Search

Abstract [Objective] Pepper is the largest vegetable crop planted in China. With the land salinization becoming more and more serious, it is urgent to accelerate the functional study of key genes related to pepper salt tolerance. It is of great significance to strengthen the study of mechanisms underlying salt tolerance in peper to promote sustainable development of the pepper industry. [Methods] In the early stage of research, CaNAC36, a NAC transcription factor family gene related to salt stress response in peppers, was discovered. Based on this, the full-length gDNA and cDNA sequences of CaNAC36 were cloned using salttolerant pepper accession PI201224 and salt-sensitive pepper accession PI438643. The expression of CaNAC36 and its interacting genes in different tissues under salt stress was quantitatively analyzed by fluorescence, and the potential relationship between CaNAC36 and its interacting genes was further explored by bioinformatics analysis. [Results] The gDNA and cDNA sequence homology of CaNAC36 in salt-tolerant and salt-sensitive materials were 99.86% and 100%, respectively. CaNAC36 showed an up-expression in roots and stems in the salt-tolerant pepper, and a down-expression in roots and leaves in the salt-sensitive peper. Throgh analyzing the annotation information of 48 genes that may interact with CaNAC36, it was found that 14 genes were belonging to transmembrane proteins, transporter proteins, water porins, chloride channel proteins, detoxifying proteins, and other genes, which may have functional interaction with CaNAC36. Further analysis revealed that PI201224 and PI438643 exhibited significant differences in the expression of five related genes, inclding Capana08g002748, Capana00g004514, Capana09g000275, Capana07g001450, Capana02g001031, at different time points and tissues under salt stress. Meanwhile, the promoter region of CaNAC36 and five associated genes was found to contain a large number of stressrelated cis-acting elements. [Conclusion] CaNAC36 was an important regulatory gene in pepper in response to salt stress, and might interact with other genes to improve salt tolerance.

Abstract Background Statistical epistasis, or “gene–gene interaction” in genetic association studies, means the nonadditive effects between the polymorphic sites on two different genes affecting the same phenotype. In the genetic association analysis of complex traits, nevertheless, the researchers haven’t found enough clues of statistical epistasis so far. Methods We developed a statistical model where the statistical epistasis was presented as an extra linkage disequilibrium between the polymorphic sites of different risk genes. The power of statistical test for identifying the gene–gene interaction was calculated and then compared in different hypothesis scenarios. Results Our results show the statistical power increases with the increasing of interaction coefficient, relative risk, and linkage disequilibrium with genetic markers. However, the power of interaction discovery is much lower than that of regular single-site association test. When rigorous criteria were employed in statistical tests, the identification of gene–gene interaction became a very difficult task. Since the criterion of significance was given to be p-value ≤ 5.0 × 10–8, the same as that of many genome-wide association studies, there is little chance to identify the gene–gene interaction in all kind of circumstances. Conclusions The lack of epistasis tends to be an inevitable result caused by the statistical principles of methods in the genetic association studies and therefore is the inherent characteristic of the research itself.

Abstract The genes of Wnt/β-catenin pathway may have potential roles in fat accumulation of Non-traumatic osteonecrosis of the femoral head (ONFH), but the effects of their variants in the pathway on ONFH development have been remained unclear. To explore the potential roles of the variants in the development of ONFH, we completed the investigation of the paired interactions as well as their related biological functions of 17 variants of GSK3β, LRP5, and FRP4 genes etc. in the pathway. The genotyping of the 17 variants were finished by MASS ARRAY PLATFORM in a 560 ONFH case–control system. The association of variants interactions with ONFH risk and clinical traits was evaluated by logistic regression analysis etc. and bioinformatics technology. The results showed that the genotype, allele frequency, and genetic models of Gsk3β rs334558 (G/A), SFRP4 rs1052981 (A/G), and LRP5 rs312778 (T/C) were significantly associated with the increased and decreased ONFH risk and clinical traits, respectively (P

Flax is a crucial fiber crop that exhibits excellent textile properties and serves as a model plant for investigating phloem fiber development. The regulation of multiple genes significantly influences fiber development, notably involving NAC (NAM, ATAF1/2, CUC2) transcription factors in forming the fiber secondary cell wall (SCW). Overexpression of LuNAC61 in flax resulted in sparse top meristematic zone leaves and significantly reduced stem cellulose content. Scanning electron microscopy and staining observations revealed a significant reduction in fiber bundles. β-Glucuronidase (GUS) staining analysis demonstrated high activity of the LuNAC61 promoter in the bast fibers of the flax stem. Additionally, several members of the LuPLATZ and LuCesA families exhibited significant coexpression with LuNAC61. Subcellular localization indicated the presence of LuPLATZ24 protein in the nucleus and cytoplasm, LuNAC61 protein exclusively in the nucleus, and LuCesA10 in the nucleus and endoplasmic reticulum. LuPLATZ24 positively regulates LuNAC61, whereas LuNAC61 negatively affects LuCesA10, suggesting the involvement of a metabolic network in regulating flax fiber development. In conclusion, this study provides a critical opportunity for a comprehensive and in-depth analysis of the mechanisms governing flax fiber development and the potential use of biotechnology to enhance flax fiber yield.

Abstract Background PRAME constitutes one of the largest multi-copy gene families in Eutherians, encoding cancer-testis antigens (CTAs) with leucine-rich repeats (LRR) domains, highly expressed in cancer cells and gametogenic germ cells. This study aims to elucidate genetic interactions between two members, Pramex1 and Pramel1, in the mouse Prame family during gametogenesis using a gene knockout approach. Result Single-gene knockout (sKO) of either Pramex1 or Pramel1 resulted in approximately 7% of abnormal seminiferous tubules, characterized by a Sertoli-cell only (SCO) phenotype, impacting sperm count and fecundity significantly. Remarkably, sKO female mice displayed normal reproductive functions. In contrast, Pramex1/Pramel1 double knockout (dKO) mice exhibited reduced fecundity in both sexes. In dKO females, ovarian primary follicle count decreased by 50% compared to sKO and WT mice, correlating with a 50% fecundity decrease. This suggested compensatory roles during oogenesis in Pramex1 or Pramel1 sKO females. Conversely, dKO males showed an 18% frequency of SCO tubules, increased apoptotic germ cells, and decreased undifferentiated spermatogonia compared to sKO and WT testes. Western blot analysis with PRAMEX1- or PRAMEL1-specific antibodies on sKO testes revealed compensatory upregulation of each protein (30–50%) in response to the other gene’s deletion. Double KO males exhibited more severe defects in sperm count and litter size, surpassing Pramex1 and Pramel1 sKO accumulative effects, indicating a synergistic enhancement interaction during spermatogenesis. Additional experiments administering trans-retinoic acid (RA) and its inhibitor (WIN18,446) in sKO, dKO, and WT mice suggested that PRAMEX1 and PRAMEL1 synergistically repress the RA signaling pathway during spermatogenesis. Conclusion Data from sKO and dKO mice unveil a synergistic interaction via the RA signaling pathway between Pramex1 and Pramel1 genes during gametogenesis. This discovery sets the stage for investigating interactions among other members within the Prame family, advancing our understanding of multi-copy gene families involved in germ cell formation and function.

Background: Statistical epistasis, or "gene–gene interaction" in genetic association studies, means the nonadditive effects between the polymorphic sites on two different genes affecting the same phenotype. In the genetic association analysis of complex traits, nevertheless, the researchers haven't found enough clues of statistical epistasis so far. Methods: We developed a statistical model where the statistical epistasis was presented as an extra linkage disequilibrium between the polymorphic sites of different risk genes. The power of statistical test for identifying the gene–gene interaction was calculated and then compared in different hypothesis scenarios. Results: Our results show the statistical power increases with the increasing of interaction coefficient, relative risk, and linkage disequilibrium with genetic markers. However, the power of interaction discovery is much lower than that of regular single-site association test. When rigorous criteria were employed in statistical tests, the identification of gene–gene interaction became a very difficult task. Since the criterion of significance was given to be p-value ≤ 5.0 × 10–8, the same as that of many genome-wide association studies, there is little chance to identify the gene–gene interaction in all kind of circumstances. Conclusions: The lack of epistasis tends to be an inevitable result caused by the statistical principles of methods in the genetic association studies and therefore is the inherent characteristic of the research itself. [ABSTRACT FROM AUTHOR]

The genes of Wnt/β-catenin pathway may have potential roles in fat accumulation of Non-traumatic osteonecrosis of the femoral head (ONFH), but the effects of their variants in the pathway on ONFH development have been remained unclear. To explore the potential roles of the variants in the development of ONFH, we completed the investigation of the paired interactions as well as their related biological functions of 17 variants of GSK3β, LRP5, and FRP4 genes etc. in the pathway. The genotyping of the 17 variants were finished by MASS ARRAY PLATFORM in a 560 ONFH case–control system. The association of variants interactions with ONFH risk and clinical traits was evaluated by logistic regression analysis etc. and bioinformatics technology. The results showed that the genotype, allele frequency, and genetic models of Gsk3β rs334558 (G/A), SFRP4 rs1052981 (A/G), and LRP5 rs312778 (T/C) were significantly associated with the increased and decreased ONFH risk and clinical traits, respectively (P < 0.001–0.0002). Particularly, the paired interactions of six variants as well as eight variants also showed statistically increased and decreased ONFH risk, bilateral hip lesions risk and stage IV risk of ONFH, respectively (P < 0.044–0.004). Our results not only at the first time simultaneously showed exact serum lipid disorder and abnormal platelet function of ONFH in the same study system with the 17 variants polymorphisms of Wnt/β-catenin pathway but also shed light on the variants closely intervening the lipid disorder and abnormal coagulation of ONFH. [ABSTRACT FROM AUTHOR]

Background: PRAME constitutes one of the largest multi-copy gene families in Eutherians, encoding cancer-testis antigens (CTAs) with leucine-rich repeats (LRR) domains, highly expressed in cancer cells and gametogenic germ cells. This study aims to elucidate genetic interactions between two members, Pramex1 and Pramel1, in the mouse Prame family during gametogenesis using a gene knockout approach. Result: Single-gene knockout (sKO) of either Pramex1 or Pramel1 resulted in approximately 7% of abnormal seminiferous tubules, characterized by a Sertoli-cell only (SCO) phenotype, impacting sperm count and fecundity significantly. Remarkably, sKO female mice displayed normal reproductive functions. In contrast, Pramex1/Pramel1 double knockout (dKO) mice exhibited reduced fecundity in both sexes. In dKO females, ovarian primary follicle count decreased by 50% compared to sKO and WT mice, correlating with a 50% fecundity decrease. This suggested compensatory roles during oogenesis in Pramex1 or Pramel1 sKO females. Conversely, dKO males showed an 18% frequency of SCO tubules, increased apoptotic germ cells, and decreased undifferentiated spermatogonia compared to sKO and WT testes. Western blot analysis with PRAMEX1- or PRAMEL1-specific antibodies on sKO testes revealed compensatory upregulation of each protein (30–50%) in response to the other gene's deletion. Double KO males exhibited more severe defects in sperm count and litter size, surpassing Pramex1 and Pramel1 sKO accumulative effects, indicating a synergistic enhancement interaction during spermatogenesis. Additional experiments administering trans-retinoic acid (RA) and its inhibitor (WIN18,446) in sKO, dKO, and WT mice suggested that PRAMEX1 and PRAMEL1 synergistically repress the RA signaling pathway during spermatogenesis. Conclusion: Data from sKO and dKO mice unveil a synergistic interaction via the RA signaling pathway between Pramex1 and Pramel1 genes during gametogenesis. This discovery sets the stage for investigating interactions among other members within the Prame family, advancing our understanding of multi-copy gene families involved in germ cell formation and function. [ABSTRACT FROM AUTHOR]

Resistant starch (RS) can help prevent diabetes and decrease calorie intake and that from plants are the main source of mankind consumption. Rice is many people's staple food and that with higher RS will help health management. A significantly positive correlation exists between apparent amylose content (AAC) of rice and its RS content. In this study, 72 accessions with moderate or high AAC were selected to explore the regulatory mechanisms and physicochemical properties on different proceeding types of rice RS. RS in raw milled rice (RSm), hot cooked rice (RSc), and retrogradation rice (RSr) showed a wide variation and distinct controlling mechanisms. They were cor-egulated by Waxy (Wx), soluble starch synthase (SS) IIb and SSI. Besides that, RSm was also regulated by SSIIa and SSIVb, RSc by granule-bound starch synthase (GBSS) II and RSr by GBSSII and Pullulanase (PUL). Moreover, Wx had significant interactions with SSIIa, SSI, SSIIb and SSIVb on RSm, but only the dominant interactions with SSIIb and SSI on RSc and RSr. Wx was the key factor for the formation of RS, especially the RSc and RSr. The genes had the highest expression at 17 days after flowering and were beneficial for RS formation. The longer the chain length of starch, the higher the RS3 content. RSc and RSrwere likely to be contained in medium-size starch granules. The findings favor understanding the biosynthesis of different subtypes of RS. [ABSTRACT FROM AUTHOR]

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Abstract Objectives To assess LRP5-/6 gene polymorphisms and its association with risk of abnormal bone mass (ABM) in postmenopausal women. Methods The study recruited 166 patients with ABM (case group) and 106 patients with normal bone mass (control group) based on bone mineral density (BMD) results. Multi-factor dimensionality reduction (MDR) was used to analyze the interaction between the Low-density lipoprotein receptor-related protein 5 (LRP5) gene (rs41494349, rs2306862) and the Low-density lipoprotein receptor-related protein 6 (LRP6) gene (rs10743980, rs2302685) and the subjects’ clinical characteristics of age and menopausal years. Results (1) Logistic regression analysis showed that the subjects with the CT or TT genotype at rs2306862 had a higher risk of ABM than those with the CC genotype (OR = 2.353, 95%CI = 1.039–6.186; OR = 2.434, 95%CI = 1.071, 5.531; P 0.9, r 2 > 0.3). AC and AT haplotypes were significantly more frequently distributed in the ABM group than in the control group, indicating that subjects carrying the AC and AT haplotypes were associated with an increased risk of ABM (P

Main conclusion: Transcriptomics and methylomics were used to identify the potential effects resulting from GM rice breeding stacks, which provided scientific data for the safety assessment strategy of stacked GM crops in China. Gene interaction is one of the main concerns for stacked genetically modified crop safety. With the development of technology, the combination of omics and bioinformatics has become a useful tool to evaluate the unintended effects of genetically modified crops. In this study, transcriptomics and methylomics were used as molecular profiling techniques to identify the potential effects of stack through breeding. Stacked transgenic rice En-12 × Ec-26 was used as material, which was obtained through hybridization using parents En-12 and Ec-26, in which the foreign protein can form functional EPSPS protein by intein-mediated trans-splitting. Differentially methylated region (DMR) analysis showed that the effect of stacking breeding on methylation was less than that of genetic transformation at the methylome level. Differentially expressed gene (DEG) analysis showed that the DEGs between En-12 × Ec-26 and its parents were far fewer than those between transgenic rice and Zhonghua 11 (ZH11), and no unintended new genes were found in En-12 × Ec-26. Statistical analysis of gene expression and methylation involved in shikimic acid metabolism showed that there was no difference in gene expression, although there were 16 and 10 DMR genes between En-12 × Ec-26 and its parents (En and Ec) in methylation, respectively. The results indicated that the effect of stacking breeding on gene expression and DNA methylation was less than the effect of genetic transformation. This study provides scientific data supporting safety assessments of stacked GM crops in China. [ABSTRACT FROM AUTHOR]

Objectives: To assess LRP5-/6 gene polymorphisms and its association with risk of abnormal bone mass (ABM) in postmenopausal women. Methods: The study recruited 166 patients with ABM (case group) and 106 patients with normal bone mass (control group) based on bone mineral density (BMD) results. Multi-factor dimensionality reduction (MDR) was used to analyze the interaction between the Low-density lipoprotein receptor-related protein 5 (LRP5) gene (rs41494349, rs2306862) and the Low-density lipoprotein receptor-related protein 6 (LRP6) gene (rs10743980, rs2302685) and the subjects' clinical characteristics of age and menopausal years. Results: (1) Logistic regression analysis showed that the subjects with the CT or TT genotype at rs2306862 had a higher risk of ABM than those with the CC genotype (OR = 2.353, 95%CI = 1.039–6.186; OR = 2.434, 95%CI = 1.071, 5.531; P < 0.05). The subjects with the TC genotype at rs2302685 had a higher risk of ABM than those with the TT genotype (OR = 2.951, 95%CI = 1.030–8.457, P < 0.05). (2) When taking the three Single-nucleotide polymorphisms (SNPs) together, the accuracy was the highest with the cross-validation consistency of 10/10 (OR = 1.504, 95%CI:1.092–2.073, P < 0.05), indicating that the LRP5 rs41494349 and LRP6 rs10743980, rs2302685 were interactively associated with the risk of ABM. (3) Linkage disequilibrium (LD) results revealed that the LRP5 (rs41494349,rs2306862) were in strong LD (D′ > 0.9, r2 > 0.3). AC and AT haplotypes were significantly more frequently distributed in the ABM group than in the control group, indicating that subjects carrying the AC and AT haplotypes were associated with an increased risk of ABM (P < 0.01). (4) MDR showed that rs41494349 & rs2302685 & rs10743980 & age were the best model for ABM prediction. The risk of ABM in "high-risk combination" was 1.00 times that of "low-risk combination"(OR = 1.005, 95%CI: 1.002–1.008, P < 0.05). (5) MDR showed that there was no significant association between any of the SNPs and menopausal years and ABM susceptibility. Conclusion: These findings indicate that LRP5-rs2306862 and LRP6-rs2302685 polymorphisms and gene–gene and gene–age interactions may increase the risk of ABM in postmenopausal women. There was no significant association between any of the SNPs and menopausal years and ABM susceptibility. [ABSTRACT FROM AUTHOR]

The present study was conducted to ascertain the gene action and inheritance of yield and various yield-attributing traits and to screen the simple sequence repeat (SSR) markers for parental polymorphism in bitter gourd (Momordica charantia L.). Two contrasting parents (S-2 and Pusa Purvi) were used for hybridization. Parental polymorphism was analysed using 100 SSR markers. DNA amplicon of size around 150-250 bp in both the parents was obtained for the 10 polymorphic SSR markers. These were used to ascertain the hybridity of F1 progeny, from which the subsequent generations were developed. Generation mean analysis, ABCD scaling test and joint scaling test were performed using the observations from six generations (parent-1, parent-2, F1, F2, back cross 1 and back cross 2). The additive effect of the genes was predominant for the quantitative traits like fruit length, diameter, weight, etc. Duplicate epistasis was observed for the majority of traits. The yield per plant was positively correlated with fruit length, diameter, weight and fruit number per plant. Chi-square test revealed the monogenic inheritance of qualitative traits (fruit tubercles and ridgeness, and shape at apex), in which 'conspicuous tubercles', 'discontinuous ridgeness' and 'acute fruit shape at apex' were dominant. These results reveal the complexity and polygenic nature of the yield. The findings obtained from the present study can be used for yield improvement in the future. For this, the polymorphic SSRs identified can also be used in genetic diversity studies, DNA fingerprinting, genetic mapping, genomics analysis, etc. [ABSTRACT FROM AUTHOR]

Knowledge of productivity and genetic control of the rate of ultra-early lines development will facilitate their use in breeding of common wheat Tritium aestivum L. for high adaptive capacity. The research focused on ultra-early lines Rico (k-65588), Rimax (k-67257) (progeny of F3 Rico × ‘Max’, k-57181), Fori 1-8 line series (progeny of F4 ‘Photon’ × Rico) and Rifor 1-13 (progeny of F7-8 Rico × ‘Forlani Roberto’), as well as on the accessions ‘Photon’ (k-55696) and ‘Forlani Roberto’ (k-42641). The varieties ‘Leningradskaya 6’ (k-64900) and ‘Leningradskaya 97’ (k-62935) were used as standards in VIR, and ‘Chelyaba 2’ (k-64379) was used in Сhelyabinsk ARI. The alleles of Vrn and Ppd genes were identified by PCR using the published allele-specific primers. Responses to vernalization (30 days at 3°C) and to a short 12-hour day were determined according to the VIR guidelines. The ultra-earliness of common wheat lines is associated with the presence of dominant alleles Vrn-A1, Vrn-B1, Vrn-D1, Ppd-B1, Ppd-D1, and possibly Eps. The shortest emergence-to-heading period at two experimental locations was noted for Rico (39.9 ± 1.49 days), which is 14.8 ± 1.22 days earlier than the development of region-adapted varieties. The Rico genotype contains Vrn-A1, Vrn-B1, Vrn-D1, Ppd-B1 and Ppd-D1. In the Rimax genotype, different alleles of the Ppd-D1 and Vrn-B1 genes were found, possibly being a result of recombination processes in Rico × ‘Max’ hybrids. Under a short photoperiod (12 hours), the Rico and Rimax genes can interact in a cumulative polymeric mode, which is not the case in long-day environments. Unlike other Rifor lines, Rifor 4 and Rifor 5, as well as ‘Forlani Roberto’, have a recessive vrn-A1a allele. However, Rifor 4 and Rifor 5 do not respond to vernalization, while ‘Forlani Roberto’ is responsive to this factor. The absence of response to vernalization in Rifor 4 and Rifor 5 possessing the recessive vrn-A1a allele is possibly provided by a complex of modifier genes along with the dominant Vrn-D1 gene, which was formed during recombination in F7-8 Rico × ‘Forlani Roberto’ hybrids. Recombinants of spring common wheat, combining ultra-earliness and relatively high ear productivity, have been identified. Grain yield per 1 m2 of new ultra-early lines in some years can reach 90% of that of the ‘Leningradskaya 97’. It is expedient to use ultra-early lines as donors of high-rate development in common wheat breeding, considering genetic peculiarities of the source lines.

Lung cancer, amongst the fast growing malignant tumors, has become the leading cause of cancer death, which deserves attention. From a prevention and treatment perspective, advances in screening, diagnosis, and treatment have driven a reduction in non-small-cell lung cancer (NSCLC) incidence and improved patient outcomes. It is of benefit that the identification of key genetic markers contributes to the understanding of disease initiation and progression. In this work, information theoretical measures are proposed to determine the collaboration between genes and specific NSCLC samples. Top mutual information observes genes of high sample classification accuracy, such as STX11, S1PR1, TACC1, LRKK2, and SRPK1. In particular, diversity exists in different gender, histology, and smoking situations. Furthermore, leading synergy detects a high-accuracy combination of two ordinary individual genes, bringing a significant gain in accuracy. We note a strong synergistic effect of genes between COL1A2 and DCN, DCN and MMP2, and PDS5B and B3GNT8. Apart from that, RHOG is revealed to have quite a few functions in coordination with other genes. The results provide evidence for gene-targeted therapy as well as combined diagnosis in the context of NSCLC. Our approach can also be extended to find synergistic biomarkers associated with different diseases. [ABSTRACT FROM AUTHOR]

Global genetic networks provide additional information for the analysis of human diseases, beyond the traditional analysis that focuses on single genes or local networks. The Gaussian graphical model (GGM) is widely applied to learn genetic networks because it defines an undirected graph decoding the conditional dependence between genes. Many algorithms based on the GGM have been proposed for learning genetic network structures. Because the number of gene variables is typically far more than the number of samples collected, and a real genetic network is typically sparse, the graphical lasso implementation of GGM becomes a popular tool for inferring the conditional interdependence among genes. However, graphical lasso, although showing good performance in low dimensional data sets, is computationally expensive and inefficient or even unable to work directly on genome-wide gene expression data sets. In this study, the method of Monte Carlo Gaussian graphical model (MCGGM) was proposed to learn global genetic networks of genes. This method uses a Monte Carlo approach to sample subnetworks from genome-wide gene expression data and graphical lasso to learn the structures of the subnetworks. The learned subnetworks are then integrated to approximate a global genetic network. The proposed method was evaluated with a relatively small real data set of RNA-seq expression levels. The results indicate the proposed method shows a strong ability of decoding the interactions with high conditional dependences among genes. The method was then applied to genome-wide data sets of RNA-seq expression levels. The gene interactions with high interdependence from the estimated global networks show that most of the predicted gene-gene interactions have been reported in the literatures playing important roles in different human cancers. Also, the results validate the ability and reliability of the proposed method to identify high conditional dependences among genes in large-scale data sets. [ABSTRACT FROM AUTHOR]

Gene pathway enrichment analysis is a widely used method to analyze whether a gene set is statistically enriched on certain biological pathway network. Current gene pathway enrichment methods commonly consider local importance of genes in pathways without considering the interactions between genes. In this paper, we propose a gene pathway enrichment method (GIGSEA) based on improved TF-IDF algorithm. This method employs gene interaction data to calculate the influence of genes based on the local importance in a pathway as well as the global specificity. Computational experiment result shows that, compared with traditional gene set enrichment analysis method, our proposed method in this paper can find more specific enriched pathways related to phenotype with higher efficiency.

Global genetic networks provide additional information for the analysis of human diseases, beyond the traditional analysis that focuses on single genes or local networks. The Gaussian graphical model (GGM) is widely applied to learn genetic networks because it defines an undirected graph decoding the conditional dependence between genes. Many algorithms based on the GGM have been proposed for learning genetic network structures. Because the number of gene variables is typically far more than the number of samples collected, and a real genetic network is typically sparse, the graphical lasso implementation of GGM becomes a popular tool for inferring the conditional interdependence among genes. However, graphical lasso, although showing good performance in low dimensional data sets, is computationally expensive and inefficient or even unable to work directly on genome-wide gene expression data sets. In this study, the method of Monte Carlo Gaussian graphical model (MCGGM) was proposed to learn global genetic networks of genes. This method uses a Monte Carlo approach to sample subnetworks from genome-wide gene expression data and graphical lasso to learn the structures of the subnetworks. The learned subnetworks are then integrated to approximate a global genetic network. The proposed method was evaluated with a relatively small real data set of RNA-seq expression levels. The results indicate the proposed method shows a strong ability of decoding the interactions with high conditional dependences among genes. The method was then applied to genome-wide data sets of RNA-seq expression levels. The gene interactions with high interdependence from the estimated global networks show that most of the predicted gene-gene interactions have been reported in the literatures playing important roles in different human cancers. Also, the results validate the ability and reliability of the proposed method to identify high conditional dependences among genes in large-scale data sets. [ABSTRACT FROM AUTHOR]

The present study was undertaken with the objective to assess the nature and magnitude of gene action for various morpho-physiological and biochemical traits in two crosses namely cross BHU 31 × HD 2733 and cross, HPYT 485 × HD 2967 in wheat. The six basic generations (P1, P2, F1, F2, B1 and B2 obtained from these crosses (made in Rabi 2018 and 2019) were evaluated for 13 quantitative traits including yield and micronutrient traits during Rabi 2020 in compact family block design with 3 replications at Research farm, RPCAU, Pusa and data were recorded on randomly selected plants per replication of each cross for all the traits. The estimation of micronutrient in wheat grains was done by X-Ray Fluorescence Spectrometry at Harvest-plus Division, ICRISAT, Hyderabad. The result regarding gene effect indicated that in both the crosses dominance and dominance × dominance effect for grain Zinc content (-29.00 & 19.18 and -9.79 & 7.04 respectively in cross I and II) and grain Iron content (-18.16 & 12.37 and -20.29 & 12.31 respectively in cross I and II) has significant role in expression of these traits. Duplicate type of gene interaction was found predominant for grain Zinc and Iron content and almost for all the traits due to opposite sign of dominance (h) and dominance × dominance (l) gene effect which tends to cancel the effect of each other in hybrid combination therefore selection should be advanced in later generation. [ABSTRACT FROM AUTHOR]

Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involved in ginsenoside biosynthesis have been cloned through orthologue analysis. Here, we report the identification of 21 genes controlling Rb1 biosynthesis by stepwise ginseng transcriptome and Rb1 content integrated analysis. We first identified the candidate genes for Rb1 biosynthesis by integrated analysis of genes with the trait from four aspects, including gene transcript differential expression between highest- and lowest-Rb1 content cultivars, gene transcript expression–Rb1 content correlation, and biological impacts of gene mutations on Rb1 content, followed by the gene transcript co-expression network. Twenty-two candidate genes were identified, of which 21 were functionally validated for Rb1 biosynthesis by gene regulation, genetic transformation, and mutation analysis. These genes were strongly correlated in expression with the previously cloned genes encoding key enzymes for Rb1 biosynthesis. Based on the correlations, a pathway for Rb1 biosynthesis was deduced to indicate the roles of the genes in Rb1 biosynthesis. Moreover, the genes formed a strong co-expression network with the previously cloned Rb1 biosynthesis genes, and the variation in the network was associated with the variation in the Rb1 content. These results indicate that Rb1 biosynthesis is a process of correlative interactions among Rb1 biosynthesis genes. Therefore, this study provides new knowledge, 21 new genes, and 96 biomarkers for Rb1 biosynthesis useful for enhanced research and breeding in ginseng. [ABSTRACT FROM AUTHOR]

The advent of the edge computing network paradigm places the computational and storage resources away from the data centers and closer to the edge of the network largely comprising the heterogeneous IoT devices collecting huge volumes of data. This paradigm has led to considerable improvement in network latency and bandwidth usage over the traditional cloud-centric paradigm. However, the next generation networks continue to be stymied by their inability to achieve adaptive, energy-efficient, timely data transfer in a dynamic and failure-prone environment—the very optimization challenges that are dealt with by biological networks as a consequence of millions of years of evolution. The transcriptional regulatory network (TRN) is a biological network whose innate topological robustness is a function of its underlying graph topology. In this article, we survey these properties of TRN and the metrics derived therefrom that lend themselves to the design of smart networking protocols and architectures.We then reviewa body of literature on bio-inspired networking solutions that leverage the stated properties of TRN. Finally, we present a vision for specific aspects of TRNs that may inspire future research directions in the fields of large-scale social and communication networks. [ABSTRACT FROM AUTHOR]

Through the artistic planning tool known to comic book artists and animators as storyboarding, students will embark on comic book–style adventures to plan, describe, and visualize the complex life of genes through the non-Mendelian concept of epistasis. Using storyboard templates, conceptual layouts, sketch booking, and cut-out genetic elements, students will construct their interpretation of the gene-gene interactions of epistasis. The incomplete story of the epistasis of human eye color will serve as the theme for this storyboard, which will also become its own assessment tool, inviting educators into a realm of a true STEAM experience. [ABSTRACT FROM AUTHOR]

Abstract Background Epistasis is the interaction between different genes when expressing a certain phenotype. If epistasis involves more than two loci it is called high-order epistasis. High-order epistasis is an area under active research because it could be the cause of many complex traits. The most common way to specify an epistasis interaction is through a penetrance table. Results This paper presents PyToxo, a Python tool for generating penetrance tables from any-order epistasis models. Unlike other tools available in the bibliography, PyToxo is able to work with high-order models and realistic penetrance and heritability values, achieving high-precision results in a short time. In addition, PyToxo is distributed as open-source software and includes several interfaces to ease its use. Conclusions PyToxo provides the scientific community with a useful tool to evaluate algorithms and methods that can detect high-order epistasis to continue advancing in the discovery of the causes behind complex diseases.

Leaf rust (LR) and stripe rust (YR) are important diseases in wheat producing areas worldwide and cause severe yield losses under favorable environmental conditions when susceptible varieties are grown. We determined the genetic basis of resistance to LR and YR in variety Borlaug 100 by developing and phenotyping a population of 198 F6 recombinant inbred lines derived from a cross with the susceptible parent Apav#1. LR and YR phenotyping were conducted for 4 and 3 seasons, respectively, at CIMMYT research stations in Mexico under artificial epidemics. Mendelian segregation analyses indicated that 3–5 LR and 2 YR genes conferred resistance in Borlaug 100. Lr46/Yr29 (1BL), Yr17 (2AS) and Yr30 (3BS) were present in the resistant parent and segregated in the RIL population based on characterization by molecular markers linked to these genes. When present alone, Lr46/Yr29 caused average 13% and 16% reductions in LR and YR severities, respectively, in RILs. Similarly, Yr17 and Yr30 reduced YR severities by 57% and 11%, respectively. The Yr30 and the Yr17 translocation were also associated with 27% and 14% reductions, respectively, in LR severity, indicating that the 3BS and 2AS chromosomal regions likely carry new slow rusting LR resistance genes, temporarily designated as LrB1 and LrB2, respectively. Additive effects of Yr30*Yr17, Yr29*Yr17 and Yr29*Yr30 on YR and LR were significant and reduced YR severities by 56%, 55%, and 45%, respectively, and LR severities by 34%, 40%, and 45%, respectively. Furthermore, interaction between the three genes was also significant, with mean reductions of 70% for YR and 54% for LR severities. Borlaug 100, or any one of the 21 lines with variable agronomic traits but carrying all three co-located resistance loci, can be used as resistance sources in wheat breeding programs.

The present study was undertaken with the objective to assess the nature and magnitude of gene action for various morpho-physiological and biochemical traits in two crosses namely cross BHU 31 × HD 2733 and cross, HPYT 485 × HD 2967 in wheat. The six basic generations (P1, P2, F1, F2, B1 and B2 obtained from these crosses (made in Rabi 2018 and 2019) were evaluated for 13 quantitative traits including yield and micronutrient traits during Rabi 2020 in compact family block design with 3 replications at Research farm, RPCAU, Pusa and data were recorded on randomly selected plants per replication of each cross for all the traits. The estimation of micronutrient in wheat grains was done by X-Ray Fluorescence Spectrometry at Harvest-plus Division, ICRISAT, Hyderabad. The result regarding gene effect indicated that in both the crosses dominance and dominance × dominance effect for grain Zinc content (-29.00 & 19.18 and -9.79 & 7.04 respectively in cross I and II) and grain Iron content (-18.16 & 12.37 and -20.29 & 12.31 respectively in cross I and II) has significant role in expression of these traits. Duplicate type of gene interaction was found predominant for grain Zinc and Iron content and almost for all the traits due to opposite sign of dominance (h) and dominance × dominance (l) gene effect which tends to cancel the effect of each other in hybrid combination therefore selection should be advanced in later generation.

Analyzing how gene interaction networks are perturbed in individuals can help identify different types of colorectal cancers, paving the way towards personalized care.

Molecular subtypes of colorectal cancer (CRC) are currently identified via the snapshot transcriptional profiles, largely ignoring the dynamic changes of gene expressions. Conversely, biological networks remain relatively stable irrespective of time and condition. Here, we introduce an individual-specific gene interaction perturbation network-based (GIN) approach and identify six GIN subtypes (GINS1-6) with distinguishing features: (i) GINS1 (proliferative, 24%~34%), elevated proliferative activity, high tumor purity, immune-desert, PIK3CA mutations, and immunotherapeutic resistance; (ii) GINS2 (stromal-rich, 14%~22%), abundant fibroblasts, immune-suppressed, stem-cell-like, SMAD4 mutations, unfavorable prognosis, high potential of recurrence and metastasis, immunotherapeutic resistance, and sensitive to fluorouracil-based chemotherapy; (iii) GINS3 (KRAS-inactivated, 13%~20%), high tumor purity, immune-desert, activation of EGFR and ephrin receptors, chromosomal instability (CIN), fewer KRAS mutations, SMOC1 methylation, immunotherapeutic resistance, and sensitive to cetuximab and bevacizumab; (iv) GINS4 (mixed, 10%~19%), moderate level of stromal and immune activities, transit-amplifying-like, and TMEM106A methylation; (v) GINS5 (immune-activated, 12%~24%), stronger immune activation, plentiful tumor mutation and neoantigen burden, microsatellite instability and high CpG island methylator phenotype, BRAF mutations, favorable prognosis, and sensitive to immunotherapy and PARP inhibitors; (vi) GINS6, (metabolic, 5%~8%), accumulated fatty acids, enterocyte-like, and BMP activity. Overall, the novel high-resolution taxonomy derived from an interactome perspective could facilitate more effective management of CRC patients.

Genetic improvement of fruit color and shape of bell pepper (Capsicum annuum var. grossum Sendt.) have been constrained by lack of adequate information on genetic control of fruit physical-chemical characteristics at the physiologically mature stage. Inheritance pattern of fruit color and shape and the nature of gene action for quantitative traits at physiological maturity were studied in six genetic populations (P1, P2, F1, F2, BC1P1, BC2P2) generated from four crosses involving parents bearing different fruit color and shape. Duplicate recessive epistasis gene action was involved in the expression of fruit color in Red × Yellow cross. The segregation pattern of the crosses Red × Purple and Red × White indicated involvement of dominant and recessive epistasis, respectively. Fruit shape segregation of the cross Blocky × Elongate indicated recessive epistasis gene interaction. The inheritance pattern indicated that fruit color and shape in bell pepper were conditioned by two genes with either dominant or recessive epistatic action. The segregation pattern of test crosses revealed involvement of two loci; there is no linkage between the genes and their two alternative alleles on both the loci. Gene action of most of the quantitative characters in the crosses 'C/4 × 8/4ʹ and 'C/4 × BC CAP Yellow' indicated predominance of non-additive gene action showing duplicate epistasis. Fruit color and shape were conditioned by two genes showing either dominant or recessive epistatic action, however, these two characters were not linked. Fruit physical and chemical traits could be improved following deferred selection through advancement of promising cross-combination. [ABSTRACT FROM AUTHOR]

The incidence of esophageal cancer has obvious genetic susceptibility. Identifying esophageal cancer-related genes plays a huge role in the prevention and treatment of esophageal cancer. Through various sequencing methods, researchers have found only a small number of genes associated with esophageal cancer. In order to improve the efficiency of esophageal cancer genetic susceptibility research, this paper proposes a method for large-scale identification of esophageal cancer-related genes by computational methods. In order to improve the efficiency of esophageal cancer genetic susceptibility research, this paper proposes a method for large-scale identification of esophageal cancer-related genes by computational methods. This method fuses graph convolutional network and logical matrix factorization to effectively identify esophageal cancer-related genes through the association between genes. We call this method GCNLMF which achieved AUC as 0.927 and AUPR as 0.86. Compared with other five methods, GCNLMF performed best. We conducted a case study of the top three predicted genes. Although the association of these three genes with esophageal cancer has not been reported in the database, studies by other reseachers have shown that these three genes are significantly associated with esophageal cancer, which illustrates the accuracy of the prediction results of GCNLMF. [ABSTRACT FROM AUTHOR]

Keywords: molluscs; molecular physiology; transcriptomics; phenotypic plasticity; toxicology; innate immune; gene interaction; molecular transport EN molluscs molecular physiology transcriptomics phenotypic plasticity toxicology innate immune gene interaction molecular transport 1 4 4 06/21/22 20220617 NES 220617 Physiology applies the basic rules of chemistry, physics, and biology to study the activities of organisms, including the study of the regulation of the synthesis of biomolecules at the molecular level, and the details of providing nutrients to support mitochondrial metabolism at the subcellular level ([4]). Molluscs have played an important role in the history of physiology, and two groups of scientists studying mollusc physiology shared the Nobel Prize in Physiology or Medicine in 1963 and 2000, respectively ([16]; [9]; [15]). In summary, the articles in this Research Topic presented recent advances in the field of molecular physiology in molluscs that will benefit molluscs physiology science for many years to come. Research into the function of the Tssk family may contribute to a better understanding of sperm development in molluscs and may contribute to the knowledge of male sterility in some bivalves. [Extracted from the article]

Jujube production is threatened by jujube witches' broom (JWB) disease, which is caused by JWB phytoplasma. The jujube TCP transcription factor (TF) ZjTCP16 may be involved in the interaction of jujube plants with JWB phytoplasma. In this study, qRT-PCR proved that the expression pattern of ZjTCP16 was altered by JWB phytoplasma. The gene functions of ZjTCP16 were analyzed by its overexpression in Arabidopsis and jujube, as well as knock-down in. The overexpression of ZjTCP16 in Arabidopsis and jujube resulted in dwarfism and small leaves, while the zjtcp16 CRISPR mutants were higher than the WT. Microscopic observation of paraffin sections of jujube stems showed that ZjTCP16 affected the size of cells. The interactions of ZjTCP16 with ZjAS2 and ZjLOB in both the cytoplasm and nucleus were demonstrated by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Yeast one-hybrid (Y1H) assays and qRT-PCR further confirmed that ZjTCP16 affected the expression of genes involved in leaf morphogenesis and cell proliferation (ZjAS1, ZjKNAT1, ZjKNAT2 and ZjKNAT6) at the mRNA level through the ZjAS2 and ZjLOB pathways. In conclusion, ZjTCP16 regulates plant growth and cell size by altering the expression pattern of morphogenesis-related genes in jujube. [ABSTRACT FROM AUTHOR]

Lung cancer, amongst the fast growing malignant tumors, has become the leading cause of cancer death, which deserves attention. From a prevention and treatment perspective, advances in screening, diagnosis, and treatment have driven a reduction in non-small-cell lung cancer (NSCLC) incidence and improved patient outcomes. It is of benefit that the identification of key genetic markers contributes to the understanding of disease initiation and progression. In this work, information theoretical measures are proposed to determine the collaboration between genes and specific NSCLC samples. Top mutual information observes genes of high sample classification accuracy, such as STX11, S1PR1, TACC1, LRKK2, and SRPK1. In particular, diversity exists in different gender, histology, and smoking situations. Furthermore, leading synergy detects a high-accuracy combination of two ordinary individual genes, bringing a significant gain in accuracy. We note a strong synergistic effect of genes between COL1A2 and DCN, DCN and MMP2, and PDS5B and B3GNT8. Apart from that, RHOG is revealed to have quite a few functions in coordination with other genes. The results provide evidence for gene-targeted therapy as well as combined diagnosis in the context of NSCLC. Our approach can also be extended to find synergistic biomarkers associated with different diseases.

Background: Epistasis is the interaction between different genes when expressing a certain phenotype. If epistasis involves more than two loci it is called high-order epistasis. High-order epistasis is an area under active research because it could be the cause of many complex traits. The most common way to specify an epistasis interaction is through a penetrance table. Results: This paper presents PyToxo, a Python tool for generating penetrance tables from any-order epistasis models. Unlike other tools available in the bibliography, PyToxo is able to work with high-order models and realistic penetrance and heritability values, achieving high-precision results in a short time. In addition, PyToxo is distributed as open-source software and includes several interfaces to ease its use. Conclusions: PyToxo provides the scientific community with a useful tool to evaluate algorithms and methods that can detect high-order epistasis to continue advancing in the discovery of the causes behind complex diseases. [ABSTRACT FROM AUTHOR]

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein--protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides. [ABSTRACT FROM AUTHOR]

As a woody plant, peony (Paeonia suffruticosa) has a long growth cycle and inefficient traditional breeding techniques. There is an urgent need in peony molecular breeding to establish an efficient and stable in vitro regeneration and genetic transformation system, in order to overcome the recalcitrant characteristics of peony regeneration and shorten the breeding cycle. The development of plant somatic embryos is an important way to establish an efficient and stable in vitro regeneration and genetic transformation system. Plant-specific WUSCHEL-related homeobox (WOX) family transcription factors play important roles in plant development, from embryogenesis to lateral organ development. Therefore, in this research, four PoWOX genes of "Fengdan" (Paeonia ostii) were cloned from the peony genome and transcriptome data of preliminary peony somatic embryos. The sequence characteristics and evolutionary relationships of the PoWOX genes were analyzed. It was demonstrated that the four PoWOX genes, named PoWOX1, PoWOX4, PoWOX11, and PoWOX13, belonged to three branches of the WOX gene family. Their expression patterns were analyzed at different stages of development and in different tissues of peony seedlings. The expression localization of the PoWOX genes was determined to be the nucleus via subcellular localization assay. Finally, the interaction protein of the PoWOX genes was identified via yeast two-hybrid assay combined with bimolecular fluorescence complementation assay. It was shown that PoWOX1 and PoWOX13 proteins could form homodimers by themselves, and PoWOX11 interacted with PoWOX1 and PoWOX13 to form heterodimers. Peony stem cell activity may be regulated from PoWOX1 and PoWOX13 by forming dimers and moving to peony stem cells through plasmodesmata. Additionally, PoWOX11–PoWOX1 and PoWOX11–PoWOX13 may play important regulatory functions in promoting the proliferation of stem cells and maintaining the homeostasis of stem cells in the SAM of peony stems. Exploring the critical genes and regulatory factors in the development of the peony somatic embryo is beneficial not only to understand the molecular and regulatory mechanisms of peony somatic embryo development but also to achieve directed breeding and improvements in efficiency through genetic engineering breeding technology to accelerate the fundamental process of molecular breeding in peony. [ABSTRACT FROM AUTHOR]

Pearl millet [ Pennisetum glaucum (L.) R. Br.] is a climate-resilient dryland cereal that has been identified as a potential staple food crop that can contribute to alleviating micronutrient malnutrition, particularly with respect to grain iron (Fe) and zinc (Zn) contents, in Sub-Saharan Africa and India. In this regard, an understanding of the inheritance pattern of genes involved in Fe and Zn contents is vital for devising appropriate breeding methods to genetically enhance their levels in grains. In this study, we aimed to determine the genetic effects underlying such inheritance and their interactions based on the generation mean analyses. Four experimental crosses and their six generations (P1, P2, F1, BCP1, BCP2, and F2) were independently evaluated in a compact family block design in 2017 rainy and 2018 summer seasons. ANOVA revealed highly significant mean squares (p < 0.01) among different generations for grain Fe and Zn contents. Six-parameter generation mean analyses revealed a predominance of additive genetic effect and a significant (p < 0.05) additive × dominant interaction for the grain Fe content. The additive genetic effect for the grain Zn content was also highly significant (p < 0.01). However, interaction effects contributed minimally with respect to most of the crosses for the grain Zn content and hence we assume that a simple digenic inheritance pattern holds true for it. Furthermore, we established that narrow-sense heritability was high for the grain Fe content (>61.78%), whereas it was low to moderate for the grain Zn content (30.60–59.04%). The lack of superior parent heterosis coupled with non-significant inbreeding depression for Fe and Zn contents in grains further confirmed the predominance of an additive genetic effect. These findings will contribute to strategizing a comprehensive breeding method to exploit the available variability of grain Fe and Zn contents for the development of biofortified hybrids of pearl millet. [ABSTRACT FROM AUTHOR]

Peppers have shown an increasing and continuous acceptance by the consumer market, standing out in the trade of potted ornamental plants. From this perspective, this study aimed to estimate the genetic parameters and genetic effects involved in the inheritance of traits referring to plant size, flowers, and fruits in a segregating generation of ornamental pepper plants (Capsicum annuum L.). The experiment was conducted in a plant nursery. Two ornamental pepper (C. annuum L.) accessions belonging to the vegetable germplasm bank of the Federal University of Paraíba (UFPB) were used as parents: UFPB 349 and UFPB 356. The experimental design was completely randomized, with five plants of each parent, 20 plants of generation F1, 88 plants of generation F2, and 40 plants of the backcross generations BC1 and BC2. Nineteen quantitative traits referring to plant, flowers, and fruits were evaluated. The data obtained were subjected to generation analysis, and the effects of the models were subjected to the t-test at 5% and 1% of significance. Highers broad- and narrow-sense heritability values were observed for plant height and pericarp thickness, suggesting the predominance of additive genetic effects in trait expression. The additive-dominant model (m, a, d) was suitable (r-value superior to 0.7) to explain the genetic parameters of most traits. However, for canopy diameter, petal diameter, pedicel length, and dry matter content, the additive-dominant model was inadequate, and the interpretation of the complete model is recommended instead. [ABSTRACT FROM AUTHOR]

The APETALA2/Ethylene-Responsive factor (AP2/ERF) gene family is a large plant-specific transcription factor family, which plays important roles in regulating plant growth and development. A role in starch synthesis is among the multiple functions of this family of transcription factors. Barley (Hordeum vulgare L.) is one of the most important cereals for starch production. However, there are limited data on the contribution of AP2 transcription factors in barley. In this study, we used the recently published barley genome database (Morex) to identify 185 genes of the HvAP2/ERF family. Compared with previous work, we identified 64 new genes in the HvAP2/ERF gene family and corrected some previously misannotated and duplicated genes. After phylogenetic analysis, HvAP2/ERF genes were classified into four subfamilies and 18 subgroups. Expression profiling showed different patterns of spatial and temporal expression for HvAP2/ERF genes. Most of the 12 HvAP2/ERF genes analyzed using quantitative reverse transcription–polymerase chain reaction had similar expression patterns when compared with those of starch synthase genes in barley, except for HvAP2-18 and HvERF-73. HvAP2-18 is homologous to OsRSR1 , which negatively regulates the synthesis of rice starch. Luciferase reporter gene, and yeast one-hybrid assays showed that HvAP2-18 bound the promoter of AGP-S and SBE1 in vitro. Thus, HvAP2-18 might be an interesting candidate gene to further explore the mechanisms involved in the regulation of starch synthesis in barley. [ABSTRACT FROM AUTHOR]

Background: Diabetes especially type 2 diabetes mellitus (T2DM) is securing the rank under five around the world and leading cause of death cardiac disease and cancer. T2DM is a severe inflammatory state mainly associated to obesity and enhanced oxidative stress. Objectives: We have investigated eleven genetic polymorphisms of seven important genes viz. IL-10, TNF-α, IL-6, adiponectin, IL-1, IL-18, and Vitamin D-receptor. We have focused to investigate the haplotypes, gene-gene interactions and their role in determining individual susceptibility to T2DM and their manifestation. Methods: Eleven genetic variants of seven important candidate genes in 440 T2DM individuals and 440 controls were genotyped using conventional polymerase chain reaction (PCR) and PCR restriction fragment length polymorphism (PCR-RFLP). All calculations were done by SPSS software and LD were analysed by haploview (SHEsis software). Results: Genotypic frequency of rs1800872, rs1800795, rs2241766, rs17846866 and rs1946518 showed highly significant association in our population. While allele frequencies of rs1800795, rs2241766 and rs1946518 showed highly significant association. The allele set of “CGGAGGTAFTB”, “CGGAGTTAFTB” and “CGGATGTCFTB” increase the chance of diabetes up to 1.6 times. This study reflects that these individuals are more susceptible of having T2DM. Conclusions: The present study will provide a new insight in the development and the manifestation of T2DM. These genetic studies showing gene interaction for the susceptibility of the disease may be used as prognostic markers and alter treatment strategies for T2DM.

Abstract Background Awns are bristle-like organs at the tips of the glumes. Wild rice has maintained long awns for successful seed propagation through seed dispersal. Seed awning is an interesting trait in rice domestication. Long awns might have been beneficial for seed gatherers in the initial phase of domestication; however, awnless phenotypes were preferably selected in a later phase with non-seed-shattering plants. Investigation of domestication loci associated with awnlessness in cultivated rice will be useful in clarifying the process and history of rice domestication. Results Quantitative trait locus (QTL) analysis for seed awning was carried out using a BC3F2 population between Oryza sativa IR36 (a cultivated donor parent with awnless phenotype) and O. rufipogon W630 (a wild recurrent parent with awns). As a result, two QTLs on chromosome 4 (corresponding to An-1 and LABA1) and one on chromosome 2 (designated as qAWNL2) were detected. Gene interaction among three seed-awning QTLs were further examined with the plants having eight different combinations of homozygous genotypes. Their awn length variation indicated that the IR36 alleles at these loci had the additive awnlessness effects in the genetic background of wild rice. The shortest awn length was observed for the plants having IR36 homozygous alleles at all loci, giving about 75% reduction in awn length. By the fine mapping, the candidate region of the novel qAWNL2 locus was delimited in a 157.4-kb region containing 22 predicted genes in Nipponbare genome. Conclusions QTL analysis revealed that three loci, An-1, LABA1 and qAWNL2, were mainly responsible for the awnlessness of O. sativa IR36. In the wild genetic background, loss-of-function alleles at three awning loci showed additive effects on length reduction. In rice domestication, awnless forms may be gradually generated through the accumulation of mutations at awning loci.

Abstract Background Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains the probability of expressing the phenotype under study given a particular allele combination. Available simulators can only create penetrance tables for well-known epistasis models involving a small number of genes and under a large number of limitations. Results Toxo is a MATLAB library designed to calculate penetrance tables of epistasis models of any interaction order which resemble real data more closely. The user specifies the desired heritability (or prevalence) and the program maximizes the table’s prevalence (or heritability) according to the input epistatic model boundaries. Conclusions Toxo extends the capabilities of existing simulators that define epistasis using penetrance tables. These tables can be directly used as input for software simulators such as GAMETES so that they are able to generate data samples with larger interactions and more realistic prevalences/heritabilities.

Rheumatoid arthritis (RA) is an autoimmune disease which can lead to progressive and functional disability. Literature data suggest that some inflammatory proteins are dysregulated in RA patients and its genetic polymorphisms may contribute to the aetiology and pathogenesis of disease in different ethnic groups. Polymorphisms in IL1β, IL18, NFKB1 and IFNG genes were studied in different populations with RA, but the analysis indicated contradictory results. Thereby, we hypothesised that polymorphisms in these genes could have a combined effect on susceptibility to and severity of disease. We evaluated the +3953 C/T IL1β (rs1143634), –137 G/C IL18 (rs187238), –94 ins/del ATTG NFKB1 (rs28362491) and +874 T/A IFNG (rs2430561) polymorphisms in the northeastern Brazilian population. Peripheral blood samples were collected and DNA extraction was conducted. The polymorphisms were evaluated by RFLP and ARMS–PCR. An association was observed in rs1143634 which showed a protective effect against development of RA in carriers of the T allele (OR = 0.58; 95% CI 0.36–0.92; p = .020). In addition, we found an association among genotypes of the rs1143634 with the HAQ index (p = .021) and rs2430561 with DAS28 (p = .029) and CDAI (p = .029). In relation to combined effects of these SNPs (C/C to rs1143634, G/G to rs187238, I/I to rs28362491 and AA to rs2430561) we found a significant association with decreased functional disability (HAQ index p

Abstract Objective Genetic factors underlying different personality traits are not entirely understood, particularly how genes interact to modulate their effect. We studied 76 patients diagnosed with borderline personality disorder (BPD), characterized by extreme levels of personality traits, especially neuroticism (N), in which we genotyped two polymorphisms, the 5HTTLPR of the Serotonin transporter (SERT) gene, and the Val66Met of the Brain-derived neurotrophic factor (BDNF) gene. Results We found an association with SERT, where S-allele carriers had significantly higher levels of N than L-homozygous. Furthermore, we found that the protective effect of L-homozygosity is only evident on A-allele carriers of the BDNF Val66Met polymorphism. Genetic constitution in SERT and BDNF seems to be important in neuroticism, the most relevant personality trait on BPD.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a climate-resilient dryland cereal that has been identified as a potential staple food crop that can contribute to alleviating micronutrient malnutrition, particularly with respect to grain iron (Fe) and zinc (Zn) contents, in Sub-Saharan Africa and India. In this regard, an understanding of the inheritance pattern of genes involved in Fe and Zn contents is vital for devising appropriate breeding methods to genetically enhance their levels in grains. In this study, we aimed to determine the genetic effects underlying such inheritance and their interactions based on the generation mean analyses. Four experimental crosses and their six generations (P1, P2, F1, BCP1, BCP2, and F2) were independently evaluated in a compact family block design in 2017 rainy and 2018 summer seasons. ANOVA revealed highly significant mean squares (p < 0.01) among different generations for grain Fe and Zn contents. Six-parameter generation mean analyses revealed a predominance of additive genetic effect and a significant (p < 0.05) additive × dominant interaction for the grain Fe content. The additive genetic effect for the grain Zn content was also highly significant (p < 0.01). However, interaction effects contributed minimally with respect to most of the crosses for the grain Zn content and hence we assume that a simple digenic inheritance pattern holds true for it. Furthermore, we established that narrow-sense heritability was high for the grain Fe content (>61.78%), whereas it was low to moderate for the grain Zn content (30.60–59.04%). The lack of superior parent heterosis coupled with non-significant inbreeding depression for Fe and Zn contents in grains further confirmed the predominance of an additive genetic effect. These findings will contribute to strategizing a comprehensive breeding method to exploit the available variability of grain Fe and Zn contents for the development of biofortified hybrids of pearl millet.