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Snake venoms are complex mixtures of toxic proteins that hold significant medical, pharmacological and evolutionary interest. To better understand the genetic diversity underlying snake venoms, we developed VenomCap, a novel exon‐capture probe set targeting toxin‐coding genes from a wide range of elapid snakes, with a particular focus on the ecologically diverse and medically important subfamily Hydrophiinae. We tested the capture success of VenomCap across 24 species, representing all major elapid lineages. We included snake phylogenomic probes in the VenomCap capture set, allowing us to compare capture performance between venom and phylogenomic loci and to infer elapid phylogenetic relationships. We demonstrated VenomCap's ability to recover exons from ~1500 target markers, representing a total of 24 known venom gene families, which includes the dominant gene families found in elapid venoms. We find that VenomCap's capture results are robust across all elapids sampled, and especially among hydrophiines, with respect to measures of target capture success (target loci matched, sensitivity, specificity and missing data). As a cost‐effective and efficient alternative to full genome sequencing, VenomCap can dramatically accelerate the sequencing and analysis of venom gene families. Overall, our tool offers a model for genomic studies on snake venom gene diversity and evolution that can be expanded for comprehensive comparisons across the other families of venomous snakes. [ABSTRACT FROM AUTHOR]

ABSTRACT Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype‐resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1‐specific and 2,702 Pda_hap2‐specific genes, and 1,118 allele‐specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non‐peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9‐bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1‐mediated anti‐aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid‐resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars. [ABSTRACT FROM AUTHOR]

In plants, recognition between resistance gene (R) and virus induces a local hypersensitive response (HR), which is accompanied by systemic acquired resistance (SAR). The dominant resistance gene N in tobacco confers resistance to tobacco mosaic virus (TMV) at both locally inoculated tissues and systemically infected tissues. However, the mechanisms underlying HR- and SAR-mediated viral inhibition are not fully revealed. In this study, we find that Nicotiana glutinosa RNA-binding protein (NgRBP) is an RNA silencing suppressor which enhances TMV-triggered HR. Stronger HR could result in stronger local and systemic RNA silencing as well as SAR. Enhanced RNA silencing in the systemically infected leaves induced by the NgRBP gene is compromised by transient expression of NahG. These results indicate that RNA silencing is activated by HR and plays a crucial role in local and systemic virus resistance. Our results reveal a crosstalk between N gene-mediated virus resistance and RNA silencing which would deepen our understanding of the established HR and SAR models. [ABSTRACT FROM AUTHOR]

ABSTRACT Dwarfing genes that are considerably reducing plant height are used in many cereals. In triticale, the rye‐derived dominant dwarfing gene Ddw1 was introgressed in commercial varieties. It has already been shown that this gene increases Fusarium head blight (FHB) susceptibility in one segregating population. We aimed for verifying this effect in the genetically unrelated doubled haploid (DH) population Cando (Ddw1) × Tritikon (ddw1), with 182 progenies in an experiment with artificial inoculation across six location–year combinations (environments). Linkage mapping was performed with DArTseq markers. The progenies significantly (p < 0.001) varied for FHB severity, plant height and heading stage with high entry‐mean heritabilities (0.85–0.98). The population showed a bimodal distribution for plant height. A significant QTL on chromosome 5RL was found for all three traits explaining 38%, 62% and 43% of the genotypic variation for FHB severity, plant height and heading stage, respectively, and most likely representing Ddw1. This gene increased FHB severity by 5.6 percentage points, delayed heading by 2.7 EC stages and reduced plant height by 29.6 cm on average. To use this gene in practical triticale breeding, the genetic background must be enriched with FHB resistance QTL to counterbalance the negative effect of Ddw1 either by introgression of major FHB QTL from exotic sources or by genomic selection within the adapted gene pool. [ABSTRACT FROM AUTHOR]

Background: The additive model of inheritance assumes that heterozygotes (Aa) are exactly intermediate in respect to homozygotes (AA and aa). While this model is commonly used in single-locus genetic association studies, significant deviations from additivity are well-documented and contribute to phenotypic variance across many traits and systems. This assumption can introduce type I and type II errors by overestimating or underestimating the effects of variants that deviate from additivity. Alternative genotype encoding strategies have been explored to account for different inheritance patterns, but they often incur significant computational or methodological costs. To address these challenges, we introduce PAGER (Phenotype Adjusted Genotype Encoding and Ranking), an efficient pre-processing method that encodes each genetic variant based on normalized mean phenotypic differences between diallelic genotype classes (AA, Aa, and aa). This approach more accurately reflects each variant's true inheritance model, improving model precision while minimizing the costs associated with alternative encoding strategies. Results: Through extensive benchmarking on SNPs simulated with both binary and continuous phenotypes, we demonstrate that PAGER accurately represents various inheritance patterns (including additive, dominant, recessive, and heterosis), achieves levels of statistical power that meet or exceed other encoding strategies, and attains computation speeds up to 55 times faster than a similar method, EDGE. We also apply PAGER to publicly available real-world data and identify a novel, relevant putative QTL associated with body mass index in rats (Rattus norvegicus) that is not detected with the additive model. Conclusions: Overall, we show that PAGER is an efficient genotype encoding approach that can uncover sources of missing heritability and reveal novel insights in the study of complex traits while incurring minimal costs. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant swine viral infectious diseases worldwide. Vaccination is a key strategy for the control and prevention of PRRS. At present, the NADC30-like PRRSV strain has become the predominant epidemic strain in China, superseding the HP-PRRSV strain. The existing commercial vaccines offer substantial protection against HP-PRRSV, but their efficacy against NADC30-like PRRSV is limited. The development of a novel vaccine that can provide valuable cross-protection against both NADC30-like PRRSV and HP-PRRSV is highly important. In this study, an infectious clone of a commercial MLV vaccine strain, GD (HP-PRRSV), was first generated (named rGD). A recombinant chimeric PRRSV strain, rGD-SX-5U2, was subsequently constructed by using rGD as a backbone and embedding several dominant immune genes, including the NSP2, ORF5, ORF6, and ORF7 genes, from an NADC30-like PRRSV isolate. In vitro experiments demonstrated that chimeric PRRSV rGD-SX-5U2 exhibited high tropism for MARC-145 cells, which is of paramount importance in the production of PRRSV vaccines. Moreover, subsequent in vivo inoculation and challenge experiments demonstrated that rGD-SX-5U2 confers cross-protection against both HP-PRRSV and NADC30-like PRRSV, including an improvement in ADG levels and a reduction in viremia and lung tissue lesions. In conclusion, our research demonstrated that the chimeric PRRSV strain rGD-SX-5U2 is a novel approach that can provide broad-spectrum protection against both HP-PRRSV and NADC30-like PRRSV. This may be a significant improvement over previous MLV vaccinations. [ABSTRACT FROM AUTHOR]

The genotype of patients with viral hepatitis B in Salah al-Din Governorate was determined through the use of Real Time PCR technology. Real Time PCR technology is the most precise method for detecting DNA and determining the genotyping of infected individuals· The study demonstrated a significant discrepancy in the genotyping of patients and that the genotype distribution in the governorate was as follows: The total number of patients in the Governorate was divided as follows: genotype A accounted for 69.0%, genotype B for 38.0%, genotype C for 35.0%, and genotype D for 61.0%. Mix genotypes were also observed in the patients, indicating that an individual possessed more than one genotype. In 6% of cases, the combination of all four genotypes (A+B+C+D) was identified, while in 10% of cases, the three-genotype combinations A+B+C, A+B+D, and A+C+D were identified. In terms of the frequency of two-genotype combinations, A+B was present in 10%, A+D in 19% (the highest among all combinations), A+C in 3%, B+C in 4%, B+D in 2%, and C+D in 3%. [ABSTRACT FROM AUTHOR]

The pathogen Plasmopara halstedii, causing downy mildew (DM), is a widespread sunflower disease which can be controlled by single dominant genes. Wild Helianthus annuus have been a valuable source of vertical resistance to control P. halstedii, but such resistance may eventually be overcome by new races of the pathogen. Alternatively, quantitative, or partial resistance, is more stable and may be combined with vertical resistance to prevent DM outbreaks. We assessed the responses of six populations of wild H. annuus naturalized in Argentina to race 710 of P. halstedii. We examined: 1) the aerial phenotype (including seedling death) using two damage scales and three disease indices, 2) the growth of the pathogen along the hypocotyls, and 3) the presence of the pathogen in the root system. We found that the evaluated sunflower wild populations had lower disease levels than the susceptible cultivated controls. A histologic analysis showed that the wild H. annuus seedlings showed cellular reactions (e.g. necrosis and the deposit of materials on the walls of invaded cells) to restrict the pathogen's growth, allowing the identification of two possible types of resistance: type I, when the growth of the pathogen was limited to the base of the hypocotyls, and type II, when the pathogen managed to invade the entire length of the hypocotyls. The wild sunflower populations also showed differential responses to root infections. A quantitative or partial genetic resistance, rather than resistance based on major genes, seems to be operating in the sampled populations. The individuals found to be resistant in each population represent promising germplasm for sunflower breeding. [ABSTRACT FROM AUTHOR]

Clubroot, a significant soil-borne disease, severely impacts the productivity of cruciferous crops. The identification and development of clubroot resistance (CR) genes are crucial for mitigating this disease. This study investigated the genetic inheritance of clubroot resistance within an F2 progeny derived from the cross of a resistant parent, designated "377", and a susceptible parent, designated "12A". Notably, "377" exhibited robust resistance to the "KEL-23" strain of Plasmodiophora brassicae, the causative agent of clubroot. Genetic analyses suggested that the observed resistance is controlled by a single dominant gene. Through Bulked Segregant Analysis sequencing (BSA-seq) and preliminary gene mapping, we localized the CR gene locus, designated as BraPb8.3, to a 1.30 Mb genomic segment on chromosome A08, flanked by the markers "333" and "sau332-1". Further fine mapping precisely narrowed down the position of BraPb8.3 to a 173.8 kb region between the markers "srt8-65" and "srt8-25", where we identified 22 genes, including Bra020861 with a TIR-NBS-LRR domain and Bra020876 with an LRR domain. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses confirmed that both Bra020861 and Bra020876 exhibit increased expression levels in the resistant parent "377" following inoculation with P. brassicae, thereby underscoring their potential as key genes implicated in BraPb8.3-mediated clubroot resistance. This study not only identifies molecular markers associated with BraPb8.3 but also enriches the genetic resources available for breeding programs aimed at enhancing resistance to clubroot. [ABSTRACT FROM AUTHOR]

SUMMARY The external appearance of fruit commodities is an essential trait that has profound effects on consumer preferences. A natural melon variety, characterized by an uneven and patchy arrangement of dark green streaks and spots on the white‐skinned rind, resembles shooting stars streaking across the sky; thus, this variety is called “Shooting Star” (SS). To investigate the mechanism underlying the SS melon rind pattern, we initially discovered that the variegated dark green color results from chlorophyll accumulation on the white skin. We then constructed a segregation population by crossing a SS inbred line with a white rind (WR) inbred line and used bulk segregant analysis (BSA) revealed that the SS phenotype is controlled by a single dominant gene, CmAPRR2, which has been previously confirmed to determine dark green coloration. Further genomic analysis revealed a hAT‐like transposable element (TE) inserted in CmAPRR2. This TE in CmAPRR2 is recurrently excised from rind tissues, activating the expression of CmAPRR2. This activation promotes the accumulation of chlorophyll, leading to the variegated dark green color on the rind, and ultimately resulting in the SS rind phenotype. Therefore, we propose that the SS phenotype results from the recurrent excision of the hAT‐like TE in CmAPRR2. [ABSTRACT FROM AUTHOR]

PURPOSE: To evaluate the relative diagnostic yield of clinical germline genomic tests in a diverse pediatric cancer population. PATIENTS AND METHODS: The KidsCanSeq study enrolled pediatric cancer patients across six sites in Texas. Germline analysis included both exome sequencing and a therapy-focused pediatric cancer gene panel. The results were categorized by participants demographics, the presence of pathogenic or likely pathogenic (P/LP) variants, and variants of uncertain significance (VUS) in cancer predisposition genes (CPGs). Pediatric actionable CPGs were defined as those with cancer surveillance recommendations during childhood. RESULTS: Cancer P/LP variants were reported by at least one platform in 103 of 578 (17.8%) participants of which 76 were dominant cancer genes (13.1%) with no significant differences by self-described race or Hispanic ethnicity. However, the proportion of participants with VUS was greater in Asian and African American participants (P =.0029). Diagnostic yield was 16.6% for exome versus 8.5% for panel (P <.0001) with 42 participants with concordant germline results. Exome-only results included P/LP variants in 30 different CPGs in 54 participants, whereas panel-only results included seven participants with a copy number or structural P/LP variants in CPGs. There was no significant difference in diagnostic yield limited to pediatric actionable CPGs (P =.6171). CONCLUSION: Approximately 18% of a diverse pediatric cancer population had germline diagnostic findings with 50% of P/LP variants reported by only one platform because of CPGs not on the targeted panel and copy number variants (CNVs)/rearrangements not reported by exome. Although diagnostic yields were similar in this diverse population, increases in VUS results were observed in Asian and African American populations. Given the clinical significance of CNVs/rearrangements in this cohort, detection is critical to optimize germline analysis of pediatric cancer populations. Germline analysis with comprehensive gene list and CNV detection is critical in pediatric oncology. [ABSTRACT FROM AUTHOR]

An experiment was carried out to evaluate the level of heterosis and combining ability in cotton. Thirty five interspecific hybrids were generated by crossing five lines viz., GMS 14, GMS 17, GMS 19, GMS 21 and GMS 27 with seven testers namely CCB26, CCB51, DB1901, CCB2, CCB6, CO18 and Suvin in line x tester mating fashion. Twelve parents along with 35 hybrids and a standard check (DCH 32) were raised in a randomized block design with two replications to evaluate the combining ability and heterosis to identify good combiners and the best hybrids with high yield and fibre quality. The lines viz., GMS 14 and GMS 17 and the testers viz., CO 18 and Suvin were found to record significant gca effects for yield and fibre quality traits. Out of the 35 hybrids, GMS 14 x CO18, GMS 27 x Suvin and GMS 17 x CO18 recorded highly positive significant sca effects for most of the traits. The ratio between additive and dominant genetic variance was less than one for all the traits, indicating the preponderance of dominant gene action or non-additive gene action. The above three crosses also exhibited high heterosis over mid parent, better parent and standard check. Hence, these hybrids could be harnessed after analyzing their performance in yield trials. [ABSTRACT FROM AUTHOR]

The present investigation was undertaken in brinjal (Solanum melongena L.) to estimate combining ability and gene action following a half diallel mating design using ten parents. The ratio of genetic variance components, σ² gca/σ² sca and σ² D/σ² A, showed dominant gene action, indicating the presence of non-additive genetic variance for days to 50% flowering, fruit yield per plant, total phenol, antioxidant activity and total soluble sugar. The traits fruits per plant, fruit girth, and fruit weight showed additive genetic variance. Among the parental genotypes, AB 15-08, ABSR 2 and AB 20- 13 were found to be good general combiners for fruit yield, fruits per plant, and total soluble solids. The three highestranking hybrids were AB 15-08 × AB 20-13, AB 15-08 × AB 20-03 and AB 20-07 × GP BRJ 224. The above hybrids would be rewarding for harnessing heterosis. [ABSTRACT FROM AUTHOR]

Breeders need to mine the underlying genes of target traits for their improvement before the inception of the breeding program. We conducted this research to decipher the number of genes along with their interactions and linkage for seed color, flower color, and anther color, and to show the reflection of genetic divergence on phenotypic variations in segregating populations by crossing diverse flax (Linum usitatissimum L.) genotypes. Seed color showed maternal effect and appeared to be controlled by two and three independent genes having dominant, duplicate, and dominant epistatic interactions varying according to cross combinations. The flower and anther color were controlled by one and two independent genes showing dominant and duplicate interactions. We observed a strong genetic linkage among seed, flower, and anther color genes. We also found that the incorporation of diverse parents in crossing resulted in more phenotypic variation, which included new phenotypic classes other than parents in the segregating population for seed color. This research will facilitate indirect selection and help in developing markers for marker‐assisted selection in flax breeding program. Core Ideas: This research examined the number of genes controlling seed color, flower color, and anther color in oilseed flax, as well as their genetic interactions.To reach conclusions, 16 crosses were made among different parents.This research will facilitate indirect selection and help in developing markers for marker‐assisted selection in flax breeding program. [ABSTRACT FROM AUTHOR]

Epidermolysis bullosa (EB) is a clinically and genetically heterogeneous group of mechanobullous diseases characterized by non-scarring blisters and erosions on the skin and mucous membranes upon mechanical trauma. The simplex form (EBS) is characterized by recurrent blister formation within the basal layer of the epidermis. It most often results from dominant mutations in the genes coding for keratin (K) 5 or 14 proteins (KRT5 and KRT14). A disruptive mutation in KRT5 or KRT14 will not only structurally impair the cytoskeleton, but it will also activate a cascade of biochemical mechanisms contributing to EBS. Skin lesions are painful and disfiguring and have a significant impact on life quality. Several gene expression studies were accomplished on mouse model and human keratinocytes to define the gene expression signature of EBS. Several key genes associated with EBS were identified as specific immunological mediators, keratins, and cell junction components. These data deepened the understanding of the EBS pathophysiology and revealed important functional biological processes, particularly inflammation. This review emphasizes the three EBS subtypes caused by dominant mutations on either KRT5 or KRT14 (localized, intermediate, and severe). It aims to summarize current knowledge about the EBS expression profiling pattern and predicted molecular mechanisms involved and to outline progress in therapy. [ABSTRACT FROM AUTHOR]

Key message: A new stripe rust resistance gene YrBDT in Chinese landrace wheat Baidatou was mapped to a 943.6-kb interval on chromosome arm 6DS and co-segregated with a marker CAPS3 developed from candidate gene TraesCS6D03G0027300. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating foliar disease of wheat. Chinese landrace wheat Baidatou has shown high resistance to a broad spectrum of Pst races at both the seedling and adult-plant stages for decades in the Longnan region of Gansu province, a hot spot for stripe rust epidemics. Here, we report fine mapping and candidate gene analysis of stripe rust resistance gene YrBDT in Baidatou. Analysis of F1, F2 plants and F2:3 lines indicated that resistance in Baidatou to Pst race CYR31 was conferred by a single dominant gene, temporarily designated YrBDT. Bulked segregant exome capture sequencing (BSE-seq) analysis revealed 61 high-confidence polymorphic SNPs concentrated in a 5.4-Mb interval at the distal of chromosome arm 6DS. Several SNPs and InDels were also identified by genome mining of DNA sampled from the parents and contrasting bulks. The YrBDT locus was mapped to a 943.6-kb (4,658,322–5,601,880 bp) genomic region spanned by markers STS2 and STS3 based on IWGSC RefSeq v2.1, including five putative disease resistance genes. There was high collinearity of the target interval among Chinese Spring RefSeq v2.1, Ae. tauschii AL8/78 and Fielder genomes. The expression level of TraesCS6D03G0027300 showed significant association with Pst infection, and a gene-specific marker CAPS3 developed from TraesCS6D03G0027300 co-segregated with YrBDT suggesting this gene as a candidate of YrBDT. The resistance gene and flanking markers can be used in marker-assisted selection for improvement of stripe rust resistance. [ABSTRACT FROM AUTHOR]

Leaf rust (caused by Puccinia triticina Erikss., Pt) is a severe foliar disease of cultivated wheat worldwide. Severe development of the disease results in significant losses in seed yield and quality. Growing immune varieties is the most rational method for Pt control in terms of effectiveness and ecological safety. However, the gene pool of cultivated wheat is very narrow for seedling Pt effective resistance genes, which hampers breeding for this trait. One of the well-known methods to broaden genetic diversity for resistance is the introgression of highly effective genes from wild relatives into the genomes of cultivated wheat. The Aegilops L. species have been proven to be perfectly suited for this purpose. No gene for Pt resistance has been transferred to wheat from Aegilops biuncialis Vis. (Lorent's goatgrass) up to now. Previously, we selected eight accessions of the species from the VIR (N.I. Vavilov All-Russian Institute of Plant Genetic Resources) genebank that showed a perfect level of resistance to leaf rust. In this research, we studied the genetic control of resistance using hybridological, phytopathological, and molecular analyses. According to the F1–F3 hybrid evaluation results, each accession possesses one dominant gene for Pt resistance, and genes in different accessions are allelic or very tightly linked. Phytopathological test clone analysis showed that this gene is not identical to Lr9, Lr19, Lr24, Lr39, and Lr47, which are effective against Pt populations in some areas of Russia. This conclusion was partially supported by the results of the identification of DNA markers specific to these genes in bread wheat. Thus, we identified one dominant gene (temporarily symbolized as LrBi1) for effective seedling Pt resistance; it is recommended for introgression to cultivated wheat via interspecific hybridization. [ABSTRACT FROM AUTHOR]

Stripe rust and powdery mildew are serious diseases that severely decrease the yield of wheat. Planting wheat cultivars with powdery mildew and stripe rust resistance genes is the most effective way to control these two diseases. Introducing disease resistance genes from related species into the wheat genome via chromosome translocation is an important way to improve wheat disease resistance. In this study, nine novel T 1 RS. 1 AL translocation lines were developed from the cross of wheat cultivar Chuannong25 (CN25) and a Chinese rye Qinling. The results of non-denaturing fluorescence in situ hybridization and PCR showed that all new lines were homozygous for the TIRS. 1 AL translocation. These new 1 RS .l AL translocation l ines exhibited strong resistance to stri pe ru st and powdery mildew. The cytogenetics results indicatedthat the resistance of the new lines was conferred by the 1RS chromosome arms, which came from Qinling rye. The genetic analysis indicated that there were new dominant resistance genes on the 1 RS chromosome arm resistant to stripe rust and powdery mildew, and their resistance patterns were different from those of y, 9, Pm8, and Pm 17 genes. In addition, the T iRS. 1 AL translocation lines generally exhibited better agronomic traits in the field relative to CN25. These T 1 RS.1 AL translocations have great potential in wheat-breeding programs in the future. [ABSTRACT FROM AUTHOR]

The article evaluated the genetics of six cucumbers (Cucumis sativus L.) cultivars and 30 hybrids based on morpho-yield traits. The dominant and epistatic gene effects managed the fruit weight in three cucumber hybrids (C-25/1, A-6, and A-9), while additive gene effects in three other hybrids were supreme. For productivity per plant, dominant genes with epistatic effects controlled these in three accessions, while additive effects played a special role in manifesting the trait in three other hybrid (C-25/1, A-6, and A-9) genes. Likewise, dominant genes with epistatic effects controlled the yield per plant trait in three accessions, while additive effects influenced the attribute in three other hybrids (C-25/1, A-6, and A-9). According to these traits, the promising hybrids were С-25/1 х С25/2, С-26 х С-25/2, С-26 х С25/1, А-9 х С-26, and А-6 х С-25/1. The cucumber F1 hybrids C-26 x C29, A-9 x A-6, and A-9 x C-25/2 showed characteristics of large fruits weighing 108.2 to 113.1 g. In the accessions, C-25/1, A-6, and A-9, the additive gene effects dominated the studied trait (σ2ĝi > σ2si). The superior-in-yield hybrid combinations were C-26 x C-29, A-9 x A-6, and A-6 x A-9, with a total fruit yield of 691 to 769 g per plant. [ABSTRACT FROM AUTHOR]

Evaluating the fitness of hybrids can provide important insights into genetic differences between species or diverging populations. We focused on surface- and cave-ecotypes of the widespread Atlantic molly Poecilia mexicana and raised F1 hybrids of reciprocal crosses to sexual maturity in a common-garden experiment. Hybrids were reared in a fully factorial 2 × 2 design consisting of lighting (light vs. darkness) and resource availability (high vs. low food). We quantified survival, ability to realize their full reproductive potential (i.e. completed maturation for males and 3 consecutive births for females) and essential life-history traits. Compared to the performance of pure cave and surface fish from a previous experiment, F1s had the highest death rate and the lowest proportion of fish that reached their full reproductive potential. We also uncovered an intriguing pattern of sex-specific phenotype expression, because male hybrids expressed cave molly life histories, while female hybrids expressed surface molly life histories. Our results provide evidence for strong selection against hybrids in the cave molly system, but also suggest a complex pattern of sex-specific (opposing) dominance, with certain surface molly genes being dominant in female hybrids and certain cave molly genes being dominant in male hybrids. [ABSTRACT FROM AUTHOR]

Dominance refers to the effect of a heterozygous genotype relative to that of the two homozygous genotypes. The degree of dominance of mutations for fitness can have a profound impact on how deleterious and beneficial mutations change in frequency over time as well as on the patterns of linked neutral genetic variation surrounding such selected alleles. Since dominance is such a fundamental concept, it has received immense attention throughout the history of population genetics. Early work from Fisher, Wright, and Haldane focused on understanding the conceptual basis for why dominance exists. More recent work has attempted to test these theories and conceptual models by estimating dominance effects of mutations. However, estimating dominance coefficients has been notoriously challenging and has only been done in a few species in a limited number of studies. In this review, we first describe some of the early theoretical and conceptual models for understanding the mechanisms for the existence of dominance. Second, we discuss several approaches used to estimate dominance coefficients and summarize estimates of dominance coefficients. We note trends that have been observed across species, types of mutations, and functional categories of genes. By comparing estimates of dominance coefficients for different types of genes, we test several hypotheses for the existence of dominance. Lastly, we discuss how dominance influences the dynamics of beneficial and deleterious mutations in populations and how the degree of dominance of deleterious mutations influences the impact of inbreeding on fitness. [ABSTRACT FROM AUTHOR]

Although cowpea mild mottle virus (CPMMV) has been reported in Brazil since 1983, it has only become a significant concern for researchers and farmers in recent years. The objective of this work was to investigate the genetic basis of CPMMV tolerance, mapping and reporting the first loci associated with this trait in common bean (cv. BRS Sublime). Phenotypic assays were carried out on 180 individual plants (F2 generation) and 180 F2:3 progenies comprising 12 plants per family and their parents (BRS Sublime, tolerant parent × CNFCT 16207, susceptible parent). CPMMV was mechanically inoculated and symptoms were evaluated at 35 days after inoculation, using a 1–5 scoring scale. A linkage map was constructed using 1695 single‐nucleotide polymorphism (SNP) and SilicoDArT markers that segregated in the F2 and F2:3 generations as expected. Markers were distributed across 11 common bean chromosomes, resulting in a total length of 2864 cM, with an average distance between markers of 1.8 cM. Phenotypic observations revealed that tolerance in cv. BRS Sublime is controlled by a single dominant gene. The main effect quantitative trait locus (QTL; CPMMV.Pv08) associated with CPMMV tolerance was identified in the terminal region on chromosome 8 (Pv08). This QTL explained approximately 77% of phenotypic variation, indicating that the inheritance of tolerance to CPMMV is monogenic, controlled by a major locus. As far as we know, this study represents the first investigation into the inheritance and genetic mapping of CPMMV tolerance in common bean, with potential for the development of elite lines with multiple virus resistance/tolerance. [ABSTRACT FROM AUTHOR]

Background: Transforming coniferous plantation into broadleaved or mixed broadleaved-coniferous plantations is the tendency of forest management strategies in subtropical China. However, the effects of this conversion on soil phosphorus (P) cycling microbial functional genes are still unknown. Methods: Soil samples were collected from 0-20, 20-40, and 40-60 cm (topsoil, middle layer, and subsoil, respectively) under coniferous Pinus massoniana (PM), broadleaved Erythrophleum fordii (EF), and their mixed (PM/EF) plantation in subtropical China. Used metagenomic sequencing to examine the alterations of relative abundances and molecular ecological network structure of soil P-cycling functional genes after the conversion of plantations. Results: The composition of P-cycling genes in the topsoil of PM stand was significantly different from that of PM/EF and EF stands (p < 0.05), and total phosphorus (TP) was the main factor causing this difference. After transforming PM plantation into EF plantation, the relative abundances of P solubilization and mineralization genes significantly increased in the topsoil and middle layer with the decrease of soil TP content. The abundances of P-starvation response regulation genes also significantly increased in the subsoil (p < 0.05), which may have been influenced by soil organic carbon (SOC). The dominant genes in all soil layers under three plantations were phoR, glpP, gcd, ppk, and ppx. Transforming PM into EF plantation apparently increased gcd abundance in the topsoil (p < 0.05), with TP and NO3--N being the main influencing factors. After transforming PM into PM/EF plantations, the molecular ecological network structure of P-cycling genes was more complex; moreover, the key genes in the network were modified with the transformation of PM plantation. Conclusion: Transforming PM into EF plantation mainly improved the phosphate solubilizing potential of microorganisms at topsoil, while transforming PM into PM/EF plantation may have enhanced structural stability of microbial P-cycling genes react to environmental changes. [ABSTRACT FROM AUTHOR]

Background: Bacterial spot of pepper (BSP), caused by four different Xanthomonas species, primarily X. euvesicatoria (Xe), poses a significant challenge in pepper cultivation. Host resistance is considered the most important approach for BSP control, offering long-term protection and sustainability. While breeding for resistance to BSP for many years focused on dominant R genes, introgression of recessive resistance has been a more recent focus of breeding programs. The molecular interactions underlying recessive resistance remain poorly understood. Results: In this study, transcriptomic analyses were performed to elucidate defense responses triggered by Xe race P6 infection by two distinct pepper lines: the Xe-resistant line ECW50R containing bs5, a recessive resistance gene that confers resistance to all pepper Xe races, and the Xe-susceptible line ECW. The results revealed a total of 3357 upregulated and 4091 downregulated genes at 0, 1, 2, and 4 days post-inoculation (dpi), with the highest number of differentially expressed genes (DEGs) observed at 2 dpi. Pathway analysis highlighted DEGs in key pathways such as plant-pathogen interaction, MAPK signaling pathway, plant hormone signal transduction, and photosynthesis – antenna proteins, along with cysteine and methionine metabolism. Notably, upregulation of genes associated with PAMP-Triggered Immunity (PTI) was observed, including components like FLS2, Ca-dependent pathways, Rboh, and reactive oxygen species (ROS) generation. In support of these results, infiltration of ECW50R leaves with bacterial suspension of Xe led to observable hydrogen peroxide accumulation without a rapid increase in electrolyte leakage, suggestive of the absence of Effector-Triggered Immunity (ETI). Furthermore, the study confirmed that bs5 does not disrupt the effector delivery system, as evidenced by incompatible interactions between avirulence genes and their corresponding dominant resistant genes in the bs5 background. Conclusion: Overall, these findings provide insights into the molecular mechanisms underlying bs5-mediated resistance in pepper against Xe and suggest a robust defense mechanism in ECW50R, primarily mediated through PTI. Given that bs5 provides early strong response for resistance, combining this resistance with other dominant resistance genes will enhance the durability of resistance to BSP. [ABSTRACT FROM AUTHOR]

Tomato spotted wilt orthotospovirus (TSWV) causes substantial economic loss to tomato production, and the Sw-5b resistance gene is widely deployed for management. Here, we show (i) the emergence of resistance-breaking (RB) TSWV strains in processing and fresh market tomato production in California over the past ten years, and (ii) evolutionary relationships with RB strains from other areas. A specific RT-PCR test was used to show the C118Y RB strain that emerged in Fresno County in 2016 quickly became predominant in the central production area and remained so through this study. In 2021, the C118Y strain was detected in the Northern production area, and was predominant in 2022. However, in 2023, the C118Y strain was unexpectedly detected in fewer spotted wilt samples from resistant varieties. This was due to emergence of the T120N RB strain, previously known to occur in Spain. A specific RT-PCR test was developed and used to show that the T120N RB strain was predominant in Colusa and Sutter counties (detected in 75–80% of samples), and detected in ~50% of samples from Yolo County. Pathogenicity tests confirmed California isolates of the T120N strain infected Sw-5b tomato varieties and induced severe symptoms. Another RB strain, C118F, was associated with spotted wilt samples of Sw-5 varieties from fresh market tomato production in southern California. Phylogenetic analyses with complete NSm sequences revealed that the C118Y and T120N RB strains infecting resistant processing tomato in California emerged locally, whereas those from fresh market production were more closely related to isolates from Mexico. Thus, widespread deployment of this single dominant resistance gene in California has driven the local emergence of multiple RB strains in different tomato production areas and types. These results further emphasize the need for ongoing monitoring for RB strains, and identification of sources of resistance to these strains. [ABSTRACT FROM AUTHOR]

Maize (Zea mays L.) C-type cytoplasmic male sterility (CMS-C) is a highly used CMS system for maize commercial hybrid seed production. Rf4 is the major dominant restorer gene for CMS-C. Inbreds were recently discovered which contain the restoring Rf4 allele yet are unable to restore fertility due to the lack of an additional gene required for Rf4's restoration. To find this additional gene, QTL mapping and positional cloning were performed using an inbred that contained Rf4 but was incapable of restoring CMS-C. The QTL was mapped to a 738-kb interval on chromosome 2, which contains a Pentatricopeptide Repeat (PPR) gene cluster. Allele content comparisons of the inbreds identified three potential candidate genes responsible for fertility restoration in CMS-C. Complementation via transformation of these three candidate genes showed that PPR153 (Zm00001eb114660) is required for Rf4 to restore fertility to tassels. The PPR153 sequence is present in B73 genome, but it is not capable of restoring CMS-C without Rf4. Analysis using NAM lines revealed that Rf4 requires the presence of PPR153 to restore CMS-C in diverse germplasms. This research uncovers a major CMS-C genetic restoration pathway and can be used for identifying inbreds suitable for maize hybrid production with CMS-C cytoplasm. [ABSTRACT FROM AUTHOR]

The aim of the study was to assess the genetic structure and quantitative heritability of cotton yield, yield components and fiber quality parameters under well-watered (100%) and deficit (50%) irrigation conditions using a complete full diallel cross method with six cotton genotypes. The F1 and F2 generations were obtained to study the effect of irrigation conditions on genotypic variation and maternal effects on the traits studied. Parental, F1 and F2 generations were growed under full and deficit irrigation conditions and selected agronomic and fiber quality traits were measured. The data were analysed using various methods, including Griffing Method I, Model I analysis of variance, full diallel table analysis of variance, Jinks-Hayman diallel hybrid analysis. The Jinks-Hayman analysis of variance showed that dominant effects were more important in the inheritance of all traits, as indicated by the negative value of the difference between the additive variance and the dominance variance (D-H1). In addition, the average degree of dominance (H1/D)1/2 was greater than 1, indicating the predominance of dominant gene action in inheritance. The study concluded that starting selection in the F5–F6 generation is appropriate for drought resistant cotton breeding studies. It also emphasised the importance of conducting drought resistant cotton breeding under drought conditions due to the differences in gene movement between well-watered irrigation and drought stress conditions. The study highlighted the importance of population selection, environmental factors, data collection and analysis interpretation in breeding studies. It suggested that the Griffing diallel analysis method is suitable for hybrid breeding studies, while the Jinks-Hayman type analysis method is suitable for studying the genetic structures of populations. [ABSTRACT FROM AUTHOR]

Geraniums (Pelargonium spp.) are ornamental plants that are widely popular because of their abundant flowering, color variability, different flower patterns, and ease of cultivation. Genetic breeding of this species aims to reduce the plant size and flower color. The objective of this study was to carry out morphoagronomic characterization of parents and F1 hybrids and to estimate the combined capacity and hybrid performance in the circulating diallel in F2 geranium (Pelargonium sp.). We obtained 18 and 275 plants from the F1 and F2 generations, respectively. Characterization of the parental genotypes and F1 and F2 hybrids was performed based on the descriptors for Pelargonium. Parents and F1 hybrids were grouped using the Tocher and UPGMA methods and diallel analyses in the F2 generation. The F1 hybrids G8, G11, and G17 exhibited color combinations suitable for commercialization and are promising for inclusion in breeding programs. The effects of general combining ability (GCA) and specific combining ability (SCA) were significant for these traits were also significant. The results showed the presence of both additive and non-additive genes. However, non-additive and dominant genes were predominant in most characteristics studied. Diallel analysis of the F2 hybrids revealed that the best hybrid combinations for reducing plant height were 14 × 11, 14 × 13, and 15 × 12. Therefore, the implementation and use of diallel analysis were efficient in selecting superior parental genotypes and producing hybrids with high yields. [ABSTRACT FROM AUTHOR]

Zooplankton is an important link between primary producers and lower trophic level organisms in the marine food web, and is an important biological basis for the formation of fishing grounds. Based on the Zooplankton samples collected by the fishery resources survey vessel "Songhang" of Shanghai Ocean University during the comprehensive scientific survey of fishery resources in the high seas of the Northwest Pacific Ocean from June to August in 2021 and 2022, the Zooplankton samples were analyzed in terms of their species composition, distributional characteristics, and their relationship with the environment. The results showed that a total of 174 Zooplankton species were collected in the surveyed area over the two years, belonging to 10 groups. Copepoda and planktonic larvae were the most abundant Zooplankton, with 95 and 22 species identified respectively, accounting for 54.6% and 12.6% of the total number of species, followed by ScyphoZoa, with 18 species identified, and Ostracoda, Tunicata, Chaetognatha, Euphausiacea, and Gastropoda with 11, 9, 6, 4 and 3 species respectively. Additionally, two species each of Polychaeta, Amphipoda, and Cladocera were identified. The dominant genes (species) included seven categories: Clausocalanus sp., Oncaea sp., Paracalanus sp., Calocalanus sp., Oithona plumifera, Oithona decipiens and Metridinidae larvae. The species diversity and dominant genes (species) composition were similar in both years. The mean Zooplankton abundance in 2021 was 732.89 ind./m³, lower than that in 2022 (1 418.88 ind./m³). The Shannon-Wiener index in 2021 was 1.57-3.16, the Evenness index was 0.54-0.91, and the abundance index was 0.84-3.36. All three indices were higher than those in 2022, which ranged from 0.66 to 2.92, 0.26 to 0.94, and 0.77 to 3.11, respectively. GAM analyses showed that Zooplankton abundance was significantly and negatively correlated with the sea-surface salinity and the water temperature in the 200 m layer, and the analyses suggested that the Kuroshio current and the Oyashio also had a certain effect on the temporal and spatial distributions of the abundance. The results of this study will provide basic information for the study of Zooplankton in the high seas of the Northwest Pacific Ocean. [ABSTRACT FROM AUTHOR]

Stripe rust (Puccinia striiformis West. f.sp. tritici, Pst) is a destructive disease that seriously threatens wheat production globally. Exploring novel resistance genes for use in wheat breeding is an urgent need, as continuous Pst evolution frequently leads to a breakdown of host resistance. Here, we identified a set of wheat–Dasypyrum villosum 01I139 (V#6) disomic introgression lines for the purpose of determining their responses to a mixture of Pst isolates CYR32, CYR33 and CYR34 at both seedling and adult-plant stages. The results showed that all introgression lines exhibited high susceptibility at the seedling stage, with infection-type (IT) scores in the range of 6–8, whereas, for chromosomes 5V#6 and 7V#6, disomic addition lines NAU5V#6-1 and NAU7V#6-1 displayed high resistance at the adult-plant stage, indicating that adult-plant resistance (APR) genes were located on them. Further, in order to transfer the stripe-rust resistance on chromosome 7V#6, four new wheat–D. villosum introgression lines were identified, by the use of molecular cytogenetic approaches, from the self-pollinated seeds of 7D and 7V#6, in double monosomic line NAU7V#6-2. Among them, NAU7V#6-3 and NAU7V#6-4 were t7V#6L and t7V#6S monosomic addition lines, and NAU7V#6-5 and NAU7V#6-6 were homozygous T7DS·7V#6L and T7DL·7V#6S whole-arm translocation lines. Stripe-rust tests and genetic analyses of chromosome 7V#6 introgression lines revealed a dominant APR gene designated as Yr7VS on the chromosome arm 7V#6S. Comparison with the homozygous T7DL·7V#6S translocation line and the recurrent parent NAU0686 showed no significant differences in yield-related traits. Thus, T7DL·7V#6S whole-arm translocation with the APR gene Yr7VS provided a valuable germplasm for breeding for resistance. [ABSTRACT FROM AUTHOR]

Background: Downy mildew is the most relevant disease of quinoa and the most widespread. Though, little is known about the genetics of resistance to this disease. The objective of this study was to identify the genomic regions controlling downy mildew resistance in quinoa and candidate genes for this trait. With this aim we carried out a GWAS analysis in a collection formed by 211 quinoa accessions from different origins. This approach was combined with inheritance studies and Bulk Segregant Analysis (BSA) in a segregating population. Results: GWAS analysis identified 26 genomic regions associated with the trait. Inheritance studies in a F2 population segregating for resistance revealed the existence of a major single dominant gene controlling downy mildew complete resistance in quinoa accession PI614911. Through BSA, this gene was found to be located in chromosome 4, in a region also identified by GWAS. Furthermore, several plant receptors and resistance genes were found to be located into the genomic regions identified by GWAS and are postulated as candidate genes for resistance. Conclusions: Until now, little was known about the genetic control of downy mildew resistance in quinoa. A previous inheritance study suggested that resistance to this disease was a quantitative polygenic trait and previous GWAS analyses were unable to identify accurate markers for this disease. In our study we demonstrate the existence of, at least, one major gene conferring resistance to this disease, identify the genomic regions involved in the trait and provide plausible candidate genes involved in defense. Therefore, this study significantly increases our knowledge about the genetics of downy mildew resistance and provides relevant information for breeding for this important trait. [ABSTRACT FROM AUTHOR]

The current breeding effort aims to develop new wheat genotypes with higher genetic potential, thereby contributing to food security. Ten wheat genotypes were crossed in a half-diallel mating design. The F1 progeny from the 45 crosses, along with their ten parents, were evaluated in a randomized block design to estimate combining ability and the nature of gene action. Analysis of variance for combining ability revealed significant mean squares for both general and specific combining abilities across all studied traits. This indicates the importance of both additive and non-additive gene effects in the inheritance of these traits. The GCA/SCA ratio suggested the predominance of non-additive genetic action for all studied traits. Only five parents (HD3086, UP 2748, WH 1105, UP 2565, and HD 2967) exhibited good general combining ability for yield and associated traits. However, but none of them were found good combiners for all traits. Twenty-one crosses exhibited significant specific combining ability for yield and associated traits. The crosses UP 2748 x HD 3059, UP2565 x HD3086, WH 1105 x UP 2526, WH 1105 x WH 1021, and HD 2967 x WH 1021 were identified as good specific combiners for higher grain yield and associated traits. Utilizing these crosses in breeding programs that exploit heterosis can lead to the creation of new wheat genotypes with a broader genetic base. This approach, which involves crossing high-performing parents for some traits with low-performing parents for others, has the potential to produce offspring with superior characteristics in the next generation due to interactions between dominant genes. [ABSTRACT FROM AUTHOR]

Simple Summary: Erect leaves are one of the important phenotypes for plants to adapt to dense planting. This study obtained the erect leaf mutant mths29 through fast neutron irradiation and directional breeding. Dynamic observation of lamina joint development in the mutant and its genetic parent Heng S29 revealed an extreme phenotype during the booting stage, characterized by the complete absence of lamina joint on the inverted second leaves and flag leaves, resulting in a close adhesion of the leaf blade to the stem and the formation of an erect leaf phenotype. Through map-based cloning, the erect leaf QTL was localized within a physical interval of 1.03 Mb on chromosome 5A, and four potential candidate genes were predicted. Here, we demonstrate that mths29 represents a novel genetic resource for erect leaf traits in wheat. This study contributes to a better understanding of lamina joint development in graminaceous and aids in shaping plant architecture for denser planting. The erect leaf plays a crucial role in determining plant architecture, with its growth and development regulated by genetic factors. However, there has been a lack of comprehensive studies on the regulatory mechanisms governing wheat lamina joint development, thus failing to meet current breeding demands. In this study, a wheat erect leaf mutant, mths29, induced via fast neutron mutagenesis, was utilized for QTL fine mapping and investigation of lamina joint development. Genetic analysis of segregating populations derived from mths29 and Jimai22 revealed that the erect leaf trait was controlled by a dominant single gene. Using BSR sequencing and map-based cloning techniques, the QTL responsible for the erect leaf trait was mapped to a 1.03 Mb physical region on chromosome 5A. Transcriptome analysis highlighted differential expression of genes associated with cell division and proliferation, as well as several crucial transcription factors and kinases implicated in lamina joint development, particularly in the boundary cells of the preligule zone in mths29. These findings establish a solid foundation for understanding lamina joint development and hold promise for potential improvements in wheat plant architecture. [ABSTRACT FROM AUTHOR]

Background/Objectives: Gene therapy's emergence has made molecular diagnosis for inherited retinal diseases clinically significant. Free genetic testing panels have improved testing access in clinical practice, yet the interpretation of results, especially variants of unknown significance (VUS), remains challenging and requires expertise. This study shares our experience in utilizing sponsored IRD panel tests by Invitae and Blueprint Genetics (BG), reporting their positivity rates, and comparing their reclassification of variants through amendments. Methods: This retrospective study analyzed genetic test reports from patients who underwent testing via Invitae or BG panels. A positive test was determined if there was a pathogenic mutation in an autosomal dominant gene, two pathogenic mutations in an autosomal recessive gene, or a pathogenic mutation in an X-linked gene in a male patient. Results: The testing positivity rates were 34.9% for Invitae (n = 109) and 42.1% for BG (n = 107). Invitae had more pathogenic variants per report (0.87 vs. 0.58 variants, p = 0.0038) and issued more amendments than BG (0.54 vs. 0.03 amendments; p < 0.01). Of the Invitae variant classification changes, 66.2% switched a VUS to benign. In the BG group, 75% of variant reclassifications changed a VUS to pathogenic. As a result of the Invitae amendments, 88% did not change the overall report result. Conclusions: While free-of-charge genetic testing panels offer valuable insights for diagnosing IRD, limitations such as low diagnostic yield and variant classification discrepancies persist between Invitae and BG. VUS should not be considered pathogenic in the clinical decision-making process. Careful interpretation of genetic testing is required. [ABSTRACT FROM AUTHOR]

In crop improvement, delineating inheritance pattern of a character guides a plant breeder to choose appropriate breeding procedure, which enables ease of improving phenotypic expression of the traits. To deduce the inheritance pattern of naked seed or fuzzless character, four parental lines involving two purely naked seed types (DHN‐1 and DHN‐10), one partial naked seed type (SP46CC) and one fully fuzzy type (OSB415) were used to develop three different types of crosses, namely, naked × naked seed type cross (N × N), partial naked × naked seed type cross (PN × N) and fuzzy × naked seed type cross (F × N). We observed that naked trait segregates in the ratio of 11 naked: 5 partial naked in N × N cross, 22 naked: 42 partial naked in PN × N cross and 22 naked: 42 partial naked: 192 fuzzy in F × N cross. Our study reports a novel four‐gene model to understand inheritance nature of naked seed character where the presence of single basic dominant fuzzy gene negates the effect of genes controlling nakedness resulting fuzzy phenotype irrespective of the number of partial fuzzyness/nakedness imparting alleles. This indicates that nakedness is recessive to fuzzyness. Based on our results, we infer observing gradations of nakedness on seeds depends on the presence of number of partial fuzzyness imparting alleles, which led to a conclusion that the trait exhibited dose‐dependent expression with one basic gene for fuzziness. [ABSTRACT FROM AUTHOR]

Summary: The exploitation of heterosis to integrate parental advantages is one of the fastest and most efficient ways of rice breeding. The genomic architecture of heterosis suggests that the grain yield is strongly correlated with the accumulation of numerous rare superior alleles with positive dominance. However, the improvements in yield of hybrid rice have shown a slowdown or even plateaued due to the limited availability of complementary superior alleles. In this study, we achieved a considerable increase in grain yield of restorer lines by inducing an alternative splicing event in a heterosis gene OsMADS1 through CRISPR‐Cas9, which accounted for approximately 34.1%–47.5% of yield advantage over their corresponding inbred rice cultivars. To achieve a higher yield in hybrid rice, we crossed the gene‐edited restorer parents harbouring OsMADS1GW3p6 with the sterile lines to develop new rice hybrids. In two‐line hybrid rice Guang‐liang‐you 676 (GLY676), the yield of modified hybrids carrying the homozygous heterosis gene OsMADS1GW3p6 significantly exceeded that of the original hybrids with heterozygous OsMADS1. Similarly, the gene‐modified F1 hybrids with heterozygous OsMADS1GW3p6 increased grain yield by over 3.4% compared to the three‐line hybrid rice Quan‐you‐si‐miao (QYSM) with the homozygous genotype of OsMADS1. Our study highlighted the great potential in increasing the grain yield of hybrid rice by pyramiding a single heterosis gene via CRISPR‐Cas9. Furthermore, these results demonstrated that the incomplete dominance of heterosis genes played a major role in yield‐related heterosis and provided a promising strategy for breeding higher‐yielding rice varieties above what is currently achievable. [ABSTRACT FROM AUTHOR]

Background: Depression and coronary heart disease (CHD) have common risk mechanisms. Common single nucleotide polymorphisms (SNPs) may be associated with the risk of depression combined with coronary heart disease. Methods: This study was designed according to the PRISMA-P guidelines. We will include case-control studies and cohort studies investigating the relationship between gene SNPs and depression and coronary heart disease comorbidities. The Newcastle- Ottawa Scale (NOS) will be used to assess the risk of bias. When measuring dichotomous outcomes, we will use the odds ratio (OR) and 95% confidence interval (95%CIs) in a case-control study. Five genetic models (allele model, homozygous model, co-dominant model, dominant model, and recessive model) will be evaluated for each included study. Subgroup analysis by ethnicity will be performed. If necessary, post hoc analysis will be made according to different types. Results: A total of 13 studies were included in this study, and the types of genes included are FKBP5 and SGK1 genes that act on glucocorticoid;miR-146a, IL-4-589, IL-6-174, TNF-a-308, CRP-717 genes that act on inflammatory mechanisms; eNOS genes from endothelial cells; HSP70 genes that act on the autoimmune response; ACE2 and MAS1 genes that act to mediate Ang(1-7) in the RAS system; 5-HTTLPR gene responsible for the transport of serotonin 5-HT and neurotrophic factor BDNF gene. There were three studies on 5-HTTLPR and BDNF genes, respectively, while there was only one study targeting FKBP5, SGK1, miR-146a, IL-4-589, IL-6-174, TNF-alpha-308, CRP-717, eNOS, HSP70, ACE2, and MAS1 genes. We did not perform a meta-analysis for genes reported in a single study, and meta-analysis was performed separately for studies exploring the 5-HTTLPR and BDNF genes. The results showed that for the 5-HTTLPR gene, there was a statistically significant association between 5-HTTLPR gene polymorphisms and depression in combination with coronary diseases (CHD-D) under the co-dominant model (LS vs LL:OR 1.76, 95%CI 1.20-2.59; SS vs LL: OR 2.80, 95%CI 1.45 to 5.41), the dominant model (LS+SS vs LL: OR 2.06, 95%CI 1.44 to 2.96), and the homozygousmodel (SS vs LL: OR 2.80 95%CI 1.45 to 5.5.41) were statistically significant for CHD-D, demonstrating that polymorphisms in the 5-HTTLPR gene are associated with the development of CHD-D and that the S allele in the 5-HTTLPR gene is likely to be a risk factor for CHD-D. For the BDNF gene, there were no significant differences between one of the co-dominant gene models (AA vs GG: OR 6.63, 95%CI 1.44 to 30.64), the homozygous gene model (AA vs GG: OR 6.63,95% CI 1.44 to 30.64), the dominant gene model (GA+AA vs GG: OR4.29, 95%CI 1.05 to 17.45), recessive gene model (AA vs GG+GA: OR 2.71, 95%CI 1.16 to 6.31), and allelemodel (A vs G: OR 2.59, 95%CI 1.18 to 5.67) were statistically significant for CHD-D, demonstrating that BDNFrs6265 gene polymorphisms are associated with the CHD-D development and that the A allele in the BDNFrs6265 gene is likely to be a risk factor for CHD-D. We analyzed the allele frequencies of SNPs reported in a single study and found that the SNPs in the microRNA146a gene rs2910164, the SNPs in the ACE2 gene rs2285666 and the SNPs in the SGK1 gene rs1743963 and rs1763509 were risk factors for the development of CHD-D. We performed a subgroup analysis of three studies involving the BDNFrs6265 gene. The results showed that European populations were more at risk of developing CHD-D than Asian populations in both dominant model (GA+AA vs GG: OR 10.47, 95%CI 3.53 to 31.08) and co-dominant model (GA vs GG: OR 6.40, 95%CI 1.98 to 20.73), with statistically significant differences. In contrast, the studies involving the 5-HTTLPR gene were all Asian populations, so subgroup analyses were not performed.We performed sensitivity analyses of studies exploring the 5-HTTLPR and BDNF rs6265 genes. The results showed that the results of the allele model, the dominant model, the recessive model, the homozygous model and the co-dominant model for both 5-HTTLPR and BDNF rs6265 genes were stable. Due to the limited number of studies of the 5-HTTLPR and BDNF genes, it was not possible to determine the symmetry of the funnel plot using Begg's funnel plot and Egger's test. Therefore, we did not assess publication bias. Discussion: SNPs of the microRNA146a gene at rs2910164, the ACE2 gene at the rs2285666 and the SGK1 gene at rs1743963 and rs1763509, and the SNPs at the 5-HTTLPR and BDNF gene loci are associated with the onset of comorbid depression in coronary heart disease. We recommend that future research focus on studying SNPs' impact on comorbid depression in coronary heart disease, specifically targeting the 5-HTTLPR and BDNF gene at rs6265. [ABSTRACT FROM AUTHOR]

Phytoremediation is a promising technology for removing the high‐toxic explosive 2,4,6‐trinitrotoluene (TNT) pollutant from the environment. Mining dominant genes is the key research direction of this technology. Most previous studies have focused on the detoxification of TNT rather than plants' TNT tolerance. Here, we conducted a transcriptomic analysis of wild type Arabidopsis plants under TNT stress and found that the Arabidopsis cytochrome P450 gene CYP81D11 was significantly induced in TNT‐treated plants. Under TNT stress, the root length was approximately 1.4 times longer in CYP81D11‐overexpressing transgenic plants than in wild type plants. The half‐removal time for TNT was much shorter in CYP81D11‐overexpressing transgenic plants (1.1 days) than in wild type plants (t1/2 = 2.2 day). In addition, metabolic analysis showed no difference in metabolites in transgenic plants compared to wild type plants. These results suggest that the high TNT uptake rates of CYP81D11‐overexpressing transgenic plants were most likely due to increased tolerance and biomass rather than TNT degradation. However, CYP81D11‐overexpressing plants were not more tolerant to osmotic stresses, such as salt or drought. Taken together, our results indicate that CYP81D11 is a promising target for producing bioengineered plants with high TNT removing capability. [ABSTRACT FROM AUTHOR]

Resistance to pre-harvest sprouting (PHS) is an agronomically important trait affecting the yield and grain quality of bread wheat. PHS resistance depends both on environmental factors and the genotypic and phenotypic properties of wheat varieties. It is known that wheat varieties with red-grain are more resistant to PHS than white-grain varieties. However, at present there are no methodological approaches that allow to unambiguously distinguish red-grain varieties according to the level of PHS resistance. The purpose of the study was to compare different methods for efficient differentiation of soft winter wheat (Triticum aestivum L.) varieties for resistance to PHS. The germination index (GI), α-amylase activity (AAA), a digital grade of the grain color and genetic bases of the wheat varieties the grain was determined in 164 winter wheat, among them 156 were red-grain. The studies were carried out at the late milk/hard dough (LM/HD; GS77-GS87) stage and the hard grain (HG; GS92-GS93) stage. Based on the dynamics of GI it was found that late LM/HD stage is the most suitable for GI evaluation. AAA was performed using the Ceralpha method and falling number (FN) evaluation. An increase in the level of AAA during grain ripening of wheat varieties was shown. A negative correlation was found between GI and FN, FN and AAA. Using the Lab color model to assess the color variation of the grain coat allow to identify 3 variants of grain color. Genetic base of wheat varieties was analyzed by means of allelic composition of the Tamyb10 gene, which participate in the formation of the red color of grain. The results indicated that digital analysis and allelic composition of the Tamyb10 cannot be used as additional criterion for separation of red-grain wheat varieties for resistance to PHS. This is despite the fact that the numerous group of the varieties contain two or more dominant Tamyb10 gene. In general, a comparison of varieties by all three parameters allow to identify a group of varieties that are most PHS resistant. This group consist of 73 red-grain varieties out of 156, while no white-grain PHS-resistant varieties were identified. [ABSTRACT FROM AUTHOR]

Wheat powdery mildew is a fungal disorder caused by Blumeria graminis f. sp. tritici (Bgt) and is a severe and significant threat to the yield and quality of its host. The most practical and environmentally friendly approach to controlling this disease is through resistance gene identification to develop resistant varieties. Wild germplasm relatives of wheat are a valuable reservoir of genes contributing to resistance against powdery mildew. In our study, we identified the Aegilops tauschii germplasm "KU-2013", exhibiting seedling resistance to Bgt isolate E09 following hexaploidization. Genetic analysis and chromosomal localization of the powdery mildew resistance gene in doubled haploid (DH) KU-2013 indicated that the disease resistance gene in DHKU-2013 is governed by a dominant gene situated in 5DS, tentatively named PmKu-2013. Following the analysis of PmKu-2013 relative to the genes at the Pm2 locus, it was inferred that PmKu-2013 represented a distinct novel gene separate from Pm2. Using molecular marker analysis, PmKu-2013 was found to be ultimately mapped between the sdau5DS5-3 and sdau5DS6-1 markers, with genetic distances of 0.6 cM and 1.3 cM, respectively. Using markers tightly linked to PmKu-2013, the genotypes of core wheat varieties from various regions were identified, laying the foundation for the transfer and utilization of PmKu-2013 in molecular-assisted selection (MAS) for breeding. [ABSTRACT FROM AUTHOR]

The latest study strategized to evaluate the maize populations by combining ability analysis under optimum and drought-stress environments to assemble the promising parental inbred lines and their hybrid populations with high productivity and resistance to drought stress. From the collection of the Trunojoyo Madura University, Indonesia, came five maize pure lines (UTM 2, UTM 7, UTM 10, UTM 19, and UTM 31) that received crossing in a complete diallel fashion to obtain 20 hybrid populations. The performance of five parental inbred lines and their 20 F1 hybrids' evaluation in crop season 2021 had a randomized complete block design with three replications under four each for optimum and droughtstress environmental conditions. Data recording ensued on grain yield and drought susceptibility index (DSI). The GCA and SCA variances revealed that grain yield had more influences from the dominant genes with maternal effects at the eight locations; hence, the parental lines have less stimulus on the hybrids' performance. The genotype UTM2 (G1) appeared resistant to drought-stress conditions based on the DSI value (0.70) and has positive GCA effects for grain yield. Therefore, it can better serve to improve drought resistance and grain yield. The results further exhibited that six maize hybrids, i.e., G3 (UTM 2 x UTM 10), G6 (UTM 7 x UTM 2), G10 (UTM 7 x UTM 31), G11 (UTM 10 x UTM 2), G22 (UTM 31 x UTM 10), and G24 (UTM 31 x UTM 19) were remarkable as commercial hybrids with high grain yield and resistance to drought stress. [ABSTRACT FROM AUTHOR]

Background: This study aimed to understand the genetic aspects and inheritance patterns that control the process of restoring fertility in the context of the A1 system of Cytoplasmic-Nuclear Male Sterility (CMS) in pearl millet. Methods: The experimentation was conducted in commercial pearl millet hybrids, utilizing three F2 populations and three BC1 populations. These populations underwent assessment during the rainy and post-rainy seasons at Rallis India Limited, Hyderabad During the Post-rainy (November-February) and summer (March-June) seasons of 2022-2023. Segregation data derived from observations on pollen shedding and seed set were gathered and subsequently, statistical analysis was performed. The Chi-square (X2) test was employed to assess the conformity of the observed segregation data to the expected genetic ratios, thus evaluating the goodness of fit. Result: The hybrid combinations MP13P025A X MP16P050R (MP7171) and MP18P069A X MP20P081R (MP7214) consistently displayed a 3:1 segregation ratio in the F2 generation and a 1:1 ratio in the BC1 generation, regardless of the rainy or post-rainy seasons. However, the cross between MP14030A and MP15P038R (MP7878) showed irregularities in both seasons due to modifiers and environmental factors. These irregularities stemmed from an excess of fertile plants (FF) in the post-rainy season or an excess of sterile plants (FS) in the summer season. These observations provide valuable insights into the genetic dynamics of the A1 Cytoplasmic-Nuclear Male Sterility (CMS) system within commercial pearl millet hybrids. The study indicates that fertility restoration in the A1-based CMS system is strongly influenced by a single Dominant gene control mechanism governing the interplay between male sterility and fertility restoration in these crosses. [ABSTRACT FROM AUTHOR]

Introduction: Variations in mutation rates among acute myeloid leukemia (AML) patients with myeloid sarcoma (MS) underscore the need for a thorough examination. This meta-analysis was conducted to fill the information gap concerning mutation frequencies in AML patients presenting with MS. Materials and methods: This study included retrospective and prospective cohorts. It examined genetic alterations in AML patients with and without MS across all age groups. The search strategy employed terms such as “acute myeloid leukemia,” “extramedullary,” “granulocytic sarcoma,” “myeloid sarcoma,” and “leukemic cutis” in the EMBASE, MEDLINE, and Scopus databases. Excluded from the study were reviews, case reports, and case series with fewer than 10 cases. Statistical analyses were performed with Review Manager 5.4 software. Results: The primary analysis incorporated data from 37 cohorts involving 5646 diagnosed AML patients and revealed a 17.42% incidence of MS. The most prevalent mutation among AML patients with MS was FLT3-ITD, with a pooled prevalence of 17.50% (95% CI 12.60% to 22.50%; I² 82.48%). The dominant fusion gene was RUNX1::RUNX1T1, displaying a pooled prevalence of 28.10% (95% CI 15.10% to 41.20%; I² 96.39%). In comparison, no significant intergroup differences were observed for NPM1, FLT3-ITD, KIT, and IDH2 mutations. Interestingly, the CEBPA mutation exhibited protective effects for MS patients, with an odds ratio of 0.51 (95% CI 0.32 to 0.81; I² 0%). Conversely, the NRAS mutation was associated with an increased risk of MS development, with an odds ratio of 5.07 (95% CI 1.87 to 13.73; I² 0%). Conclusion: This meta-analysis sheds light on the prevalence of genetic mutations in AML patients with MS, providing insights into the unique characteristics of the mutations and their frequencies. These discoveries are crucial in informing therapeutic and prognostic decisions for individuals with myeloid sarcoma. [ABSTRACT FROM AUTHOR]

Spinach (Spinacia oleracea) is an economically important leafy vegetable grown in the United States and world-wide. The downy mildew pathogen, Peronospora effusa (Pfs), is a major biotic constraint impacting spinach production and quality. The use of resistant cultivars is an economical and environmentally-friendly management option especially in organic production systems. As new races of the pathogen continue to appear, there is a need to continue to select for resistance to the emerging races. The objectives of this study were to evaluate a set of spinach hybrids and F2 breeding populations for resistance to Pfs race 5 to develop a better understanding of the genetics of downy mildew resistance. Also, we screened 39 commercial spinach cultivars for resistance to a recently identified race, Pfs race 19. The genetics of resistance to Pfs 5 was determined by greenhouse inoculations of F1 progeny (individual crosses between near isogenic lines, NIL3 or NIL1 and susceptible genotype, Viroflay) and F2 population progeny (cross between Califlay and susceptible Viroflay). Two hybrids were examined for resistance to Pfs 5. The results indicated that resistance conferred at the RPF1 or the RPF3 loci in a heterozygous (Rr) condition to Pfs 5 was completely dominant. Also, Chi-square analysis of the segregation pattern in the F2 population showed that resistance to Pfs race 5 was conferred by a single dominant gene. A total of 22 out of 39 spinach commercial cultivars were resistant to the newly reported Pfs race 19 and could be used in breeding programs to develop new cultivars with resistance to Pfs 19. [ABSTRACT FROM AUTHOR]

Cowpea is an essential economic crop in underdeveloped and developing countries mainly grown by small farmers. In terms of seed yield and some agricultural characteristics, this study was carried out to determine the genetic structures and the general and specific adaptability of the genotypes. The trial, which included F1 hybrids and parents, was established under Konya ecological conditions with 3 replications in 2020 in the "Random Blocks Trial" design. Based on the results of the preliminary analysis of variance, it was determined that there was sufficient variation in the hybrid populations formed in terms of all traits examined. Nonadditive and dominant genes were found to be important in all traits examined. In the study, general adaptability was found to be important for the other traits examined, except the seed number per pod, seed number per plant, seed yield per plant, and protein yield per plant, and the effects of special adaptability were significant for all traits examined. Considering their general combining abilities, it was found that Ülkem, Sırma, and Pekşen cultivars should be used as rootstocks in breeding programs aimed at increasing yield and Pekşen and Ülkem cultivars in breeding programs to increase protein levels. When the specific combining abilities, heterosis and heterobeltiosis values are evaluated together, the hybrid combinations "Pekşen × Sırma", "Ülkem × Pekşen" and "Karagöz × Sırma" with the best performance in terms of, seed yield per plant and "Pekşen × Amazon", "Sırma × Pekşen", "Sırma × Karagöz" and "Ülkem × Pekşen" with the most outstanding give better performance in terms of protein ratio were found to be promising. [ABSTRACT FROM AUTHOR]

In this study, it was aimed to determine the benthic macroinvertebrate fauna of Demre Stream in Antalya. Benthic macroinvertebrate samples were taken seasonally from 12 stations determined on Demre Stream between April 2015 and December 2015 and the obtained individuals belonging to Clitellata, Rhabditophora, Gastropoda, Insecta, and Arachnida groups Macroinvertebrate based clustering of stations was calculated by using UPGMA analysis. The lowest similarity was determined between the 3rd and 10th stations, and the highest similarity was between the 8th and 11th stations. Simpson and Shannon-Wiener diversity indices were applied to determine the diversity values of the stations. According to both diversity indices, the highest diversity value was reached at the 5th station, while the lowest diversity value was reached at the 3rd station. This study is the first study to determine the benthic fauna of the Demre Stream and therefore all the groups identified are the first records for the Demre Stream. [ABSTRACT FROM AUTHOR]

Fruit pubescence (trichome) is an important characteristic and is controlled by a single dominant gene (G/g), resulting in peaches and nectarines. The length and/or density of fruit fuzz varies greatly among different peach cultivars. However, little is known about fruit trichome development in peaches. In this study, significant differences in fruit trichome length and density were identified between 'XT1' and its bud mutation 'BM', showing much higher values for 'BM'. Comparative transcriptome analysis was performed, and 987 differentially expressed genes (DEGs) were identified, which were confirmed by qRT-PCR. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses showed that genes involved in defense response, secondary metabolites and plant hormone signal transduction may also be related to the development of peach fruit trichomes. By integrating other transcriptome data, we finally determined 47 DEGs that might participate in peach trichome development, including five plant-hormone-related genes. The promoter analysis showed that one abscisic-acid-related gene, Prupe.6G072400 (abscisic acid 8′-hydroxylase 2), and one auxin-related gene, Prupe.3G074900 (auxin-responsive protein IAA1), have obvious differences in the cis-acting elements of the promoters between 'XT1' and 'BM'. The results of this study will provide a valuable resource illustrating the mechanism of fruit trichome development in peaches and benefit future genomic research. [ABSTRACT FROM AUTHOR]

The article focuses on the survival and adaptation of the first human settlers in the Canary Islands over a millennium, exploring topics such as their isolated existence, distinct genetic ties to North Africa, and the challenges they faced in an arid environment. It mentions the research, conducted by local archaeologists, delves into questions about the settlers' seafaring skills, agricultural practices, and societal dynamics.

Key message: Powdery mildew resistance gene PmXNM, originated from the Chinese wheat landrace Xiaonanmai, was delimited to a 300.7-kb interval enriched with resistance genes. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally devastating disease threatening the yield and quality of wheat worldwide. The use of broad-spectrum disease resistance genes from wheat landraces is an effective strategy to prevent this pathogen. Chinese wheat landrace Xiaonanmai (XNM) was immune to 23 tested Bgt isolates at the seedling stage. The F1, F2, and F2:4 progenies derived from the cross between XNM and Chinese Spring (CS) were used in this study. Genetic analysis revealed that powdery mildew resistance in XNM was controlled by a single dominant gene, temporarily designated PmXNM. Bulked segregant analysis and molecular mapping delimited PmXNM to the distal terminal region of chromosome 4AL flanked by markers caps213923 and kasp511718. The region carrying the PmXNM locus was approximately 300.7 kb and contained nine high-confidence genes according to the reference genome sequence of CS. Five of these genes, annotated as disease resistance RPP13-like proteins 1, were clustered in the target region. Haplotype analysis using the candidate gene-specific markers indicated that the majority of 267 common wheat accessions (75.3%) exhibited extensive gene losses at the PmXNM locus, as confirmed by aligning the targeted genome sequences of CS with those of other sequenced wheat cultivars. Seven candidate gene-specific markers have proven effective for marker-assisted introgression of PmXNM into modern elite cultivars. [ABSTRACT FROM AUTHOR]