sensitive Alere™ malaria Ag P.f rapid diagnostic test mRDT had similar outcome in the same samples as detected by the HRP2-based mRDT. Microscopy and RT-PCR confirmed four out of the eight infections detected by both rapid diagnostic tests as true positive and RT-PCR further detected three false negative samples by the two mRDTs providing a sub-microscopic malaria prevalence of 3.3%. Single nucleotide polymorphism in Pfdhps gene associated with sulphadoxine resistance revealed the presence of S613 mutant genotypes in three of the seven positive isolates and isolates with mixed wild/mutant genotype at codon A613S. Furthermore, four mixed genotypes at the A581G codon were also recorded while the other Pfdhps codons (A436G, A437G and K540E) showed the presence of wild type alleles. In the Pfdhfr gene, there were mutations in 28.6%, 28.6%, and 85.7% at the I51, R59 and N108 codons respectively. Mixed wild and mutant type genotypes were also observed in 28.6% each of the N51I, and C59R codons. For the Pfcrt, two haplotypes CVMNK and CVIET were observed. The SVMNT was altogether absent. Triple mutant CVIET 1(14.3%) and triple mutant + wild genotype CVIET + CVMNK 1(14.3%) were observed. The Pfmdr1 haplotypes were single mutants YYND 1(14.3%); NFND 1(14.3%) and double mutants YFND 4(57.1%); YYDD 1(14.3%). [ABSTRACT FROM AUTHOR]

Cystic fibrosis (CF), an autosomal recessive disease, is caused by variants in both alleles of the CF transmembrane conductance regulator (CFTR) gene. A new assay based on allele-specific polymerase chain reaction and high-resolution melting analysis was developed for the detection of 18 CF-causing CFTR variants previously identified in Cuba and Latin America. The assay is also useful for zygosity determination of mutated alleles and includes internal controls. The reaction mixtures were normalized and evaluated using blood samples collected on filter paper. The evaluation of analytical parameters demonstrated the specificity and sensitivity of the method to detect the included CFTR variants. Internal and external validations yielded a 100% agreement between the new assay and the used reference tests. This assay can complement CF newborn screening not only in Cuba but also in Latin America. [ABSTRACT FROM AUTHOR]

Soybean [Glycine max (L.) Merr.] is an excellent source of protein for humans, but several allergenic and antinutritional components such as P34, lectin, Kunitz Trypsin Inhibitor (KTI), and 7S α′ subunit proteins exist in the raw mature seed. Genetic elimination of these factors would be the appropriate method to improve soybean food quality. The objective of this research was to develop a new soybean line with a tetra null recessive genotype (titilelecgy1cgy1p34p34) based on Mendelian inheritance. Four germplasms were used to develop the tetra null strain. A total of 322 F2 seeds were obtained from the cross of parent 1 and parent 2. For four proteins of KTI, lectin, 7S α′ subunit and P34, and segregation ratio of 107:30:37:8:35:9:14:3:33:9:14:0:13:3:5:2 was observed (χ2 = 9.41, P = 0.9 ~ 0.5). Two F2 seeds possessing the tetra null genotype (cgy1cgy1titilelep34p34) were selected. Confirmation of the Tetra null genotype (titilelecgy1cgy1p34p34—absence of KTI, lectin, 7S α′ subunit and P34 proteins) was verified on the random F3 seeds of the two lines selected. The seed color for both selection lines was yellow and the hilum color was buff. The seed weights (g/100 seeds) for the two selected lines were 12.2 and 12.0 g. This paper is the first to investigate the genetic segregation ratio and selection of tetra null genotype for four proteins of P34, lectin, KTI and 7S α′ subunit proteins in soybean. [ABSTRACT FROM AUTHOR]

Candida albicans, a normal member of the human microbiome and an opportunistic fungal pathogen, undergoes several morphological transitions. One of these transitions is white–opaque switching, where C. albicans alternates between 2 stable cell types with distinct cellular and colony morphologies, metabolic preferences, mating abilities, and interactions with the innate immune system. White-toopaque switching is regulated by mating type; it is repressed by the a1/α2 heterodimer in a/α cells, but this repression is lifted in a/a and α/α mating type cells (each of which are missing half of the repressor). The widely used C. albicans reference strain, SC5314, is unusual in that white–opaque switching is completely blocked when the cells are a/α; in contrast, most other C. albicans a/α strains can undergo white–opaque switching at an observable level. In this paper, we uncover the reason for this difference. We show that, in addition to repression by the a1/α2 heterodimer, SC5314 contains a second block to white–opaque switching: 4 transcription regulators of filamentous growth are upregulated in this strain and collectively suppress white–opaque switching. This second block is missing in the majority of clinical strains, and, although they still contain the a1/α2 heterodimer repressor, they exhibit a/α white–opaque switching at an observable level. When both blocks are absent, white–opaque switching occurs at very high levels. This work shows that white–opaque switching remains intact across a broad group of clinical strains, but the precise way it is regulated and therefore the frequency at which it occurs varies from strain to strain. [ABSTRACT FROM AUTHOR]

HLA and disease studies by using single allele statistics have been fruitless during the last 40 years for explaining association pathogenesis of the associated diseases.Other approaches are necessary to untangle this puzzle. We aim to revisit complement alleleism in humans and primates for both studying MHC and disease association to complotypes and extended MHC haplotypes in order to also explain the positive directional selection of maintaining immune response genes (complement, MHC adaptive and MHC non-specific genes) that keeps these three type of genes together in a short chromosome stretch (MHC) for million years. These genes may be linked to conjointly avoid microbes attack and autoimmunity. In the present paper, it is obtained a new Bf chimpanzee allele, provisionaly named Patr-Bf*A:01,that differs from other Bf alleles by having CTG at eleventh codon of exon 2 in order to start the newly suggested methodology and explain functional and evolutionary MHC obscure aspects. Exons 1 to 6 of Ba fragment of Bf gene were obtained from chimpanzee. This new chimpanzee Factor B allele (Patr-Bf*A:01) is to be identical to a infrequent human Bf allele (SNP rs641153); it stresses the strong evolutive pressure upon certain alleles that are trans specific. It also may apply to MHC extended haplotipes which may conjointly act to start an adequate immune response. It is the first time that a complement MHC class III allele is described to undergo trans species evolution,in contrast to class I and class II alleles which had already been reported. Allelism of complement factors are again proposed for studying MHC complement genes, complotypes, and extended MHC haplotypes which may be more informative that single MHC marker studies. [ABSTRACT FROM AUTHOR]

HLA and disease studies by using single allele statistics have been fruitless during the last 40 years for explaining association pathogenesis of the associated diseases.Other approaches are necessary to untangle this puzzle. We aim to revisit complement alleleism in humans and primates for both studying MHC and disease association to complotypes and extended MHC haplotypes in order to also explain the positive directional selection of maintaining immune response genes (complement, MHC adaptive and MHC non-specific genes) that keeps these three type of genes together in a short chromosome stretch (MHC) for million years. These genes may be linked to conjointly avoid microbes attack and autoimmunity. In the present paper, it is obtained a new Bf chimpanzee allele, provisionaly named Patr-Bf*A:01,that differs from other Bf alleles by having CTG at eleventh codon of exon 2 in order to start the newly suggested methodology and explain functional and evolutionary MHC obscure aspects. Exons 1 to 6 of Ba fragment of Bf gene were obtained from chimpanzee. This new chimpanzee Factor B allele (Patr-Bf*A:01) is to be identical to a infrequent human Bf allele (SNP rs641153); it stresses the strong evolutive pressure upon certain alleles that are trans specific. It also may apply to MHC extended haplotipes which may conjointly act to start an adequate immune response. It is the first time that a complement MHC class III allele is described to undergo trans species evolution,in contrast to class I and class II alleles which had already been reported. Allelism of complement factors are again proposed for studying MHC complement genes, complotypes, and extended MHC haplotypes which may be more informative that single MHC marker studies. [ABSTRACT FROM AUTHOR]

Common bean has become very popular and widespread among the population since its introduction to Azerbaijan in the second half of the 18th century. The paper represents for the first time the genetic diversity and anthracnose resistance of 37 common bean accessions cultivated in Azerbaijan. ISSR marker characterization in the present study revealed a total of 47 bands, with 33.6% of average polymorphism. The polymorphism information content (PIC) and genetic diversity index (GDI) for each primer were in the range of 0.25–0.48 (mean 0.35) and 0.45–0.73 (mean 0.59), respectively, indicating a moderate level of genetic diversity in the current collection. UNJ tree showed that the common bean accessions tended to cluster according to the local and introduced gene pools, indicating the same original sources of these accessions, which is also supported by PCo analysis. Screening with linked SCAR markers revealed the existence of common bean genotypes with single or multiple Co resistance alleles. Among studied genes Co-4 locus and its alleles were found in all samples, followed by Co-6 (40.5%) and Co-34 (16%). Three genotypes had all studies resistance loci, while 12 had Co-4 and Co-6, and 3 had Co-4 and Co-34 . The results could provide valuable information for future common bean breeding activities and conservation. The use of genotypes with two or more resistance genes as donor parents can accelerate the development of new common bean cultivars with durable resistance to anthracnose. [ABSTRACT FROM AUTHOR]

In the diffusion approximation of the neutral Wright–Fisher model, the expected time until fixation or loss of a neutral allele is proportional to the initial entropy of the distribution of the allele in the population. No explanation is known for this coincidence. In this paper, we show that the rate of entropy dissipation is proportional to the number of segregating alleles. Since the final fixed state has zero entropy, the expected lifetime of segregating alleles is proportional to the initial entropy in the system. We show that classical formulae on the average time to loss of segregating alleles and the expected time to fixation of the last segregating allele stem from these properties of the diffusion process. We also extend our results to the case of population size changing in time. The dissipation of heterozygosity and entropy shows that superlinear population growth leads to infinite expected fixation times, i.e., neutral alleles in fast-growing populations could segregate forever without ever becoming fixed or disappearing by genetic drift. [ABSTRACT FROM AUTHOR]

The paper presents the results of the microsatellite genotyping of hybrid lizards D.armeniaca × D. valentini from sympatric populations of Armenia. Triploid individuals are identified based on the totality of the Du281 and Du47G loci and their origin is determined. It is shown that the hybrids contain both alleles of the maternal parthenospecies D. armeniaca and alleles of the paternal species D. valentini. [ABSTRACT FROM AUTHOR]

Wisent Bison bonasus is an example of a species saved from extinction and reintroduced into nature after a few decades of captive breeding. There were only twelve founders of the Lowland–Caucasian line (LC) and even fewer (seven out of twelve) of Lowland (LB) animals. The genetic diversity in studies based on pedigree or markers is very low. In this paper, we present a summary of the long-term genetic monitoring conducted for the worldwide population of European bison. We summarized the long-term genetic monitoring studies conducted on the worldwide population of wisents to date. We genotyped 2227 wisents from two genetic lines (LC and LB) and different populations at ten microsatellite loci. We found low polymorphism, with only 2.7 alleles per locus, and much lower values of observed heterozygosity (0.380 and 0.348 in the LC and LB lines, respectively) than expected heterozygosity. The difference between the lines is only noticeable in allele proportions, so the number of markers is not enough to distinguish the two genetic lines. We also present the genetic distance among four free-roaming populations that are geographically close to each other. We found that the genetic distance of one of them is larger than that of the others, which could be the effect of genetic drift. [ABSTRACT FROM AUTHOR]

Background: Osteoarthritis of the knee is an irreversible disease that causes great pain, and genetic factors play an important role in its occurrence and development. There have been many studies on the correlation between ADAM12 polymorphisms and genetic susceptibility to osteoarthritis, but the results remain inconclusive. Methods: Papers from PubMed, Web of Science, EMbase, Springer, SCOPUS, Google Scholar and other databases were systematically retrieved with a cut-off of January 2022. All case–control studies on ADAM12 rs3740199, rs1871054, rs1044122, and rs1278279 polymorphisms and osteoarthritis were searched. Fixed or random effects models were used for pooled analysis with OR values and 95% confidence intervals (CI), and publication bias was assessed. In addition, the false-positive reporting probability test was used to assess the confidence of a statistically significant association. Results: Eleven articles were included, which included 3332 patients with osteoarthritis and 5108 healthy controls. Meta-analysis showed that the rs1871054 polymorphism of ADAM12 was associated with osteoarthritis in dominant, recessive, allelic, and homozygote genetic models [C vs. T: OR = 1.34 95% CI (1.05, 1.71), P < 0.001]. Our subgroup analysis revealed an association between the ADAM12 polymorphism rs1871054 in Asians and osteoarthritis [C vs. T: OR = 1.61, 95% CI (1.25, 2.08), P < 0.001], albeit this was only for three studies. In addition, the ADAM12 polymorphism rs1871054 is associated with osteoarthritis in patients younger than 60 years of age [C vs. T: OR = 1.39, 95% CI (1.01, 1.92), P = 0.289]; however, the ADAM12 gene rs3740199, rs1044122, and rs1278279 site polymorphisms were not significantly. Furthermore, when assessing the confidence of the positive results, the positive results were found to be credible (except for Age < 60). Conclusion: Polymorphism at the rs1871054 site of ADAM12 is associated with genetic susceptibility to osteoarthritis, but rs3740199, rs1044122, and rs1278279 site polymorphisms are not. [ABSTRACT FROM AUTHOR]

Objective: The genetic factors responsible for the etiopathogenesis of childhood acute leukemia have been extensively investigated. Highresolution expression analysis of the whole genome, and results of gene studies including whole genome sequencing, copy number changes of DNA, loss of heterozygosity and epigenetic changes revealed the classification of acute lymphoblastic leukemia (ALL). A variable number of tandem repeats (VNTRs) can regulate many biological processes, including gene transcription, protein function, morphological development, and cancer formation. They may also play a role in many disorders in humans such as labile repeat expansions. In this paper, our aim was to compare the genotype and allele frequencies in VNTR variants of XRCC4, eNOS, and PER3 between pediatric ALL patients and healthy controls. Methods: Seventy-four high-risk pediatric ALL patients (82.4% B-ALL, 17.6% T-ALL) who were consecutively admitted to the Pediatric Hematology Units of İstanbul Medical Faculty and Yeni Yuzyıl Medical Faculty and 100 healthy volunteers were included in this case-control study. VNTRs of three genes were analyzed using the polymerase chain reaction method. Results: The frequency of the eNOS VNTR 4a/4a genotype was found to be higher in the pediatric patients with ALL compared to the healthy controls (p=0.044) and the risk factor for childhood ALL was found to be 8.382 (95% confidence interval =0.985-71.262). The frequency of eNOS 4/a allele was found to be higher in the childhood ALL group compared to the controls (p=0.013). The frequencies of the 5R/5R genotype and 5R allele of the PER3 VNTR were found to be significantly lower in the childhood ALL patients (p=0.039 and p=0.015, respectively). Conclusion: Our results show that functional variants of the eNOS and PER3 genes may have an important relationship with the etiopathogenesis of childhood ALL. Further studies including larger groups and different ethnic populations are needed to determine the effect of VNTR variants on the risk of developing childhood ALL. [ABSTRACT FROM AUTHOR]

Scientific studies have provided evidence that there is a relationship between violent and aggressive behaviors and addictions. Genes involved with the reward system, specifically the brain reward cascade (BRC), appear to be associated with various addictions and impulsive, aggressive, and violent behaviors. In our previous research, we examined the Taq A1 allele (variant D2 dopamine receptor gene) and the DAT-40 base repeat (a variant of the dopamine transporter gene) in 11 Caucasian boys at the Brown School in San Marcus, Texas, diagnosed with intermittent explosive disorder. Thirty supernormal controls were screened to exclude several reward–deficit behaviors, including pathological violence, and genotyped for the DRD2 gene. Additionally, 91 controls were screened to exclude ADHD, pathological violence, alcoholism, drug dependence, and tobacco abuse, and their results were compared with DAT1 genotype results. In the schoolboys vs. supercontrols, there was a significant association with the D2 variant and a trend with the dopamine transporter variant. Results support our hypothesis and the involvement of at least two gene risk alleles with adolescent violent/aggressive behaviors. This study and the research presented in this paper suggest that violent/aggressive behaviors are associated with a greater risk of addiction, mediated via various genes linked to the BRC. This review provides a contributory analysis of how gene polymorphisms, especially those related to the brain reward circuitry, are associated with violent behaviors. [ABSTRACT FROM AUTHOR]

Rapid DNA profiling of casework samples is a powerful tool that can support law enforcement agencies in the quick apprehension of perpetrators before they re-offend or escape the jurisdiction. This present study evaluated the feasibility of direct PCR amplification, using the microFLOQ™ Direct swab, for generating DNA profiles (from bloodstains) within 3 h. The swab tip is coated with nylon fibers pre-treated with cell lysing agent, which allows for the direct PCR amplification of collected samples without DNA extraction and quantification, thereby shortening the time required to obtain a DNA profile. Samples collected were directly amplified using GlobalFiler™ PCR Amplification Kit with and without the presence of a PCR additive. Addition of the PCR additive enhanced the peak heights of DNA profiles by approximately 2 fold. Hence, an additive could improve results obtained in the absence of a DNA purification step, especially since casework samples may contain PCR inhibitors. Subsequently, these swabs, amplified using the GlobalFiler™ PCR Amplification Kit with PCR additive, were evaluated on common substrates encountered in routine casework samples submitted with bloodstains, such as denim jeans, knife blade, tissue paper, leather belt, shirt, and blood swabs. The minimum peak heights observed were generally above the analytical and stochastic thresholds established by the laboratory. Finally, the microFLOQ™ Direct swab workflow was compared to the laboratory's standard workflow of DNA profiling comprising of conventional processing steps such as extraction using the DNA-IQ™ chemistry on Maxwell® 16, followed by quantification, amplification and capillary electrophoresis. The average peak heights of the DNA profiles generated by direct PCR amplification were similar or exceeded those generated using the standard workflow. This study clearly demonstrates that direct PCR amplification using microFLOQ™ Direct swab can be used in a rapid workflow to obtain DNA profiles from casework samples. [ABSTRACT FROM AUTHOR]

Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g., erect leaves, short stems) that—while beneficial to the group—decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields. Some traditional breeding approaches select for "selfish" traits that can reduce yield in high-density monocultures. This paper proposes a simple method to identify plant genotypes that express more cooperative versus more competitive traits, based on how they grow in different social environments, and applies this method to a genetic study with Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

The DRB4*01:03:01:02N null allele is predominantly associated with the HLA‐DRB1*07–DQB1*03:03 haplotype. Several recent reports demonstrated a less frequent association of DRB4*01:03:01:02N with DRB1*04 carrying haplotypes in different populations. The ability to identify the presence of null alleles is extremely important in the setting of both solid organ transplants and hematopoietic cell transplants, and characterization of haplotypes carrying null alleles is crucial. In this paper, we report for the first time, an association of DRB4*01:03:01:02N null allele with a DRB1*04:07–DQB1*03:02 haplotype. [ABSTRACT FROM AUTHOR]

We introduce a within-sample SNP calling method, called the "butterfly method", that improves the quality of SNP calling with the Illumina Infinium Omni5-4 SNP Kit. This was done by improving how no-calls are determined from allele signal intensities. High confidence of SNP allele calling is extremely important in forensic genetics and clinical diagnostics. This paper is accompanied by two open-source R packages, omni54manifest and snpbeadchip that make SNP calling easy by helping with bookkeeping and giving easy access to meta-information about the SNPs typed with the Illumina Infinium Omni5-4 Kit (including chromosome, probe type, and SNP bases). We compared the results from our method with those obtained with the Illumina GenomeStudio software (which does not provide sample and SNP specific genotype probabilities or other quality measures), and with whole-genome sequencing (WGS). Given the signal intensities, the SNP calling quality was optimised using a threshold for the a posteriori probability of a SNP belonging to a SNP cluster. By lowering the a posteriori probability threshold for no-calls, we obtained a higher call rate than GenomeStudio. Using a higher a posteriori probability threshold, we achieved a higher concordance with the WGS data than GenomeStudio. Our method had SNP call and concordance rates with WGS data of approximately 99%. [ABSTRACT FROM AUTHOR]

This paper considers how polygenic local adaptation and reproductive isolation between hybridizing populations is influenced by linkage disequilibria (LD) between loci, in scenarios where both gene flow and genetic drift counteract selection. It shows that the combined effects of multi-locus LD and genetic drift on allele frequencies at selected loci and on heterozygosity at neutral loci are predicted accurately by incorporating (deterministic) effective migration rates into the diffusion approximation (for selected loci) and into the structured coalescent (for neutral loci). Theoretical approximations are tested against individual-based simulations and used to investigate conditions for the maintenance of local adaptation on an island subject to one-way migration from a differently adapted mainland, and in an infinite-island population with two habitats under divergent selection. The analysis clarifies the conditions under which LD between sets of locally deleterious alleles allows these to be collectively eliminated despite drift, causing sharper and (under certain conditions) shifted migration thresholds for loss of adaptation. Local adaptation also has counter-intuitive effects on neutral (relative) divergence: FST is highest for a pair of subpopulations belonging to the same (rare) habitat, despite the lack of reproductive isolation between them. Author summary: Environmental adaptation often involves spatially heterogeneous selection at many genetic loci. Thus, the evolutionary consequences of hybridisation between populations adapted to different environments depend on the coupled dynamics of multiple loci under selection, migration and genetic drift, making them challenging to predict. Here, I introduce theoretical approximations that accurately capture the effect of such coupling on allele frequencies at individual loci, while also accounting for the stochastic effects of genetic drift. I then use these approximations to study hybridisation in a metapopulation consisting of many interconnected subpopulations, where each subpopulation belongs to one of two habitats under divergent selection. The analysis clarifies how subpopulations belonging to a rare habitat can maintain local adaptation despite high levels of migration if net selection against multi-locus genotypes is stronger than a threshold which depends on the relative abundances of the two habitats. Further, local adaptation in a metapopulation can significantly elevate FST between subpopulations belonging to the same habitat, even though these are not reproductively isolated. These findings highlight the importance of carefully considering the genetic architecture and spatial context of divergence when interpreting patterns of genomic differentiation between speciating populations. [ABSTRACT FROM AUTHOR]

Introduction: Aetiology of psoriasis is complex with risk factors involving both environmental triggers and genetic background. Although the best characterized genetic risk factor for psoriasis is HLA-C*06 allele, a number of other variants were associated with the disease. Aim: In the current paper we have conducted a confirmation study for SNPs located in 9 gene regions in a casecontrol analysis of 507 psoriatic patients and 396 controls from the Polish population. Material and methods: Subsequently the impact of genetic variants on response to topical and NB-UVB therapy (reduction in the Psoriasis Area and Severity Index) was analysed. Results: Significant differences in genotype and/or allelic frequency were observed for the following SNPs: rs33980500 (TRAF3IP2), rs582757 (TNFAIP3I), rs12188300 (IL12B), rs28998802 (NOS2), and rs2233278 (TNIP1). None of the genetic factors was associated with treatment outcome. Conclusions: Although the genetic variants have an impact on the disease risk, they are unlikely to be useful in personalization of topical therapy. [ABSTRACT FROM AUTHOR]

Collecting, conserving, and using peanut germplasm depends on our ability to comprehend genetic variability in gene banks. The peanut genetic resources are not well characterized for their conservation and potential future use. Increased use of exotic and interspecific derivatives is required to reduce the yield gap, identify new alleles, and introduce them. We assessed the genetic diversity and organization of an 83-germplasm peanut population. Ninety polymorphic markers generated 326 alleles, and the similarity matrix formed three main clusters. Polymorphism information content (PIC) ranged from 0.09 to 0.85, indicating greater genetic diversity in these genotypes. Germplasm from exotic collections had the highest levels of diversity, followed by released cultivars, and interspecific derivatives had the lowest levels of diversity. The number of private alleles in interspecific derivatives, exotic collections, and cultivars was 1, 6, and 3, respectively. Overall, several SSRs showed a high probability of null alleles. In addition, gene diversity and allelic richness were 0.526 and 3.18, respectively. Analysis of molecular variance revealed variation both within and between individuals. Principal coordinate analysis and population structure analysis subdivided all germplasm lines into three populations. Bottleneck analysis revealed that all three populations experienced genetic bottlenecks, as a shifted mode was observed. This paper highlights the importance of using microsatellite markers to study the diversity of interspecific derivatives, including recently developed ones, and create effective conservation programs. [ABSTRACT FROM AUTHOR]

Lodging is one of the important reasons for rapeseed yield reduction. Increasing the lignin content in aerial part has become an effective way to improve rapeseed lodging resistance. However, knowledge of the genetic basis underlying lignin content in rapeseed is limited. Therefore, we undertook association mapping to identify quantitative trait nucleotides (QTNs) associated with lignin content in the stalk and taproot of 125 natural rapeseed accessions across three independent environments by BLUP mixed line model. Among the natural population, lignin content ranged from 6.05% and 12.76% for the stalk, and 3.21% and 12.33% for the taproot with massive phenotypic variation. Four QTL regions were identified for total lignin content in stalk and taproot, qBnADL.C09.1 and qBnADL.C09.2 with phenotypic variance ranging from 6.05% to 12.76% in stalk and BnADL.A05.1 and qBnADL.A09.1 from 3.21% to 12.33% in taproot. Lignin content significantly differed between superior and alternative alleles, with 4 haplotype groups. We identified 2 putative candidate genes based on the haplotype QTNs for lignin content, e.g., BnLI.C09 and BnRPS17. Combining with the RNA-seq data, identified 3 candidate genes with lignin pathway, e.g., BnLAC17 , BnF8H and BnDIR20. This study provides novel insights into the lodging improvement of high lignin content and also facilitates the MAS for low lignin straw selection of rapeseed. • The recycling and reuse of agricultural waste, such as rapeseed straw, requires fundamental work to understand genetic control of lignin. • In this paper, we used the GWAS and RNA-seq methods to discover superior alleles and candidate genes for lignin content in rapeseed. • This knowledge can improve the economic value by regulating lignin content by genes and superior alleles, increasing the development of biomass energy and lodging resistance of rapeseed. [ABSTRACT FROM AUTHOR]

Synthetic gene drive constructs could, in principle, provide the basis for highly efficient interventions to control disease vectors and other pest species. This efficiency derives in part from leveraging natural processes of dispersal and gene flow to spread the construct and its impacts from one population to another. However, sometimes (for example, with invasive species) only specific populations are in need of control, and impacts on non-target populations would be undesirable. Many gene drive designs use nucleases that recognise and cleave specific genomic sequences, and one way to restrict their spread would be to exploit sequence differences between target and non-target populations. In this paper we propose and model a series of low threshold double drive designs for population suppression, each consisting of two constructs, one imposing a reproductive load on the population and the other inserted into a differentiated locus and controlling the drive of the first. Simple deterministic, discrete-generation computer simulations are used to assess the alternative designs. We find that the simplest double drive designs are significantly more robust to pre-existing cleavage resistance at the differentiated locus than single drive designs, and that more complex designs incorporating sex ratio distortion can be more efficient still, even allowing for successful control when the differentiated locus is neutral and there is up to 50% pre-existing resistance in the target population. Similar designs can also be used for population replacement, with similar benefits. A population genomic analysis of CRISPR PAM sites in island and mainland populations of the malaria mosquito Anopheles gambiae indicates that the differentiation needed for our methods to work can exist in nature. Double drives should be considered when efficient but localised population genetic control is needed and there is some genetic differentiation between target and non-target populations. Author summary: Some disease vectors, invasive species, and other pests cannot be satisfactorily controlled with existing interventions, and new methods are required. Synthetic gene drive systems that are able to spread though populations because they are inherited at a greater-than-Mendelian rate have the potential to form the basis for new, highly efficient pest control measures. The most efficient such strategies use natural gene flow to spread a construct throughout a species' range, but if control is only desired in a particular location then these approaches may not be appropriate. As some of the most promising gene drive designs use nucleases to target specific DNA sequences, it ought to be possible to exploit sequence differences between target and non-target populations to restrict the spread and impact of a gene drive. In this paper we propose using two-construct "double drive" designs that exploit pre-existing sequence differences between target and non-target populations. Our approaches maintain the efficiencies associated with only small release rates being needed and can work if the differentiated locus is selectively neutral and if the differentiation is far from complete, and therefore expand the range of options to be considered in developing genetic approaches to control pest species. [ABSTRACT FROM AUTHOR]

Announces the co-winners of the 1999 Fulker Award for a paper appearing in 'Behavior Genetics.' 'Oviposition-Site Preference in Drosophila Following Interspecific Gene Transfer of the Alcohol Dehydrogenase Locus,' by Mark L. Siegal and Daniel L. Hartl; 'Distinguishing Population Stratification from Genuine Allelic Effects with Mx: Association of ADH2 with Alcohol Consumption,' by Mike Nale and colleagues.

In this paper we discuss bifurcations of equilibria in the symmetric viability model with weak selection. Overcoming the difficulties from irrational fractions of the 4 parameters in determining the signs of determinant and trace, we find that the system has at most 5 interior equilibria, 4 edge equilibria and 4 corner equilibria and give a complete qualitative analysis for all equilibria in both hyperbolic cases and non-hyperbolic cases, including the case of fully null degeneracy. On this basis we display all bifurcations of equilibria such as pitchfork bifurcation, transcritical bifurcation and bifurcations at corner equilibria of fully null degeneracy, which is of codimension 2 but none of known results of codimension 2 can be applied to. We further discuss the unfolding system of fully null degeneracy, displaying all its bifurcations and giving bifurcation curves analytically. Our results provide an intuitive basis for us to predict the genetic composition of a population and provide the basic mathematical theory for the protection and loss of alleles. [ABSTRACT FROM AUTHOR]

In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10−100 for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (Ae). Ae > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The Ae for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High Ae loci can also be useful in missing persons cases. Finally, high Ae microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher Ae microhaplotypes can outperform the standard CODIS markers. [ABSTRACT FROM AUTHOR]

In his 1972 paper ‘The apportionment of human diversity’, Lewontin showed that, when averaged over loci, genetic diversity is predominantly attributable to differences among individuals within populations. However, selection can alter the apportionment of diversity of specific genes or genomic regions. We examine genetic diversity at the human leucocyte antigen (HLA) loci, located within the major histocompatibility complex (MHC) region. HLA genes code for proteins that are critical to adaptive immunity and are well-documented targets of balancing selection. The single-nucleotide polymorphisms (SNPs) within HLA genes show strong signatures of balancing selection on large timescales and are broadly shared among populations, displaying low FST values. However, when we analyse haplotypes defined by these SNPs (which define ‘HLA alleles’), we find marked differences in frequencies between geographic regions. These differences are not reflected in the FST values because of the extreme polymorphism at HLA loci, illustrating challenges in interpreting FST. Differences in the frequency of HLA alleles among geographic regions are relevant to bone-marrow transplantation, which requires genetic identity at HLA loci between patient and donor. We discuss the case of Brazil's bone marrow registry, where a deficit of enrolled volunteers with African ancestry reduces the chance of finding donors for individuals with an MHC region of African ancestry. [ABSTRACT FROM AUTHOR]

Relatives tend to have more DNA in common than unrelated people. The closer the biological relationship, the higher the chance of alleles being identical by descent between the individuals. Therefore, when considering a mixed DNA profile, close relatives of the true contributor may not always be excluded as a possible contributor to a mixture due to allele sharing. In these situations, it might be more appropriate under the alternate proposition to consider that the DNA could have originated from a relative of the person of interest rather than an unrelated individual. The probabilistic genotyping software STRmix™ automatically provides LRs considering close biological relatives as alternate sources of the DNA. In this paper, we investigate the support for siblings of the true contributor to a mixture (who are not present in the mixture themselves). We interpret the mixtures and assign LRs using STRmix™ and investigate whether the resulting LRs could be used to indicate whether the true contributor could be a sibling of the POI. Most siblings will have one or more alleles that are not observed in the mixture profile. Support for siblings to have contributed can only occur when allelic dropout is a possibility at the loci where the siblings have alleles that are not observed in the profile. In these data, that was only observed in components with assigned template of 588 rfu or less. [ABSTRACT FROM AUTHOR]

In this paper, we describe 10 novel HLA alleles discovered, submitted and officially named in the calendar years 2022 through the end of 2023. [ABSTRACT FROM AUTHOR]

Varieties of spring bread wheat with the Ppd-D1a allele are insensitive to the photoperiod and are widespread in the world. The overwhelming majority of spring bread wheat cultivars in Russia are sensitive to the length of daylight. Incorporation of the Ppd-D1a allele in Russian cultivars of spring soft wheat will make it possible to accelerate breeding, using one to two additional vegetations per year. The aims of this paper are to (1) consider a trend of distribution of the Ppd-D1a allele among spring bread wheat of the Northern Hemisphere, (2) reveal an influence of the Ppd-D1a allele on agronomic traits of spring bread wheat, and (3) designate the main ways of breeding work for creation of Russian spring bread wheat with insensitivity to the photoperiod. The frequency of the Ppd-D1a allele increases from countries at high latitude to those at low latitude. The influence of the Ppd-D1a allele on agronomic traits depends on the geographic latitude where the experiment takes place and leads to a reduction of the period from seedling to heading, plant height, spikelets per spike, and protein content and to an increase in duration of green leaves after heading. The Ppd-D1a allele has a negative effect on wheat yield north of 50° N. The high frequency of the Ppd-D1a allele in Canadian spring bread wheat varieties indicates that this allele can become widespread in some regions of Russia. The negative effects caused by this allele can be compensated by reasonable selection of parents for hybridization. [ABSTRACT FROM AUTHOR]

Polymorphisms of the ACTN3 and ACE genes related to athletic performance are controversial due to those who favor differences between ethnicity and athletic status. However, although the above is the subject of debate through genetics, it is known that the potential benefits of the R + I allele fall on anaerobic performance and the carriers of the X + D allele on aerobic performance, biologically indicative that the genotype RX + DD + II is the key to the excellent performance of athletes with similar physical abilities and makes both power and endurance phenotypes important. The objective of this paper was to select and describe the studies that support the association of the genotype of the ACTN3 and ACE genes with the performance of individual sports athletes, considered elite for their high sports performance. 1,153 articles on the subject were reviewed and only 13 were included in the research. The results obtained indicate that athletes with the RR/RX + ID/DD genotype stand out in speed/power and those with the XX + II genotype in endurance. In conclusion, it is possible that there is a specific genetic structure associated with the polymorphisms of the ACTN3 and ACE genes that allow them to be predisposed to a high level of anaerobic and/or aerobic performance. [ABSTRACT FROM AUTHOR]

Over a century after the first description of a polymorphism controlled by a supergene, these genetic architectures still puzzle biologists. Supergenes are groups of tightly linked loci facilitating the co-segregation of combinations of alleles underlying alternative, complex adaptive strategies. The suppression of recombination at supergenes is generally caused by polymorphic chromosomal rearrangements, such as inversions. The existence of inversion polymorphisms and supergene raises theoretical and empirical questions. Why do these architectures evolve? How can alternative combinations of alleles be formed? How and why is polymorphism maintained? The purpose of this paper is to provide answers to these questions by reviewing recent advances in the study of Heliconius numata, an Amazonian butterfly displaying a striking diversity of wing color patterns. In a broad context, this review highlightsmechanisms that play an important role in the evolution of new genomic architecture and in the adaptation of species. [ABSTRACT FROM AUTHOR]

[Objective] The purpose of this paper was to explore the genetic diversity of the tea variety ’Zijuan’ and its mutagenesis progeny.[Method] The selected ’Zijuan’ and ’Zijuan’ mutated progeny were investigated from several aspects of botanical characters, biochemical components and EST-SSR markers. [Result] It was found that the color of buds and leaves of 15 materials were similar to that of ’Zijuan’,only two materials in the leaf shape of mature leaves that were the same as ’Zijuan’,which was lanceolate, and the others were elliptic or long elliptic. There were 9 materials with the same leaf color as ’Zijuan’,all of which are purple green, while 7 materials were yellow-green. Among the variation coefficients of biochemical components in spring and summer, the highest variation coefficient was anthocyanin, which reached 72.16% in spring and 77.86% in summer. The content of anthocyanin changed more in summer than in spring. A total of 165 alleles were detected by microsatellite markers, the average number of alleles was 7.5,the effective number of alleles was 2.562,Shannon information index was 0.997,polymorphic information content was 0.492,observed heterozygosity was 0.629,and expected heterozygosity was 0.565. [Conclusion] The above analysis results of traits, physiological and biochemical characteristics and microsatellite markers showed that the mutant progeny of ’Zijuan’ had a relatively rich genetic diversity. [ABSTRACT FROM AUTHOR]

HLA‐G allele frequencies were studied in Yucatán (Mexico) Maya Amerindians by a direct exon DNA sequencing technique. It is described that Mayas are probably one of the first populations together with Olmecs that populated Meso America and that important HLA genetic differences between Mexican and Guatemalan Mayas support that Maya languages were imposed to several neighbouring Amerindian groups. HLA‐G*01:01:02, HLA‐G*01:01:01 and HLA‐G*01:04:01 are the most frequent alleles in this population. It is remarkable that HLA‐G*01:05N allele was not found in the population in accordance with similar results found in another Amerindians. Also, protein allele HLA‐G*01:04 frequency is found not to differ to those found in another far or close living Amerindians in contrast to other World populations. It seems that while high HLA‐G*01:05N frequency is found in Iran and Middle East populations, probably where this allele appeared within an ancestral HLA‐A*19 group of alleles haplotype and it is maintained by unknown evolutionary forces, Amerindians do not have a high frequency because a founder effect or because required natural evolutionary forces do not exist in America. Finally, we believe useful to study HLA‐G evolution for its physiopathology understanding in addition to the many papers on statistics on HLA‐G and in vitro models that are yearly published. [ABSTRACT FROM AUTHOR]

Complex genetic diseases may be modulated by a large number of epistatic interactions affecting a polygenic phenotype. Identifying these interactions is difficult due to computational complexity, especially in the case of higher-order interactions where more than two genomic variants are involved. In this paper, we present BitEpi, a fast and accurate method to test all possible combinations of up to four bi-allelic variants (i.e. Single Nucleotide Variant or SNV for short). BitEpi introduces a novel bitwise algorithm that is 1.7 and 56 times faster for 3-SNV and 4-SNV search, than established software. The novel entropy statistic used in BitEpi is 44% more accurate to identify interactive SNVs, incorporating a p-value-based significance testing. We demonstrate BitEpi on real world data of 4900 samples and 87,000 SNPs. We also present EpiExplorer to visualize the potentially large number of individual and interacting SNVs in an interactive Cytoscape graph. EpiExplorer uses various visual elements to facilitate the discovery of true biological events in a complex polygenic environment. [ABSTRACT FROM AUTHOR]

Context: Hepatitis C Virus (HCV) infection is amajor cause of chronic cirrhosis and hepatocellular carcinoma. Approximately 30% of infected persons with HCV spontaneously clear the viral infection; but, some of the remaining patients develop chronic HCV. Studies showthatHLAmoleculesplay animportant role intheoutcomeof HCVinfectionby influencing the efficiencyof the antiviral immune response to HCV infection. It is now known that polymorphisms in HLA loci are associated with HCV susceptibility or clearance. The purpose of the present study was to systematically review the studies that reported the association of HLA class II alleles (HLA-DQ and HLA-DR) with the outcome of HCV infection. Evidence Acquisition: Studies were identified by searching electronic databases, including PubMed and Scopus. A total of 12,265 relevant studies were identified by the electronic search, of which a total of 19 eligible papers were identified that were meta- analyzed for the association between HLA class II alleles and the outcome of HCV infection. Results: Subjects carryingHLA-DQB1*0301,HLA-DQB1*0501,HLA-DRB1*1303,HLA-DRB1*1201,HLA-DRB1*0401,HLA-DRB1*0101, andHLA- DRB1*1101 alleles were significantly associated with higher spontaneous clearance of HCV infection. Conclusions: The data fromthe current study confirm that several polymorphisms in HLA-DQ and HLA-DR loci are correlated with the clearanceof HCVinfection. Identifyingthesepolymorphismsmay contribute toabetterunderstandingof immunemechanisms of HCV clearance or persistence. [ABSTRACT FROM AUTHOR]

Introduction: Numerous human migrations between Bosnia and Herzegovina and Serbia’s northern province of Vojvodina have led to the increased mixing of these population's genetic pool, leading to a reduction in genetic differences. The question is whether there are now genetic differences between the mentioned populations. Methods: Short Tandem Repeat (STR) loci D2S1338 and D18S51 were used in this paper to compare the diversity of alleles and genotypes between the populations of Vojvodina and one of the two Bosnia’s entities, the Republic of Srpska (RS). Three hundred ninety unrelated persons, 140 persons from the RS and 260 from Vojvodina, were analysed. The PowerPlex ESX16 System commercial kit was used for profiling persons from the territory of the RS and the AmpF/STR Identifiler commercial kit for persons from Vojvodina. The Mann-Whitney U-test was used for statistical analysis. Results: Data analysis concluded a significant deviation in the allele frequency of the D18S51 locus where p = 0.021. There was no statistically significant deviation in the D2S1338 locus allele frequency between these two populations. It was also found that there is a statistically significant deviation in the genotype frequencies of these two populations for the analysed genetic markers. Conclusion: This study confirms the existence of a significant deviation of allelic frequency for the D18S51 gene locus and a significant deviation of both gene markers frequency of genotypes. [ABSTRACT FROM AUTHOR]

In order to solve the problem that symbiotic organisms search algorithm converge slowly and easy to fall into the local optimum, combining quantum genetic algorithm theory, this paper proposed a real-coded quantum symbiotic organisms search algorithm( RQSOS). First, this paper presented the concept of the difference degree based on the principle of triangular fuzzy number, and constructed a variable component vector and a pair of probability amplitude of a allele in a chromosome that could carry more information and enhance the diversity of the solutions. Then it proposed the mode of rotary learning based on the Archimedes spiral, which strengthened the exploration ability of the solution space. Finally it updated the difference degree based on SOS, and carried out the population learning and mutation operations based on the value of the difference degree which could make the whole population evolution rapidly towards the optimal direction and reduced the probability of falling into local optimum. It was verified by numerical optimization and cloud task scheduling problem, and the simulation results show that the RQSOS algorithm can significantly improve the convergence speed and optimization ability, which is a feasible and effective algorithm. [ABSTRACT FROM AUTHOR]

Fifteen full-length wheat grain avenin-like protein coding genes (TaALP) were identified on chromosome arms 7AS, 4AL, and 7DS of bread wheat with each containing five genes. Besides the aand b-type ALPs, a c type was identified in the current paper. Both a and b types have two subunits, named x and y types. The five genes on each of the three chromosome arms consisted of two xtype genes, two y-type genes, and one c-type gene. The a-type genes were typically of 520 bp in length, whereas the b types were of 850 bp in length, and the c type was of 470 bp in length. The ALP gene transcript levels were significantly up-regulated in Blumeria graminis f. sp. tritici (Bgt)-infected wheat grain caryopsis at early grain filling. Wild emmer wheat [(WEW), Triticum dicoccoides] populations were focused on in our paper to identify allelic variations of ALP genes and to study the influence of natural selection on certain alleles. Consequently, 25 alleles were identified for TdALP-bx-7AS, 13 alleles were identified for TdALP-ax-7AS, 7 alleleswere identified for TdALP-ay-7AS, and 4 alleles were identified for TdALP-ax-4AL. Correlation studies on TdALP gene diversity and ecological stresses suggested that environmental factors contribute to the ALP polymorphism formation in WEW. Many allelic variants of ALPs in the endosperm of WEW are not present in bread wheat and therefore could be utilized in breeding bread wheat varieties for better quality and elite plant defense characteristics. [ABSTRACT FROM AUTHOR]

The domestic rabbit (Oryctolagus cuniculus) has a huge variability in terms of color patterns and fur color. One of the sources of variability is the A locus. The present paper aims at describing the color patterns that result from the recombination of alleles located at A locus. The color patterns of rabbit fur are determined by allelic and non-allelic interactions. Locus A is one that includes, in order of dominance, the alleles A, at and a. Recombining these alleles in different genomic contexts results in a large number of possible color patterns. [ABSTRACT FROM AUTHOR]

Three published papers in this journal have considered the proposition that, under a Wahlund effect caused by population mixture, a positive correlation is expected between single-locus values of FIS for a sample from the mixture and FST between the populations contributing to the mixture. Two of the papers assumed unbiased samples to estimate FST but did not consider possible effects of null alleles; the other paper focused on effects of nulls but used biased samples that also included Wahlund effects to estimate FST. The result is an information gap regarding scenarios that include null alleles but have unbiased estimates of FST. Simulations were used to fill this information gap, with the following results: 1) converting ~10% of alleles to nulls substantially reduced apparent heterozygosity and substantially increased FIS, with few exceptions; 2) adding null alleles also increased FST at most loci, although the effect was much more modest; 3) null alleles generally degraded correlations between FIS and FST, but the relationship remained relatively strong for FST ≥ 0.06; and 4) null alleles had only a small effect on correlations between r2, a measure of linkage disequilibrium between pairs of loci, and the product of FST values for those loci. These results argue for some caution in interpreting FIS × FST correlations under conditions where null alleles might be common and suggest that two-locus analyses might provide more robust assessments of Wahlund effects. [ABSTRACT FROM AUTHOR]

In this paper, we describe 15 novel HLA alleles discovered and officially named in the calendar years 2019 through the first half of 2021. [ABSTRACT FROM AUTHOR]

Genetic nurturing, the effect of parents' genotypes on offspring phenotypes through parental phenotypic transmission, can be modeled in terms of gene-culture interactions. This paper first uses a simple one-locus, two-phenotype gene-culture cotransmission model to compute the effect of genetic nurturing in terms of regression of children's phenotypes on transmitted and nontransmitted alleles. With genetic nurturing, interpreting heritability and hence the meaning of "missing heritability" becomes problematic. Other factors, for example, population subdivision and assortative mating, generate similar signals to those of genetic nurturing, namely, correlation between parents' nontransmitted alleles and children's phenotypes. Corrections must be made for these to isolate the signal of genetic nurturing. Finally, a unified causal framework is constructed for genetic nurturing, population subdivision, and assortative mating. Causal and noncausal paths from transmitted and nontransmitted alleles to children's phenotypes are identified and investigated in the presence of genetic nurturing, population subdivision, and assortative mating. Using causal analysis, assumptions made in inferring direct and indirect effects are then clarified and evaluated in a broader causal context. [ABSTRACT FROM AUTHOR]

Genomic selection has been successfully implemented in plant and animal breeding. The transition of parental selection based on phenotypic characteristics to genomic selection (GS) has reduced breeding time and cost while accelerating the rate of genetic progression. Although breeding methods have been adapted to include genomic selection, parental selection often involves truncation selection, selecting the individuals with the highest genomic estimated breeding values (GEBVs) in the hope that favorable properties will be passed to their offspring. This ensures genetic progression and delivers offspring with high genetic values. However, several favorable quantitative trait loci (QTL) alleles risk being eliminated from the breeding population during breeding. We show that this could reduce the mean genetic value that the breeding population could reach in the long term with up to 40%. In this paper, by means of a simulation study, we propose a new method for parental mating that is able to preserve the genetic variation in the breeding population, preventing premature convergence of the genetic values to a local optimum, thus maximizing the genetic values in the long term. We do not only prevent the fixation of several unfavorable QTL alleles, but also demonstrate that the genetic values can be increased by up to 15 percentage points compared with truncation selection. [ABSTRACT FROM AUTHOR]

Sex determination is one of the major developmental events in higher metazoans, where complex molecular mechanisms define two physiologically and behaviorally distinct organisms still genetically compatible. In honey bees, the sex determination cascade is initiated by the allelic composition of complementary sex determiner (csd) gene: males develop from hemi or homozygous embryos, whereas females develop from heterozygous embryos. In females, different alleles of csd lead to the formation of female-specific variants of feminizer (fem) and doublesex (dsx). In males, male-specific variants of fem and dsx are formed by default. In this paper, we investigated the genes of sex determination in the stingless bees Melipona quadrifasciata, Scaptotrigona postica, and Frieseomelitta varia. Our results revealed that the architecture of fem and dsx transcripts is highly conserved among the three stingless bee species, and also with honey bees. [ABSTRACT FROM AUTHOR]

[Objective] The present paper aimed to explore the endangered mechanism of natural resources and provide basis for the conservation of wild Fraxinus hupehensis. [Method] The genetic diversity of 196 individuals from 10 natural populations of Fraxinus hupehensis were analyzed by using cpSSR molecular markers, and the the UPGMA cluster of 10 populations was constructed. [Results] The 30 polymorphic hands were amplified from 6 primers. The genetic; diversity at populations level (Percentage of polymorphic loci; FPL = 25.75 % , Nei’s gene diversity index: h = 0.0974 ,Shannon’ s information index: I = 0.1440, the observed number of alleles: Na = 1.2575 , the effective number of alleles: Ne = 1.1712) was lower than that at the species level (PPL = 75.00 % h =0.1720 , I =0. 22732, Na = 1.7500,Ne = 1.2756). The Nm (gene flow) value and the coffieient of gene differentiation (Gst) was 0. 6942 and 0. 4189 Respectively, and the genetic; distance ranged from 0.0329 to 0. 1569. Based on the genetic identity (0.8548-0.9676) ,10 natural populations were divided into 4 groups. [Conclusion ]The total genetic* diversity of F. hupehensis was at a moderate level. The genetic variation mainly occurred within the populations (58. 11%), and the genetic differentiation among the populations was not obvious. Therefore, it is important to protect the populations with rich genetic diversity. [ABSTRACT FROM AUTHOR]

This manuscript is a continuation of this laboratory's journey to identifying novel HLA alleles while performing routine clinical HLA laboratory testing. Since our last paper, we have identified an additional 28 novel HLA alleles that are identified and described herein. One novel allele was found in two unrelated patients that were HLA typed for different reasons at two different times, suggesting that novel alleles may be much more frequent than previously expected. If the rate of identification is hindered by bioinformatics challenges, there is a great potential for our patients to suffer needlessly from incomplete information in either diagnostics or unrecognized incompatibilities with potential donors. [ABSTRACT FROM AUTHOR]

Classical stochastic demography predicts that environmental stochasticity reduces population growth rates and, thereby, can increase extinction risk. In contrast, in a 1978 Theoretical Population Biology paper, Gillespie demonstrated with his stochastic additive scale and concave fitness function (SAS-CFF) model that environmental stochasticity can promote genetic diversity. Extending the SAS-CFF to account for demography, I examine the simultaneous effects of environmental stochasticity on genetic diversity and population persistence. Explicit expressions for the per-capita growth rates of rare alleles and the population at low-density are derived. Consistent with Gillespie's analysis, if the log-fitness function is concave and allelic responses to the environment are not perfectly correlated, then per-capita growth rates of rare alleles are positive and genetic diversity is maintained in the sense of stochastic persistence i.e. allelic frequencies tend to stay away from zero almost-surely and in probability. Alternatively, if the log-fitness function is convex, then per-capita growth rates of rare alleles are negative and an allele asymptotically fixates with probability one. If the population's low-density, per-capita growth rate is positive, then the population persists in the sense of stochastic persistence, else it goes asymptotically extinct with probability one. In contrast to per-capita growth rates of rare alleles, the population's per-capita growth rate is a decreasing function of the concavity of the log-fitness function. Moreover, when the log-fitness function is concave, allelic diversity increases the population's per-capita growth rate while decreasing the per-capita growth rate of rare alleles; when the log-fitness function is convex, environmental stochasticity decreases the per-capita growth rate of rare alleles, but increases the population's per-capita growth rate. Collectively, these results (i) highlight how mechanisms promoting population persistence may be at odds with mechanisms promoting genetic diversity, and (ii) provide conditions under which population persistence relies on existing standing genetic variation. [ABSTRACT FROM AUTHOR]

Background: Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. Results: In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5 M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm. A single gene (Glyma.01 g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. Conclusion: These results suggest that the new region on chromosome 1 harbors a promising resistance QTL to SSR that can be used in soybean breeding program. [ABSTRACT FROM AUTHOR]