Search Results (36)

The common bean (Phaseolus vulgaris L.) cultivar Jalo Vermelho carries the Co-12 gene, which confers resistance to both Andean and Mesoamerican races of Colletotrichum lindemuthianum. Despite its importance for breeding programs, the genomic location and candidate genes underlying this resistance remain poorly defined. The Co-12 locus was fine-mapped using a biparental population derived from the cross Jalo Vermelho × Crioulo 159. A total of 172 F₂ plants were used to generate 172 F_2:3 families, which were phenotyped after inoculation with race 1545 of C. lindemuthianum. Segregation analysis confirmed a 1:2:1 Mendelian ratio, consistent with a single dominant resistance gene. Genotyping of resistant and susceptible plants using the BARBean6K_3 Illumina BeadChip (5398 SNP markers) mapped Co-12 to chromosome Pv04, between 1695 bp (ss715649768) and 9,651,954 bp (ss715646644). Subsequent fine mapping with simple sequence repeat (SSR) markers delimited the locus to a 41 kb genomic interval flanked by BARCPVSSR04557 and BARCPVSSR04570. Within this region, three candidate genes were identified, including one encoding a gamma-glutamyl-GABA enzyme and two encoding lipid transfer proteins (LTP2). Lipid transfer proteins are widely recognized components of plant defense; however, their association with anthracnose resistance in the common bean has not been previously reported. The identification of LTP2 genes within the Co-12 interval suggests a previously unrecognized resistance mechanism and expands the current understanding of host defense pathways in Phaseolus vulgaris. The markers identified here provide valuable tools for marker-assisted selection and will facilitate efficient introgression of Co-12 into common bean cultivars. Full article

Leaf color mutants are commonly characterized by altered chlorophyll content and aberrant chloroplast development, making them valuable models for investigating photosynthetic mechanisms and chloroplast biogenesis. In this study, an albino mutant was isolated from a population of transgenic maize breeding lines. Genetic analysis indicated that the mutant phenotype is inherited in a Mendelian manner and is controlled by a single nuclear locus. This was supported by a χ² test performed on the T₂ generation, which confirmed a segregation ratio consistent with 3:1 (176:68, χ² = 1.07 < χ²_0.05 = 3.84, p > 0.05). Microscopic examination revealed the absence of normally developed chloroplasts in mutant cells. Further expression analysis of chloroplast genes via Northern blotting and quantitative real-time PCR (qRT-PCR) suggested that the mutation impairs the regulation of plastid-encoded polymerase (PEP)-dependent chloroplast gene expression. Notably, PCR-based co-segregation analysis indicated that the mutant phenotype is associated with the entire inserted vector sequence, rather than a point mutation or a small genomic deletion. In conclusion, this paper reports the isolation and phenotypic characterization of an etiolated mutant from a transgenic maize breeding population, including comparative ultrastructural analysis of chloroplasts, co-segregation validation, and chloroplast gene expression profiling. These results enhance our understanding of the physiological and molecular mechanisms underlying chlorophyll-deficient mutations in plants. Full article

Stropharia rugosoannulata is a widely cultivated edible fungus with high economic and nutritional value. It is a tetrapolar heterothallic basidiomycete. The development of single nucleotide polymorphism (SNP) markers for mating-type identification holds considerable promise for enhancing breeding efficiency. In our study, one group of test crosses and three-round mating experiments from one parental strain were conducted in order to ascertain the mating type in this species. Segregation distortion in mating types was observed after single-spore isolation, which was deviated from Mendelian inheritance. The monokaryotic strain Q25 was derived from the dikaryotic mycelium S1 of S. rugosoannulata. The genome map of strain Q25 with 48.27 Mb and 14 chromosomes was constructed using genomic, transcriptomic, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies. The locations of mating-type loci were identified using genomic annotation. The mating-type A locus is located in chromosome 1, with the gene sequence of β-fg, HD2, HD1, and MIP. The mating-type B locus is located in chromosome 12. It contains five pheromone receptors and five pheromone precursor genes. Two pairs of highly specific and stable primers were designed based on SNP loci in A and B mating types. A1, A2, B1, and B2 alleles were precisely distinguished with these primers, which were subsequently applied in cultivation experiments. This study lays a foundation for the precise breeding of S. rugosoannulata. Full article

In Lolium perenne, a novel growth habit mutant, named VIROIZ, was recovered following colchicine treatment, and it was confirmed to maintain the diploid chromosome number (2n = 2x = 14). The mutation affected the stem morphology by inducing prolific axillary shoot formation at nodal zones, resulting in a spreading growth habit that can extend to ~70 cm in width. Inheritance analysis based on single-plant evaluations in crosses with wild-type plants (F₁, n = 285; F₂, n = 380) and in selfed progeny (S₁, n = 255) consistently showed ~40% expression of the spreading phenotype, deviating from classical Mendelian ratios and indicating complex genetic control. Phenotypic selection further distinguished divergent classes: positively selected lines (C1⁺) averaged 3.90 axillary tillers per stem, whereas negatively selected lines (C1⁻) averaged only 0.22. Partial sequencing of 11 candidate genes implicated in shoot architecture, covering 40–90% of full-length DNA, did not provide a conclusive explanation for the altered stem growth. Notably, a single point mutation was observed in CRT3 (an endoplasmic reticulum chaperone that interacts with brassinosteroid signaling) highlighting it as a primary target for future studies. Cytological analysis of meiosis in F₁ hybrids between VIROIZ and wild-type plants revealed irregular chromosome pairing with persistent univalents (2–4 per cell), supporting the presence of structural chromosomal rearrangements that may disrupt gene organization and function in VIROIZ. The non-Mendelian segregation of the spreading phenotype, together with the observed meiotic irregularities, suggests that the mutation affects regulatory genes responsive to hormonal signals controlling axillary meristem initiation. The mutant represents a valuable resource for turf-type L. perenne breeding and for studying hormonal regulation of shoot morphogenesis in Poaceae. Full article

Mugalzhar horses are a relatively young native breed of Kazakhstan, prized for meat and milk production and adaptation. This study was conducted to investigate genetic diversity and pinpoint genomic regions associated with selection signatures in this breed using whole-genome sequence data. Variant calling yielded a total of 21,722,393 high-quality variants, including 19,495,163 SNPs and 2,227,230 indels. Most variants were located in introns and intergenic regions, while only 1.94% were exonic. Estimates of genetic diversity were moderate, with expected and observed heterozygosity and nucleotide diversity of 0.2325, 0.2402, and 0.0021, respectively. We identified nine adaptive candidate genes (SCAPER, FHAD1, MMP15, ADGRE1, CMKLR1, MRPL15, ZNF667, CCDC66, and LOC100055310), harboring high-impact exonic variants in the homozygote state for an alternative allele. No deleterious segregating variants associated with Mendelian traits were found in this population, while seven variants linked to coat color and gaitedness were detected in a low frequency heterozygous state. Our findings suggest that there are certain genomic regions subjected to ancient selection footprints during the ancestor breed formation and adaptation. The outcome of this study serves as a foundation for future genomic-driven strategies, a broader utilization of this breed, and a reference for genomic studies on other horse breeds. Full article

Microsatellite markers are widely used in aquaculture for genetic analysis and breeding programs, but challenges such as segregation distortion and allelic instability can impact their effectiveness in parentage verification and inheritance studies. This study evaluated 15 microsatellite loci in seven experimental olive flounder (Paralichthys olivaceus) families bred through 1:1 full-sibling crosses, assessing their utility for accurate parentage and inheritance stability. Parentage assignments were conducted within an expanded pool of 647 candidate parents (including the actual 14 parents), encompassing both closely related and moderately distant individuals. Despite increased genetic diversity, assignments maintained a high accuracy rate (99.6%), demonstrating marker robustness. Differences in delta values highlighted the influence of genetic backgrounds on assignment clarity, with some groups showing reduced distinctiveness in the expanded pool. Segregation distortion was observed at certain loci, deviating from Mendelian inheritance, likely due to meiotic drive and post-zygotic selection. These findings underscore the need for empirical validation of microsatellite loci for stable inheritance and reliable parentage in diverse breeding programs, especially with genetically similar spawners. Full article

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with japonica rice Koshihikari as the recipient and indica rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, qWRG9 on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, qWRG9 was narrowed to a 1.2 Mb region. Additionally, a BC₄F₂ segregating population confirmed that low WRG was a dominant trait governed by the major QTL qWRG9, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC₄F₂ population revealed that rice grains carrying the Indica-type qWRG9 allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement. Full article

Myotonia congenita is a hereditary, non-dystrophic skeletal muscle disorder associated with muscle stiffness due to delayed muscle relaxation after contraction. We review myotonia congenita in domesticated animals and humans and investigated suspected myotonia congenita in a flock of Merino sheep in Australia. In 2020, a property in New South Wales reported a four-year history of lambs that would fall on disturbance before rapidly recovering, with 13 affected sheep identified in 2020. Episodes were associated with a short period of tetanic spasms and a stiff gait upon rising. Lambs were otherwise normal between episodes, although over time, lost body condition and occasionally died from misadventure. An inherited condition was considered from limited pedigree information and a preliminary diagnosis of myotonia congenita was made based on clinical presentation. Biochemistry from four sheep found variable, but typically mild increases in creatine kinase (CK) and aspartate aminotransferase (AST). Modified electromyography on six affected sheep found irregular electrical activity within the muscle. For four sheep, there were no consistent significant abnormalities on post mortem examination and histopathology—typical for this condition. A review of the Online Mendelian Inheritance in Man (OMIM) and Online Mendelian Inheritance in Animals (OMIA) databases was conducted to summarise information about myotonia congenita in humans and eight non-human species of animals. Comparing the characteristic clinical presentation, pathology and electromyography data of affected Merino sheep to similar conditions in other species assisted the identification of likely candidate genes. Whole genome sequencing of two affected lambs detected a missense variant in CLCN1 (NC_056057.1:g.107930611C>T; XM_004008136.5:c.844C>T; XP_004008185.4:p.(P282S)), with a predicted deleterious effect on protein function. An SNP genotyping assay was developed, and the variant segregated with the disease in 12 affected sheep and obligate carrier rams under an assumed recessive mode of inheritance. Identifying a likely causal variant and developing a diagnostic test allows screening of suspected affected or carrier Merino sheep for early intervention to reduce propagation of the variant within flocks. Full article

The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in their genome by multiplex PCR, which is utilized for genotyping of 332 half-sib plants of Ziziphus jujuba.This cost-effective method makes as much as possible to utilize the same amount of each pair of various targeted loci primers. After PCR amplification of targeted genome parts, the mixed products can be directly used in a next-generation sequencing platform. We concomitantly amplified 10 unique SNP loci at 10 different chromosomes of male JingZao 39 plants in 332 half-sib plants and sequenced them on the Illumina Novaseq 6000 platform. Analysis of SNP genotyping accuracy of 332 half-sib plants showed that all 10 unique SNPs in all 332 plants were correctly amplified in this multiplex PCR method. Furthermore, based on Mendelian inheritance, we identified 124 full-sib plants that have 10 unique SNPs in their genomes. These results were further confirmed by whole genome resequencing of 82 randomly selected half-sib plants, and the identity-by-descent values of all full-sib plants were between 0.4399 to 0.5652. This study displayed a cost-effective multiplex PCR method and proper identification of pollen parent through specific SNPs in half-sib progenies and firstly obtained a full-sib population between ‘Wuhezao’ and ‘JingZao 39’, segregating for stone and stoneless fruit. Full article

Color development in various rice organs results from the complementary expression of genes involved in anthocyanin biosynthesis. The Purple pericarp (Prp) trait and the Purple leaf (Pl) trait both display epistasis, relying on the complement of the Pb and Pp genes for pericarp coloration and the Pl and Pp genes for leaf coloration, respectively. However, there is still genetic uncertainty in identifying the genes responsible for the various color expressions and intensities of rice grain pericarp and leaves. In this study, we characterized the inheritance patterns of color development and the mode of anthocyanin pigments in rice by crossing two parental mutant lines. YUM051, exhibiting dark purple leaves (Pl^w) and purple pericarp (Prp), was crossed with YUM144, which displayed light purple leaves (Plⁱ) and a white pericarp (prp). The F1 plants exhibited dark purple leaves with purple pericarps, indicating the dominant nature of the purple leaf (Pl) and purple pericarp (Prp) traits. The rice Prp traits display a complementary interaction, reflected in a 9:7 ratio of purple to white pericarp. However, the Prp trait followed Mendelian segregation with a 3:1 ratio of purple to white pericarp in this cross, indicating homozygous dominant Pp alleles in both parental plants. Meanwhile, the segregation of the purple leaf color in the F₂ generation of this cross followed complementary inheritance, exhibiting a 9:7 segregation ratio between purple leaves and greenish leaves with purple leaf margins. Moreover, the co-segregation of Prp and Pl traits in the cross between YUM051 (Pl^w) and YUM144 (Plⁱ) plants did not adhere to the Mendelian 9:3:3:1 independent assortment ratio, confirming that the Pl gene and Pb gene are linked on the same chromosome. Cyanidin-3-O-glucoside (C3G) was detected in the leaves of all progeny resulting from the Pl^w and Plⁱ cross. However, C3G was exclusively identified in the seeds of offspring carrying the dominant Pb gene. Therefore, the Pl^w and Plⁱ alleles are Pl genes responsible for purple leaf color, while the Pb gene is responsible for purple pericarp color in rice; these genes function independently of each other. Full article

Grifola frondosa is a valuable edible fungus with high nutritional and medicinal values. The mating systems of fungi not only offer practical strategies for breeding, but also have far-reaching effects on genetic variability. Grifola frondosa has been considered as a sexual species with a tetrapolar mating system based on little experimental data. In the present study, one group of test crosses and six groups of three-round mating experiments from two parental strains were conducted to determine the mating system in G. frondosa. A chi-squared test of the results of the test-cross mating experiments indicated that they satisfied Mendelian segregation, while a series of three-round mating experiments showed that Mendelian segregation was not satisfied, implying a segregation distortion phenomenon in G. frondosa. A genomic map of the G. frondosa strain, y59, grown from an LMCZ basidiospore, with 40.54 Mb and 12 chromosomes, was generated using genome, transcriptome and Hi-C sequencing technology. Based on the genomic annotation of G. frondosa, the mating-type loci A and B were located on chromosomes 1 and 11, respectively. The mating-type locus A coded for the β-fg protein, HD1, HD2 and MIP, in that order. The mating-type locus B consisted of six pheromone receptors (PRs) and five pheromone precursors (PPs) in a crossed order. Moreover, both HD and PR loci may have only one sublocus that determines the mating type in G. frondosa. The nonsynonymous SNP and indel mutations between the A₁B₁ and A₂B₂ mating-type strains and the reference genome of y59 only occurred on genes HD2 and PR1/2, preliminarily confirming that the mating type of the y59 strain was A₁B₂ and not A₁B₁. Based on the genetic evidence and the more reliable molecular evidence, the results reveal that the mating system of G. frondosa is tetrapolar. This study has important implications for the genetics and hybrid breeding of G. frondosa. Full article

Periodic fever syndromes include autoinflammatory disorders (AID) that involve innate immunity. These disorders are characterized by recurrent fevers and aberrant multi-organ inflammation, without any involvement of T or B cells or the presence of autoantibodies. A complex genetic architecture has been recognized for many AID. However, this complexity has only been partially uncovered for familial Mediterranean fever and other conditions that have a classical monogenic origin and Mendelian transmission. Several gene panels are currently available for molecular diagnosis in patients suspected of having AID. However, even when an extensive number of genes (up to 50–100) are tested in a cohort of clinically selected patients, the diagnostic yield of AID ranges between 15% and 25%, depending on the clinical criteria used for patient selection. In the remaining 75–85% of cases, it is conceivable that the causative gene or genes responsible for a specific condition are still elusive. In these cases, the disease could be explained by variants, either recessive or dominant, that have a major effect on unknown genes, or by the cumulative impact of different variants in more than one gene, each with minor additive effects. In this study, we focused our attention on five familial cases of AID presenting with classical autosomal dominant transmission. To identify the probable monogenic cause, we performed exome sequencing. Through prioritization, filtering, and segregation analysis, we identified a few variants for each family. Subsequent bioinformatics evaluation and pathway analysis helped to narrow down the best candidate genes for each family to FCRL6, PKN1, STAB1, PTDGR, and VCAM1. Future studies on larger cohorts of familial cases will help confirm the pathogenic role of these genes in the pathogenesis of these complex disorders. Full article

Congenital hypogonadotropic hypogonadism (cHH)/Kallmann syndrome (KS) is a rare genetic disorder with variable penetrance and a complex inheritance pattern. Consequently, it does not always follow Mendelian laws. More recently, digenic and oligogenic transmission has been recognized in 1.5–15% of cases. We report the results of a clinical and genetic investigation of five unrelated patients with cHH/KS analyzed using a customized gene panel. Patients were diagnosed according to the clinical, hormonal, and radiological criteria of the European Consensus Statement. DNA was analyzed using next-generation sequencing with a customized panel that included 31 genes. When available, first-degree relatives of the probands were also analyzed to assess genotype–phenotype segregation. The consequences of the identified variants on gene function were evaluated by analyzing the conservation of amino acids across species and by using molecular modeling. We found one new pathogenic variant of the CHD7 gene (c.576T>A, p.Tyr1928) and three new variants of unknown significance (VUSs) in IL17RD (c.960G>A, p.Met320Ile), FGF17 (c.208G>A, p.Gly70Arg), and DUSP6 (c.434T>G, p.Leu145Arg). All were present in the heterozygous state. Previously reported heterozygous variants were also found in the PROK2 (c.163del, p.Ile55*), CHD7 (c.c.2750C>T, p.Thr917Met and c.7891C>T, p.Arg2631*), FLRT3 (c.1106C>T, p.Ala369Val), and CCDC103 (c.461A>C, p.His154Pro) genes. Molecular modeling, molecular dynamics, and conservation analyses were performed on three out of the nine variants identified in our patients, namely, FGF17 (p.Gly70Arg), DUSP6 (p.Leu145Arg), and CHD7 p.(Thr917Met). Except for DUSP6, where the L145R variant was shown to disrupt the interaction between β6 and β3, needed for extracellular signal-regulated kinase 2 (ERK2) binding and recognition, no significant changes were identified between the wild-types and mutants of the other proteins. We found a new pathogenic variant of the CHD7 gene. The molecular modeling results suggest that the VUS of the DUSP6 (c.434T>G, p.Leu145Arg) gene may play a role in the pathogenesis of cHH. However, our analysis indicates that it is unlikely that the VUSs for the IL17RD (c.960G>A, p.Met320Ile) and FGF17 (c.208G>A, p.Gly70Arg) genes are involved in the pathogenesis of cHH. Functional studies are needed to confirm this hypothesis. Full article

The great diversity of color patterns observed among amphibians is largely explained by the differentiation of relatively few pigment cell types during development. Mexican axolotls present a variety of color phenotypes that span the continuum from leucistic to highly melanistic. The melanoid axolotl is a Mendelian variant characterized by large numbers of melanophores, proportionally fewer xanthophores, and no iridophores. Early studies of melanoid were influential in developing the single-origin hypothesis of pigment cell development, wherein it has been proposed that all three pigment cell types derive from a common progenitor cell, with pigment metabolites playing potential roles in directing the development of organelles that define different pigment cell types. Specifically, these studies identified xanthine dehydrogenase (XDH) activity as a mechanism for the permissive differentiation of melanophores at the expense of xanthophores and iridophores. We used bulked segregant RNA-Seq to screen the axolotl genome for melanoid candidate genes and identify the associated locus. Dissimilar frequencies of single-nucleotide polymorphisms were identified between pooled RNA samples of wild-type and melanoid siblings for a region on chromosome 14q. This region contains gephyrin (Gphn), an enzyme that catalyzes the synthesis of the molybdenum cofactor that is required for XDH activity, and leukocyte tyrosine kinase (Ltk), a cell surface signaling receptor that is required for iridophore differentiation in zebrafish. Wild-type Ltk crispants present similar pigment phenotypes to melanoid, strongly implicating Ltk as the melanoid locus. In concert with recent findings in zebrafish, our results support the idea of direct fate specification of pigment cells and, more generally, the single-origin hypothesis of pigment cell development. Full article

Background: Inherited isolated nail clubbing is a very rare Mendelian condition in humans, characterized by enlargement of the terminal segments of fingers and toes with thickened nails. Mutations in two genes have been reported to cause isolated nail clubbing in humans, which are the SLCO2A1 gene and the HPGD gene. Objectives: An extended Pakistani family having two affected siblings born of unaffected consanguineous union was included in the study. Predominant isolated congenital nail clubbing (ICNC) without any other systemic abnormalities was observed, which we aimed to characterize at clinico-genetic level. Methods: Whole exome coupled with Sanger sequencing were employed to uncover the sequence variant as a cause of the disease. Furthermore, protein modeling was carried out to reveal the predicted possible effect of the mutation at the protein level. Results: Whole exome sequencing data analysis revealed a novel biallelic sequence variant (c.155T>A; p.Phe52Tyr) in the SLCO2A1 gene. Further, Sanger sequencing analysis validated and confirmed the segregation of the novel variant in the entire family. Subsequently, protein modeling of the wild-type and mutated SLCO2A1 revealed broad-scale change, which might compromise the proteins’ secondary structure and function. Conclusion: The present study adds another mutation to the SLCO2A1-related pathophysiology. The involvement of SLCO2A1 in the pathogenesis of ICNC may open exciting perceptions of this gene in nail development/morphogenesis. Full article