Search Results (34)

Familial dysbetalipoproteinemia (FD) is a prevalent and highly atherogenic hyperlipoproteinemia associated with the ε2/ε2 APOE genotype or rare APOE variants. The contributions of additional genetic and clinical factors to the FD phenotype remain unclear. We investigated these factors in both autosomal recessive and autosomal dominant forms of FD. Targeted (n = 4666) and exome (n = 194) sequencing were used to identify the ε2/ε2 APOE genotype or rare FD-causative APOE variants. Twenty-four lipid-related genes and forty variants included in a polygenic risk score for hypertriglyceridemia (HTG) were analyzed. FD was defined by the presence of FD variants and triglycerides (TG) ≥ 1.5 mmol/L (main study group). The comparison group consisted of patients with FD variants but TG < 1.5 mmol/L. Univariable and multivariable regression analyses were performed. A total of 71 unrelated subjects were identified (45.1% male, median age 50 years). FD was diagnosed in 52 patients, while 19 had FD variants only. Age (p = 0.019), elevated polygenic risk for HTG (p = 0.001), and the presence of metabolic syndrome components (p = 0.014) were independently associated with the FD phenotype. TG levels were significantly associated with polygenic burden (0.05 mmol/L per percentile), the presence of additional rare lipid-related variants (7.0 mmol/L), and glucose metabolism disorders (3.62 mmol/L), together explaining 30% of TG variance in cross-validated model. These results highlight the interplay of genetic and metabolic factors in FD development and support the integration of HTG genetic risk scores and metabolic control into personalized FD management. Full article

Background: The regulation of oil and protein contents in cottonseed is governed by a complex genetic network. Gaining insight into the mechanisms controlling these traits is necessary for dissecting the formation patterns of cottonseed quality. Method: In this study, Xinluzhong 37 (P₁) and Xinluzhong 51 (P₂) were selected as parental lines for two reciprocal crosses: P₁ × P₂ (F₁) and its reciprocal P₂ × P₁ (F₁′). Each F1 was selfed and backcrossed to both parents to generate the F₂ (F₂′), B₁ (B₁′), and B₂ (B₂′) generations. To assess nutritional traits in hairy (non-delinted) and lint-free (delinted) seeds, two indicators, oil content and protein content, were measured in both seed types. Joint segregation analysis was employed to analyze the inheritance of these traits, based on a major gene plus polygene model. Results: In the orthogonal crosses, the CVs for the four nutritional traits ranged at 2.710–7.879%, 4.086–11.070%, 2.724–6.727%, and 3.717–9.602%. In the reciprocal crosses, CVs ranged at 2.710–8.053%, 4.086–9.572%, 2.724–6.376%, and 3.717–8.845%. All traits exhibited normal or skewed-normal distributions. For oil content in undelinted/delinted seeds, polygenic heritabilities in the orthogonal cross were 0.64/0.52, and 0.40/0.36 in the reciprocal cross. For protein content, major-gene heritabilities in the orthogonal cross were 0.79 (undelinted) and 0.78 (delinted), while those in the reciprocal cross were both 0.62. Conclusions: Oil and protein contents in cottonseeds are quantitative traits. In both orthogonal and reciprocal crosses, oil content is controlled by multiple genes and is shaped by additive, dominance, and epistatic effects. Protein content, in contrast, is largely controlled by two major genes along with minor genes. In the P₁ × P₂ combination, major genes act through additive, dominance, and epistatic effects, while in the P₂ × P₁ combination, their effects are additive only. In both combinations, minor genes contribute through additive and dominance effects. In summary, the oil content in cottonseed is mainly regulated by polygenes, whereas the protein content is primarily determined by major genes. These genetic features in both linted, and lint-free seeds may offer a theoretical foundation for molecular breeding aimed at improving cottonseed oil and protein quality. Full article

Brassica crops, cultivated as vegetables, oilseeds, and forages, are vital economic resources in agricultural production. However, black rot caused by Xanthomonas campestris pv. campestris (Xcc) poses a significant threat to the production of these crops. This study aimed to enhance the resistance resource pool for Brassica crops by evaluating 29 inbred lines and 52 commercial cultivars of B. rapa through an inoculation test. Among these, 11 inbred lines, such as ‘E5’ and ‘LW’, and 8 commercial cultivars, such as ‘QX’ and ‘SY’, demonstrated high resistance. We constructed a genetic segregating population (P₁, P₂, F₁, F₂) using the highly resistant line ‘E5’ and the highly susceptible line ‘E4’ as parents. Utilizing a major gene plus polygenic mixed inheritance model for genetic analysis, our findings indicate that the resistance to black rot in ‘E5’ is governed by a pair of additive-dominant polygenes, and the main gene heritability is 93.43%. Furthermore, transmission electron microscopy examination revealed numerous autophagic structures in the xylem parenchyma cells of the highly resistant line ‘E5’, while the highly susceptible line exhibited cell necrosis, indicating that the resistant material might protect mesophyll cells and adjacent structures through programmed cell death. This research contributes novel genetic materials for breeding disease-resistant varieties, enhances our understanding of Xcc invasion mechanisms and host defense traits, and establishes a theoretical framework for the effective prevention and control of these diseases. Full article

Studying fruit genetic trends, heterosis, and growth traits in pear hybrid progeny provides the foundation for variety breeding. The aim of this research is to reveal the trait performance of the hybrid progeny of Chinese white pear and Western pear and provide a theoretical basis for other breeders to predict the trait performance of their hybrid progeny when selecting Eastern pear and Western pear as parents. Our research team constructed a ‘Yuluxiang’ × ‘Xianghongli’ interspecific hybrid population in 2015, and in 2023, we conducted a two-year investigation of 16 traits in 140 hybrid progeny, including 11 fruit traits and 5 growth traits, and analyzed and compared the genetic variation and heterosis of traits, as well as the correlation between various traits. The results showed that the hybrid progeny was widely segregated for single fruit weight (FW), soluble solid (SS) content, and titratable acid (TA) content and conformed to a normal distribution, with quantitative genetic traits under polygenic control. The highest two-year coefficients of variation for TA were 54.42% in 2023 and 39.17% in 2024. A genetic trend of decreasing FW was observed, which was greatly influenced by the male sex. The ratio of soft soluble flesh to crispy flesh was 1:1, and the gene controlling this trait may be a quality trait controlled by a single gene. The traits that showed transgressive heterosis for two years included fruit longitudinal diameter (FLoD), fruit shape index (FSI), and TA, and those that showed negative heterosis included FW, SS, leaf longitudinal diameter (LLoD), and leaf lateral diameter (LLaD). Correlation analysis indicated that the progeny of crosses in this combination, which had red fruit skin, may also present red early flowering color (EFC) and young leaf color (YLC), reddish brown annual branch color (ABC), and lower FSI, fruit stalk length (FSL), LLaD, and TA. Thus, at the seedling stage, individuals with red-colored fruit may be screened by observing the color of young leaves and young stems and the lateral diameter of the leaves. Principal component analysis showed that among the 16 traits included in six principal components, peel color (PC), FLoD, 2024SS, fruit tape (FT), and FSI were the main factors causing differences in fruit phenotypes. This study systematically elucidated the genetic trends of agronomic traits in pears and will provide a theoretical basis for the selection of parents and early selection of hybrid progeny in pear hybrid breeding. Full article

Assessing the nutritional quality of silage maize (Zea mays L.) hinges largely on its oil content, a complex quantitative trait influenced by multiple genes. Mining candidate genes within oil content-related quantitative trait loci (QTLs) can provide genetic resources and a theoretical foundation for cultivating high-oil silage maize varieties. This study employed 274 doubled haploid (DH) lines derived from the parental lines BY4944 and DNF34-2 to perform main gene plus polygene mixed genetic analysis and complex interval mapping (CIM), with the goal of pinpointing oil content-related QTLs and genes distributed across the Z. mays L. genome. Leveraging 5400 single nucleotide polymorphism (SNPs), a high-resolution silage maize genetic linkage map covering 3864.51 cM was constructed with an average interval between markers of 0.74 cM. Analysis of the map revealed 13 oil content-related QTLs. The most significant large-effect QTL (qOIL-1-1), located on chromosome 1 within the region spanning 240.93 Mb to 256.57 Mb, exhibited a logarithm of odds (LOD) score of 3.34 and explained 5.06% of oil content-related phenotypic variation. Within these QTLs, 617 genes were annotated. Through transcriptome analysis combined with quantitative real-time polymerase chain reaction (RT-qPCR), five candidate genes potentially associated with oil content were predicted and subsequently validated within these genetic loci. This research underscores the potential of identifying candidate genes to enhance breeding efforts aimed at augmenting oil content, thereby advancing animal husbandry practices. Full article

Objective: Yield traits are crucial for cotton breeding. Analyzing the yield traits of terrestrial cotton and exploring their genetic mechanisms through a primary gene + multigene hybrid genetic model provide a theoretical basis for selecting high-quality cotton varieties and identifying associated molecular markers. Methods: Completing the construction of the six populations (P1, P2, F1, F2, B1, B2) using Xinluzhong 37 as the female parent and Xinluzhong 51 as the male parent. Six yield traits were assessed: single boll weight, boll number per plant, lint yield per plant, seed cotton per plant, lint percentage, and seed index. Data were tested for normal distribution, and the inheritance patterns of yield traits were analyzed through combined primary gene + polygenic analysis. Results: The coefficients of variation for the six yield traits ranged from 37.368% to 53.905%, 33.335% to 58.524%, 34.132% to 57.686%, 8.721% to 12.808%, 1.842% to 6.283%, and 8.783% to 12.580%, respectively. These traits displayed either normal or skewed normal distributions. The optimal genetic model for single boll weight and seed index was PG-ADI, while MX2-ADI-AD best fit the traits of boll number per plant and lint percentage. For lint yield per plant and seed cotton per plant, the 2MG-ADI model was optimal. The polygenic heritability for single boll weight was 29.58%; for boll number per plant, main gene heritability was 25.19%, with 0% heritability for polygenes; for lint yield per plant, the heritability of the main gene was 23.47%. For seed cotton per plant, the heritability of main genes was 15.38%, with lint percentage showing 63.25% heritability for main genes and 0.08% for polygenes, and seed index with 45.93% heritability due to polygenes. Overall, single boll weight and seed index were predominantly polygenic, while boll number per plant and lint percentage were largely controlled by main gene inheritance. The inheritance of lint yield per plant and seed cotton per plant was also primarily governed by main genes. Full article

Pregnancy-associated glycoproteins (PAGs) are a polygenic family with many scattered genes and pseudogenes resulting from the duplication or fusion of a pseudogene with expression beginning in the trophoblast during the peri-implantation period and continuing in the trophectoderm. In this study, single-nucleotide polymorphism (SNP) and insertion/deletion (InDels) in the open reading frame (nine exons) of crossbreed pigs are reported for the first time. Novel SNPs/InDels were researched using genomic DNA templates isolated from the leukocytes of crossbreed pigs (N = 25), which were amplified, gel-out-purified, and sequenced. Sixteen SNPs and one InDel (g.6961_6966 Ins TGCCAA) were identified in the crossbreed pigs. In silico analysis revealed that among 16 SNPs, only 10 SNPs cause amino acid (aa) substitutions, and InDel codes asparagine (N²⁹⁸) and alanine (A²⁹⁹). The results provide a novel broad-based database (main pattern) that will be critical for future research into the possible correlations between the SNP genotypes of the pPAG2-L subfamily in pigs of various breeds whose reproductive traits are known. Full article

Soybean being a major cash crop provides half of the vegetable oil and a quarter of the plant proteins to the global population. Seed size traits are the most important agronomic traits determining the soybean yield. These are complex traits governed by polygenes with low heritability as well as are highly influenced by the environment as well as by genotype x environment interactions. Although, extensive efforts have been made to unravel the genetic basis and molecular mechanism of seed size in soybean. But most of these efforts were majorly limited to QTL identification, and only a few genes for seed size were isolated and their molecular mechanism was elucidated. Hence, elucidating the detailed molecular regulatory networks controlling seed size in soybeans has been an important area of research in soybeans from the past decades. This paper describes the current progress of genetic architecture, molecular mechanisms, and regulatory networks for seed sizes of soybeans. Additionally, the main problems and bottlenecks/challenges soybean researchers currently face in seed size research are also discussed. This review summarizes the comprehensive and systematic information to the soybean researchers regarding the molecular understanding of seed size in soybeans and will help future research work on seed size in soybeans. Full article

Petioles of non-heading Chinese cabbage are not only an important edible part but also a conduit for nutrient transport, holding significant agricultural and research value. In this study, we conducted a comprehensive genetic analysis of petiole-related traits using a segregating population. Modern quantitative genetic approaches were applied to investigate the genetic regulation of petiole thickness. The results indicated that petiole thickness is a quantitative trait, and the identified genetic model was consistent with two pairs of additive-dominant main genes and additive-dominant polygenes (2MG-AD). BSA-seq analysis identified a major effect of QTL controlling petiole thickness on chromosome A09: 42.08–45.09 Mb, spanning 3.01 Mb, designated as QTL-BrLH9. Utilizing InDel markers, the interval was narrowed down to 51 kb, encompassing 14 genes with annotations for 10 of them. Within the interval, four mutated genes were detected. Combined with gene annotation, protein sequence analysis, and homology alignment, it was found that BraA09g063520.3C’s homologous gene SMXL6 in Arabidopsis (Arabidopsis thaliana (L.) Heynh) is an inhibitor of the coding and synthesis of the strigolactone pathway. Strigolactone (SLs) plays an important role in plant growth and development. The cloning results showed that multiple frameshift mutations and non-synonymous mutations occurred on the exon. The qPCR results showed that the expression of the gene was significantly different between the two parents at the adult stage, so it was speculated that it would lead to changes in petiole thickness. BraA09g063520.3C was predicted as the final candidate gene. Full article

Maize is the crop which is most commonly exposed to toxigenic fungi that produce many toxins that are harmful to humans and animals alike. Preharvest grain yield loss, preharvest toxin contamination (at harvest), and storage loss are estimated to be between 220 and 265 million metric tons. In the past ten years, the preharvest mycotoxin damage was stable or increased mainly in aflatoxin and fumonisins. The presence of multiple toxins is characteristic. The few breeding programs concentrate on one of the three main toxigenic fungi. About 90% of the experiments except AFB1 rarely test toxin contamination. As disease resistance and resistance to toxin contamination often differ in regard to F. graminearum, F. verticillioides, and A. flavus and their toxins, it is not possible to make a food safety evaluation according to symptom severity alone. The inheritance of the resistance is polygenic, often mixed with epistatic and additive effects, but only a minor part of their phenotypic variation can be explained. All tests are made by a single inoculum (pure isolate or mixture). Genotype ranking differs between isolates and according to aggressiveness level; therefore, the reliability of such resistance data is often problematic. Silk channel inoculation often causes lower ear rot severity than we find in kernel resistance tests. These explain the slow progress and raise skepticism towards resistance breeding. On the other hand, during genetic research, several effective putative resistance genes were identified, and some overlapped with known QTLs. QTLs were identified as securing specific or general resistance to different toxicogenic species. Hybrids were identified with good disease and toxin resistance to the three toxigenic species. Resistance and toxin differences were often tenfold or higher, allowing for the introduction of the resistance and resistance to toxin accumulation tests in the variety testing and the evaluation of the food safety risks of the hybrids within 2–3 years. Beyond this, resistance breeding programs and genetic investigations (QTL-analyses, GWAM tests, etc.) can be improved. All other research may use it with success, where artificial inoculation is necessary. The multi-toxin data reveal more toxins than we can treat now. Their control is not solved. As limits for nonregulated toxins can be introduced, or the existing regulations can be made to be stricter, the research should start. We should mention that a higher resistance to F. verticillioides and A. flavus can be very useful to balance the detrimental effect of hotter and dryer seasons on aflatoxin and fumonisin contamination. This is a new aspect to secure food and feed safety under otherwise damaging climatic conditions. The more resistant hybrids are to the three main agents, the more likely we are to reduce the toxin losses mentioned by about 50% or higher. Full article

Brugada syndrome (BrS) is an inherited cardiac channelopathy first diagnosed in 1992 but still considered a challenging disease in terms of diagnosis, arrhythmia risk prediction, pathophysiology and management. Despite about 20% of individuals carrying pathogenic variants in the SCN5A gene, the identification of a polygenic origin for BrS and the potential role of common genetic variants provide the basis for applying polygenic risk scores for individual risk prediction. The pathophysiological mechanisms are still unclear, and the initial thinking of this syndrome as a primary electrical disease is evolving towards a partly structural disease. This review focuses on the main scientific advancements in the identification of biomarkers for diagnosis, risk stratification, pathophysiology and therapy of BrS. A comprehensive model that integrates clinical and genetic factors, comorbidities, age and gender, and perhaps environmental influences may provide the opportunity to enhance patients’ quality of life and improve the therapeutic approach. Full article

In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction. Full article

Inflammatory bowel disease (IBD) is an illness with increasing prevalence, particularly in emerging countries, which can have a substantial impact on the quality of life of the patient. The illness is rather heterogeneous with different evolution among patients. A machine learning approach is followed in this paper to identify potential genes that are related to IBD. This is done by following a Monte Carlo simulation approach. In total, 23 different machine learning techniques were tested (in addition to a base level obtained using artificial neural networks). The best model identified 74 genes selected by the algorithm as being potentially involved in IBD. IBD seems to be a polygenic illness, in which environmental factors might play an important role. Following a machine learning approach, it was possible to obtain a classification accuracy of 84.2% differentiating between patients with IBD and control cases in a large cohort of 2490 total cases. The sensitivity and specificity of the model were 82.6% and 84.4%, respectively. It was also possible to distinguish between the two main types of IBD: (1) Crohn’s disease and (2) ulcerative colitis. Full article

Psoriasis is a systemic inflammatory disease that associates with multiple comorbidities. It involves complex interactions between environmental factors and polygenic predisposition. The IL-17 family is one of the main actors in the pathogenesis of psoriasis. Secondary nonresponse is common, especially during the long-term use of TNF-α inhibitors, but it is not uncommon even for newer biologics, such as IL-17 inhibitors. Identification of clinically useful biomarkers of treatment efficacy and safety would enable optimal treatment selection, improve patient quality of life and outcome, and reduce healthcare costs. To our knowledge, this is the first study to evaluate the relationship between genetic polymorphism of IL-17F (rs763780) and IL-17RA (rs4819554) and response to biological treatment and other clinical data in bio-naive and secondary non-responders psoriasis patients in Romania and Southeastern Europe. We performed a prospective, longitudinal, analytical cohort study of 81 patients diagnosed with moderate-to-severe chronic plaque psoriasis who received biological treatments for the first time. Of the 79 patients treated with TNF-α inhibitors, 44 experienced secondary nonresponse. All patients were genotyped for the two SNPs in IL-17F and IL-17RA genes. The rs763780 polymorphism in the IL-17F gene could be an attractive candidate biomarker for predicting which patients will respond to anti-TNF-α therapies. Another emergent association of rs4819554 in IL-17RA with the risk of nail psoriasis and a higher BMI in moderate-to-severe plaque psoriasis patients is described. Full article

Powdery mildew (PM) of wheat caused by Blumeria graminis f. sp. tritici is among the most important wheat diseases, causing significant yield and quality losses in many countries worldwide. Considerable progress has been made in resistance breeding to mitigate powdery mildew. Genetic host resistance employs either race-specific (qualitative) resistance, race-non-specific (quantitative), or a combination of both. Over recent decades, efforts to identify host resistance traits to powdery mildew have led to the discovery of over 240 genes and quantitative trait loci (QTLs) across all 21 wheat chromosomes. Sources of PM resistance in wheat include landraces, synthetic, cultivated, and wild species. The resistance identified in various genetic resources is transferred to the elite genetic background of a well-adapted cultivar with minimum linkage drag using advanced breeding and selection approaches. In this effort, wheat landraces have emerged as an important source of allelic and genetic diversity, which is highly valuable for developing new PM-resistant cultivars. However, most landraces have not been characterized for PM resistance, limiting their use in breeding programs. PM resistance is a polygenic trait; therefore, the degree of such resistance is mostly influenced by environmental conditions. Another challenge in breeding for PM resistance has been the lack of consistent disease pressure in multi-environment trials, which compromises phenotypic selection efficiency. It is therefore imperative to complement conventional breeding technologies with molecular breeding to improve selection efficiency. High-throughput genotyping techniques, based on chip array or sequencing, have increased the capacity to identify the genetic basis of PM resistance. However, developing PM-resistant cultivars is still challenging, and there is a need to harness the potential of new approaches to accelerate breeding progress. The main objective of this review is to describe the status of breeding for powdery mildew resistance, as well as the latest discoveries that offer novel ways to achieve durable PM resistance. Major topics discussed in the review include the genetic basis of PM resistance in wheat, available genetic resources for race-specific and adult-plant resistance to PM, important gene banks, and conventional and complimentary molecular breeding approaches, with an emphasis on marker-assisted selection (MAS). Full article