Independent Genes Research Articles

Genetic elements associated with antimicrobial resistance among avian pathogenic Escherichia coli.

BackgroundAvian-pathogenic Escherichia coli (APEC) are pathogenic strains of E. coli that are responsible for one of the most predominant bacterial disease affecting poultry worldwide called avian colibacillosis. This study describes the genetic determinants implicated in antimicrobial resistance among APEC isolated from different broiler farms in Egypt.Methods A total of 116 APEC were investigated by serotyping, antimicrobial resistance patterns to 10 antimicrobials, and the genetic mechanisms underlying the antimicrobial-resistant phenotypes.ResultsAntibiogram results showed that the highest resistance was observed for ampicillin, tetracycline, nalidixic acid, and chloramphenicol. The detected carriage rate of integron was 29.3% (34/116). Further characterization of gene cassettes revealed the presence gene cassettes encoding resistance to trimethoprim (dfrA1, dfrA5, dfrA7, dfrA12), streptomycin/spectinomycin (aadA1, aadA2, aadA5, aadA23), and streptothricin (sat2). To our knowledge, this the first description of the presence of aadA23 in APEC isolates. Analysis of other antimicrobial resistance types not associated with integrons revealed the predominance of resistance genes encoding resistance to tetracycline (tetA and tetB), ampicillin (bla TEM), chloramphenicol (cat1), kanamycin (aphA1), and sulphonamide (sul1 and sul2). Among ciprofloxacin-resistant isolates, the S83L mutation was the most frequently substitution observed in the quinolone resistance-determining region of gyrA (56.3%). The bla TEM and bla CTX−M−1 genes were the most prevalent among APEC isolates producing extended-spectrum beta-lactamase (ESβL).ConclusionsThese findings provided important clues about the role of integron-mediated resistance genes together with other independent resistance genes and chromosomal mutations in shaping the epidemiology of antimicrobial resistance in E. coli isolates from poultry farms in Egypt.

Predominance of SCCmec types IV and V among biofilm producing device-associated Staphylococcus aureus strains isolated from tertiary care hospitals in Mysuru, India

IntroductionDevice associated infections caused by Staphylococcus aureus in hospitalised patients is a serious healthcare problem. The present study was designed to determine the prevalence of biofilm-producing MRSA in device-associated infections. MethodsDevice-associated S. aureus strains (n=200) obtained from two tertiary care hospitals in Mysuru city, India were screened for biofilm production, antibiotic resistance, Panton-Valentine Leucocidin genes, SCCmec-types, spa-types, and intercellular adhesion (icaAD) dependent and independent genes. The efficacy of antibiotics (linezolid, vancomycin and rifampicin) on biofilms was studied using MTT assay, and the results were correlated with the occurrence of ica-dependent and independent factors. ResultsMultidrug resistance was observed in 155 strains (77.5%), and 124 strains (62%) were identified as biofilm producers. Methicillin resistance was identified in 145 strains (72.5%), and SCCmec typing of these isolates revealed high prevalence of type IV and type V. They also showed increased prevalence of pvl gene. icaAD was identified in 65 isolates, with 37 isolates showing both icaAD and ica-independent genes. spa types t852 and t657 were predominantly observed in MRSA isolates. Those isolates that had both ica-dependent and ica-independent genes showed more resistance to the screened antibiotics than the ica-dependent alone. ConclusionThis study reports a high prevalence of SCCmec type IV and V in biofilm producing S. aureus strains isolated from device-associated infections. Increased prevalence of pvl in SCCmec types IV and V strains suggests the role of community associated S. aureus in device-associated infections. The simultaneous presence of ica-dependent and independent genes increased the antibiotic resistance in established biofilms. Thus, S. aureus on medical devices is a potential risk for patients.

Efficient and Heritable Targeted Mutagenesis in Mosses Using the CRISPR/Cas9 System.

Targeted genome modification by RNA-guided nucleases derived from the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has seen rapid development in many organisms, including several plant species. In the present study, we succeeded in introducing the CRISPR/Cas9 system into the non-model organism Scopelophila cataractae, a moss that exhibits heavy metal tolerance, and the model organism Physcomitrella patens Utilizing the process by which moss plants regenerate from protoplasts, we conducted targeted mutagenesis by expression of single-chain guide RNA (sgRNA) and Cas9 in protoplasts. Using this method, the acquisition rate of strains exhibiting phenotypic changes associated with the target genes was approximately 45-69%, and strains with phenotypic changes exhibited various insertion and deletion mutations. In addition, we report that our method is capable of multiplex targeted mutagenesis (two independent genes) and also permits the efficient introduction of large deletions (∼3 kbp). These results demonstrate that the CRISPR/Cas9 system can be used to accelerate investigations of bryology and land plant evolution.

Genetic Analysis of Resistance to Soybean Mosaic Virus in PI 438307 Soybean Accession

Soybean mosaic virus (SMV) is the most prevalent viral pathogen and economic threat to soybean production worldwide. Three independent genes harboring SMV resistance have been identified: Rsv1, Rsv3, and Rsv4. Although the resistance genes (R‐genes) have been found in some germplasm, usually they provide protection to some, but not all, viral strains. The objective of this research was to identify a new source of SMV resistance in Korean soybean accession PI 438307. The soybean genotype PI 438307 was crossed with susceptible parent ‘Essex’ (rsv), and differential parents PI 96983 (Rsv1), L29 (Rsv3), and V94‐5152 (Rsv4). F2 plants and F2:3 lines derived from all four cross combinations were screened with SMV‐G7 strain. Additionally, F2 plants obtainSed from PI 438307 (R) × Essex (S) were genotyped with two simple sequence repeat (SSR) markers on chromosome 2 (MLG D1b). Inheritance and allelic studies revealed that resistance to SMV in PI 438307 is controlled by a single dominant gene allelic to the Rsv4 locus. PI 438307 exhibited unique symptomology when compared to reported Rsv4 alleles in V94‐5152, PI 88788 and Beeson. PI 438307 was resistant to SMV‐G1 through G6 and resistant at seedling stages to SMV‐G7. Therefore, it was proposed that the new allele Rsv4‐v might be assigned to the SMV resistance in this soybean accession. Soybean sources carrying Rsv4 alleles are rare among the soybean germplasm and confer resistance to all or most SMV strains; therefore, this allele may be a good choice for breeding programs in the future.

Genome-Wide Gene/Genome Dosage Imbalance Regulates Gene Expressions in Synthetic Brassica napus and Derivatives (AC, AAC, CCA, CCAA).

Gene/genome dosage balance is an essential evolutionary mechanism for organisms to ensure a normal function, but the underlying causes of dosage-imbalance regulation remain poorly understood. Herein, the serial Brassica hybrids/polyploids (AC, AAC, CCA, CCAA) with different copies of A and C subgenomes from the same two parents of Brassica rapa and Brassica oleracea were synthesized to investigate the effects of genome dosages on gene expressions and interactions by using RNA-Seq. The expression changes of A- and C-subgenome genes were consistent with dosage alterations. Dosage-dependent and -independent genes were grouped according to the correlations between dosage variations and gene expressions. Expression levels of dosage-dependent genes were strongly correlated with dosage changes and mainly contributed to dosage effects, while those of dosage-independent genes gave weak correlations with dosage variations and mostly facilitated dosage compensation. More protein–protein interactions were detected for dosage-independent genes than dosage-dependent ones, as predicted by the dosage balance hypothesis. Dosage-dependent genes more likely impacted the expressions by trans effects, whereas dosage-independent genes preferred to play by cis effects. Furthermore, dosage-dependent genes were mainly associated with the basic biological processes to maintain the stability of the growth and development, while dosage-independent genes were more enriched in the stress response related processes to accelerate adaptation. The present comprehensive analysis of gene expression dependent/independent on dosage alterations in Brassica polyploids provided new insights into gene/genome dosage-imbalance regulation of gene expressions.

"Soldier's Heart": A Genetic Basis for Elevated Cardiovascular Disease Risk Associated with Post-traumatic Stress Disorder.

“Soldier's Heart,” is an American Civil War term linking post-traumatic stress disorder (PTSD) with increased propensity for cardiovascular disease (CVD). We have hypothesized that there might be a quantifiable genetic basis for this linkage. To test this hypothesis we identified a comprehensive set of candidate risk genes for PTSD, and tested whether any were also independent risk genes for CVD. A functional analysis algorithm was used to identify associated signaling networks. We identified 106 PTSD studies that report one or more polymorphic variants in 87 candidate genes in 83,463 subjects and controls. The top upstream drivers for these PTSD risk genes are predicted to be the glucocorticoid receptor (NR3C1) and Tumor Necrosis Factor alpha (TNFA). We find that 37 of the PTSD candidate risk genes are also candidate independent risk genes for CVD. The association between PTSD and CVD is significant by Fisher's Exact Test (P = 3 × 10−54). We also find 15 PTSD risk genes that are independently associated with Type 2 Diabetes Mellitus (T2DM; also significant by Fisher's Exact Test (P = 1.8 × 10−16). Our findings offer quantitative evidence for a genetic link between post-traumatic stress and cardiovascular disease, Computationally, the common mechanism for this linkage between PTSD and CVD is innate immunity and NFκB-mediated inflammation.

Selection of Reference Genes for Quantitative Real-Time RT-PCR Studies in Tomato Fruit of the Genotype MT-Rg1.

Quantitative real-time RT-PCR (qRT-PCR) has become one of the most widely used methods for accurate quantification of gene expression. Since there are no universal reference genes for normalization, the optimal strategy to normalize raw qRT-PCR data is to perform an initial comparison of a set of independent reference genes to assess the most stable ones in each biological model. Normalization of a qRT-PCR experiment helps to ensure that the results are both statistically significant and biologically meaningful. Tomato is the model of choice to study fleshy fruit development. The miniature tomato (Solanum lycopersicum L.) cultivar Micro-Tom (MT) is considered a model system for tomato genetics and functional genomics. A new genotype, containing the Rg1 allele, improves tomato in vitro regeneration. In this work, we evaluated the expression stability of four tomato reference genes, namely CAC, SAND, Expressed, and ACTIN2. We showed that the genes CAC and Exp are the best reference genes of the four we tested during fruit development in the MT-Rg1 genotype. Furthermore, we validated the reference genes by showing that the expression profiles of the transcription factors FRUITFULL1 and APETALA2c during fruit development are comparable to previous reports using other tomato cultivars.

Mitochondrial Defects Confer Tolerance against Cellulose Deficiency.

Because the plant cell wall provides the first line of defense against biotic and abiotic assaults, its functional integrity needs to be maintained under stress conditions. Through a phenotype-based compound screening approach, we identified a novel cellulose synthase inhibitor, designated C17. C17 administration depletes cellulose synthase complexes from the plasma membrane in Arabidopsis thaliana, resulting in anisotropic cell elongation and a weak cell wall. Surprisingly, in addition to mutations in CELLULOSE SYNTHASE1 (CESA1) and CESA3, a forward genetic screen identified two independent defective genes encoding pentatricopeptide repeat (PPR)-like proteins (CELL WALL MAINTAINER1 [CWM1] and CWM2) as conferring tolerance to C17. Functional analysis revealed that mutations in these PPR proteins resulted in defective cytochrome c maturation and activation of mitochondrial retrograde signaling, as evidenced by the induction of an alternative oxidase. These mitochondrial perturbations increased tolerance to cell wall damage induced by cellulose deficiency. Likewise, administration of antimycin A, an inhibitor of mitochondrial complex III, resulted in tolerance toward C17. The C17 tolerance of cwm2 was partially lost upon depletion of the mitochondrial retrograde regulator ANAC017, demonstrating that ANAC017 links mitochondrial dysfunction with the cell wall. In view of mitochondria being a major target of a variety of stresses, our data indicate that plant cells might modulate mitochondrial activity to maintain a functional cell wall when subjected to stresses.

Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases

Purpose:Diagnostic exome sequencing (DES) is now a commonly ordered test for individuals with undiagnosed genetic disorders. In addition to providing a diagnosis for characterized diseases, exome sequencing has the capacity to uncover novel candidate genes for disease.Methods:Family-based DES included analysis of both characterized and novel genetic etiologies. To evaluate candidate genes for disease in the clinical setting, we developed a systematic, rule-based classification schema.Results:Testing identified a candidate gene among 7.7% (72/934) of patients referred for DES; 37 (4.0%) and 35 (3.7%) of the genes received evidence scores of “candidate” and “suspected candidate,” respectively. A total of 71 independent candidate genes were reported among the 72 patients, and 38% (27/71) were subsequently corroborated in the peer-reviewed literature. This rate of corroboration increased to 51.9% (27/52) among patients whose gene was reported at least 12 months previously.Conclusions:Herein, we provide transparent, comprehensive, and standardized scoring criteria for the clinical reporting of candidate genes. These results demonstrate that DES is an integral tool for genetic diagnosis, especially for elucidating the molecular basis for both characterized and novel candidate genetic etiologies. Gene discoveries also advance the understanding of normal human biology and more common diseases.Genet Med19 2, 224–235.

Fine Mapping of Two Additive Effect Genes for Awn Development in Rice (Oryza sativa L.).

Awns, important domestication and agronomic traits in rice (Oryza sativa L.), are conferred by polygenes and the environment. Near isogenic line (NIL) pairs BM33 and BM38 were constructed from crosses between awnless japonica cv Nipponbare as recurrent parent, and lines SLG or Funingxiaohongmang (awned japonica accessions), respectively, as donors. In order to study the genetic and molecular mechanism of awning, two unknown, independent genes with additive effects were identified in a cross between the NILs. To map and clone the two genes, a BC4F4 population of 8,103 individuals and a BC4F6 population of 11,206 individuals were constructed. Awn3-1 was fine mapped to a 101.13 kb genomic region between Indel marker In316 and SNP marker S9-1 on chromosome 3. Nine predicted genes in the interval were annotated in the Rice Annotation Project Database (RAP-DB), and Os03g0418600 was identified as the most likely candidate for Awn3-1 through sequence comparisons and RT-PCR assays. Awn4-2 was fine mapped to a 62.4 kb genomic region flanked by simple sequence repeat (SSR) marker M1126 and Indel maker In73 on chromosome 4L. This region contained the previously reported gene An-1 that regulates awn development. Thus, An-1 may be the candidate gene of Awn4-2. These results will facilitate cloning of the awn genes and thereby provide an understanding of the molecular basis of awn development.

ROR2 is epigenetically inactivated in the early stages of colorectal neoplasia and is associated with proliferation and migration.

BackgroundColorectal cancer (CRC) is closely linked to Wnt signalling, with 94 % of cases exhibiting a Wnt related mutation. ROR2 is a receptor tyrosine kinase that is thought to repress β-catenin dependent Wnt signalling. Our study aims to determine if ROR2 is epigenetically silenced in CRC and determine if in vitro silencing of ROR2 potentiates Wnt signalling, and alters the proliferative, migratory or invasive potential of cells.MethodsROR2 expression was examined in CRC cell lines and patient adenomas using qRT-PCR, while COBRA and bisulphite sequencing was used to analyse ROR2 promoter methylation. 258 patient primary tumour samples from publicly available databases were also examined for ROR2 expression and methylation. In addition, the functional effects of ROR2 modulation were investigated in HCT116 cells following ROR2 siRNA knockdown and in RKO and SW620 cells following ectopic ROR2 expression.ResultsReduced ROR2 expression was found to correlate with ROR2 promoter hypermethylation in colorectal cancer cell lines, carcinomas and adenomas. ROR2 expression was downregulated in 76.7 % (23/30) of CRC cell lines with increasing ROR2 promoter hypermethylation correlating with progressively lower expression. Analysis of 239 primary tumour samples from a publicly available cohort also found a significant correlation between reduced ROR2 expression and increased promoter methylation. Methylation analysis of 88 adenomas and 47 normal mucosa samples found greater percentage of adenoma samples to be methylated. Additional analysis also revealed that adenoma samples with reduced ROR2 expression also possessed ROR2 promoter hypermethylation. ROR2 knockdown in the CRC cell line HCT116 significantly decreased expression of the β-catenin independent Wnt targets genes JNK and NFATC1, increased cellular proliferation and migration but decreased invasion. When ROR2 was ectopically expressed in RKO and SW620 cells, there was no significant change to either cellular proliferation or migration.ConclusionROR2 is frequently epigenetically inactivated by promoter hypermethylation in the early stages of colorectal neoplasia and this may contribute to colorectal cancer progression by increasing cellular proliferation and migration.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-016-2576-7) contains supplementary material, which is available to authorized users.

Transvection in Drosophila: trans-interaction between yellow enhancers and promoter is strongly suppressed by a cis-promoter only in certain genomic regions

Transvection is a phenomenon of interallelic communication whereby enhancers of one allele can activate a promoter located on the homologous chromosome. It has been shown for many independent genes that enhancers preferentially act on the cis-linked promoter, but deletion of this promoter allows the enhancers to act in trans. Here, we tested whether this cis-preference in the enhancer-promoter interaction could be reconstituted outside of the natural position of a gene. The yellow gene was chosen as a model system. Transgenic flies were generated that carried the yellow gene modified by the inclusion of the strategically placed recognition sites for the Cre and Flp recombinases. To facilitate transvection, an endogenous Su(Hw) insulator (1A2) or gypsy insulator was placed behind the yellow gene. Independent action of the recombinases produced a pair of derivative alleles, one containing the promoter-driven yellow gene, and the other, the enhancers and promoter that failed to produce a functional yellow protein. As a result, we observed strong transvection in many genomic regions, suggesting that a complete cis-preference of the enhancer-promoter interactions is mainly restricted to genes in their natural loci.

Genetic analysis and QTL mapping of traits related to head shape in cabbage (Brassica oleracea var. capitata L.)

Traits related to head shape, including Hvd (head vertical diameter), Htd (head transverse diameter), and Hsi (head shape index, the ratio of Hvd/Htd), are very important agronomic traits associated with both yield and quality in cabbage (Brassica oleracea var. capitata L.). However, reports of inheritance analysis and quantitative trait locus (QTL) mapping of these traits remain rare. In this study, a double haploid (DH) population with 130 lines constructed from a cross between 24-5 (inbred line, oblate head)×01-88 (inbred line, round head) was used to analyze inheritance and to detect QTLs related to Htd and Hsi using major gene plus polygene mixed inheritance analysis and inclusive composite interval mapping (ICIM). The results indicated that Htd was controlled by two independent major genes and polygenes with recessive-epistatic effects. Hsi was controlled by two linkage major genes and polygenes with cumulative effects. A genetic linkage map with 48 insertions or deletions (InDel) and 149 simple sequence repeat (SSR) markers was constructed based on the DH population, with a total length of 866.2cM and an average interval length of 4.40cM. Fourteen QTLs for Htd and Hsi were identified on six chromosomes based on two years of phenotypic data with ICIM. Ten of the QTLs explained greater than 10.0% of the phenotypic variance, and five QTLs could be repeatedly detected in two years. For Htd, two major QTLs, Htd 3.1 and Htd 8.1, explained 19.16–24.56% and 11.25–21.55% of the phenotypic variation in the two years, respectively. For Hsi, two major QTLs, Hsi 7.1 and Hsi 7.2, explained 22.30–24.93% and 14.85–16.79% of phenotypic variation in the two years, respectively. The results from QTL mapping and genetic analysis in both years were partially consistent and complemented each other. Our results provide a foundation for further research on genetic regulation, gene cloning and molecular marker-assisted selection (MAS) for head shape in cabbage.

Fatty acid desaturase 1 knockout mice are lean with improved glycemic control and decreased development of atheromatous plaque.

Delta-5 desaturase (D5D) and delta-6 desaturase (D6D), encoded by fatty acid desaturase 1 (FADS1) and FADS2 genes, respectively, are enzymes in the synthetic pathways for ω3, ω6, and ω9 polyunsaturated fatty acids (PUFAs). Although PUFAs appear to be involved in mammalian metabolic pathways, the physiologic effect of isolated D5D deficiency on these pathways is unclear. After generating >4,650 knockouts (KOs) of independent mouse genes and analyzing them in our high-throughput phenotypic screen, we found that Fads1 KO mice were among the leanest of 3,651 chow-fed KO lines analyzed for body composition and were among the most glucose tolerant of 2,489 high-fat-diet-fed KO lines analyzed by oral glucose tolerance test. In confirmatory studies, chow- or high-fat-diet-fed Fads1 KO mice were leaner than wild-type (WT) littermates; when data from multiple cohorts of adult mice were combined, body fat was 38% and 31% lower in Fads1 male and female KO mice, respectively. Fads1 KO mice also had lower glucose and insulin excursions during oral glucose tolerance tests along with lower fasting glucose, insulin, triglyceride, and total cholesterol levels. In additional studies using a vascular injury model, Fads1 KO mice had significantly decreased femoral artery intima/media ratios consistent with a decreased inflammatory response in their arterial wall. Based on this result, we bred Fads1 KO and WT mice onto an ApoE KO background and fed them a Western diet for 14 weeks; in this atherogenic environment, aortic trees of Fads1 KO mice had 40% less atheromatous plaque compared to WT littermates. Importantly, PUFA levels measured in brain and liver phospholipid fractions of Fads1 KO mice were consistent with decreased D5D activity and normal D6D activity. The beneficial metabolic phenotype demonstrated in Fads1 KO mice suggests that selective D5D inhibitors may be useful in the treatment of human obesity, diabetes, and atherosclerotic cardiovascular disease.

Revealing rate-limiting steps in complex disease biology: The crucial importance of studying rare, extreme-phenotype families.

The major challenge in complex disease genetics is to understand the fundamental features of this complexity and why functional alterations at multiple independent genes conspire to lead to an abnormal phenotype. We hypothesize that the various genes involved are all functionally united through gene regulatory networks (GRN), and that mutant phenotypes arise from the consequent perturbation of one or more rate-limiting steps that affect the function of the entire GRN. Understanding a complex phenotype thus entails unraveling the details of each GRN, namely, the transcription factors that bind to cis regulatory elements affected by sequence variants altering transcription of specific genes, and their mutual feedback relationships. These GRNs can be identified through their rate-limiting steps and are best uncovered by genomic analyses of rare, extreme phenotype families, thus providing a coherent molecular basis to complex traits and disorders.

Proglucagons in vertebrates: Expression and processing of multiple genes in a bony fish.

In contrast to mammals, where a single proglucagon (PG) gene encodes three peptides: glucagon, glucagon-like peptide 1 and glucagon-like peptide 2 (GLP-1; GLP-2), many non-mammalian vertebrates carry multiple PG genes. Here, we investigate proglucagon mRNA sequences, their tissue expression and processing in a diploid bony fish. Copper rockfish (Sebastes caurinus) express two independent genes coding for distinct proglucagon sequences (PG I, PG II), with PG II lacking the GLP-2 sequence. These genes are differentially transcribed in the endocrine pancreas, the brain, and the gastrointestinal tract. Alternative splicing identified in rockfish is only one part of this complex regulation of the PG transcripts: the system has the potential to produce two glucagons, four GLP-1s and a single GLP-2, or any combination of these peptides. Mass spectrometric analysis of partially purified PG-derived peptides in endocrine pancreas confirms translation of both PG transcripts and differential processing of the resulting peptides. The complex differential regulation of the two PG genes and their continued presence in this extant teleostean fish strongly suggests unique and, as yet largely unidentified, roles for the peptide products encoded in each gene.

Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.).

BackgroundSeed dormancy is an adaptive trait employed by flowering plants to avoid harsh environmental conditions for the continuity of their next generations. In cereal crops, moderate seed dormancy could help prevent pre-harvest sprouting and improve grain yield and quality. We performed a genome wide association study (GWAS) for dormancy, based on seed germination percentage (GP) in freshly harvested seeds (FHS) and after-ripened seeds (ARS) in 350 worldwide accessions that were characterized with strong population structure of indica, japonica and Aus subpopulations.ResultsThe germination tests revealed that Aus and indica rice had stronger seed dormancy than japonica rice in FHS. Association analysis revealed 16 loci significantly associated with GP in FHS and 38 in ARS. Three out of the 38 loci detected in ARS were also detected in FHS and 13 of the ARS loci were detected near previously mapped dormancy QTL. In FHS, three of the association loci were located within 100 kb around previously cloned GA/IAA inactivation genes such as GA2ox3, EUI1 and GH3-2 and one near dormancy gene, Sdr4. In ARS, an association signal was detected near ABA signaling gene ABI5. No association peaks were commonly detected among the sub-populations in FHS and only one association peak was detected in both indica and japonica populations in ARS. Sdr4 and GA2OX3 haplotype analysis showed that Aus and indica II (IndII) varieties had stronger dormancy alleles whereas indica I (IndI) and japonica had weak or non-dormancy alleles.ConclusionThe association study and haplotype analysis together, indicate an involvement of independent genes and alleles contributing towards regulation and natural variation of seed dormancy among the rice sub-populations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0340-2) contains supplementary material, which is available to authorized users.

Single independent genes confer resistance to faba bean rust (Uromyces viciae-fabae) in the current Australian cultivar Doza and a central European line Ac1655

Faba bean (Vicia faba L.) is one of the oldest grain legumes and is grown in many countries for both human consumption and animal feed. Faba bean rust, caused by Uromyces viciae-fabae, is a serious disease of faba beans in the subtropical agricultural region of Australia. Experiments were conducted to assess the genetic variation for rust resistance in Australian faba bean germplasm and to determine the genetic basis of rust resistance in selected germplasm. Resistant lines were identified, subsequently crossed to agronomically suitable parents and the ensuing progeny were evaluated for resistance. Many derived lines showed a higher level of resistance than the current cultivars, although none were rated immune. This level of resistance was considered adequate for reliable crop production when combined with limited fungicide application. Genetic studies from the seedling test of F2 and F3 progenies derived from two crosses based on two different sources of resistance showed three distinct responses; highly resistant, moderately resistant and susceptible. However, no homozygous family with a moderate response was found in the F3 progeny test, hence, this infection type could not be attributed to independent gene(s). The segregation ratio in both F2 and F3 in the population derived from Doza#12035, a selection from the commercial cultivar Doza, indicated a single dominant gene was responsible for conferring resistance. In the other population developed from the resistant parent Ac1655, it is likely that also a single dominant gene confers resistance even though the F3 segregation ratio deviated significantly from a one gene hypothesis. An allelism test revealed that each of the resistant parents (Doza#12035 and Ac1655) carried a single and independent gene for resistance, thus providing at least two genes for breeders to choose or pyramid for improving the rust resistance in faba bean.

Identification of fertility restorers among Assam rice cultivars by phenotyping and molecular screening approaches

In three line hybrid rice seed production the combination of a CMS line, maintainer line and restorer line are involved in the development of hybrids. The wild abortive CMS is extensively used in commercial hybrid seed production. The fertility restoration of wild abortive CMS is governed by two independent dominant Rf genes viz., Rf4 and Rf3. The present study was conducted with the objective of molecular characterization rice genotypes from Assam, India and to identify restorers for hybrid rice breeding programme. A total one hundred and eleven hybrids were generated and evaluated for their pollen and spikelet fertility. Based on molecular screening twenty five genotypes were identified to carry only Rf4 gene and three genotypes identified to carry both Rf3 and Rf4 genes. These identified restorers in the present study would be a usable restores for hybrid rice breeding in north east India. Molecular diversity for fertility restoration using NTSYS package formed two clusters among the tested genotypes, cluster A represented a landrace Terabali from Assam and cluster B with all other genotypes.

Complex Approach to Species-Specific Detection of Cowpox Virus

Objective of the study is to develop and validate the method for species-specific detection of cowpox virus (CPV). Materials and methods. Utilized were oligonucleotide primers and fluorescence-labeled probes for genus-specific detection of orthopoxviruses (OPV) and species-specific detection of cowpox and ectromelia viruses (EV). Pairs of fluorescent dyes and corresponding fluorescence extinguishers were embodied into probes in accordance with their specificity: OPV-specific probe contained FAM/BHQ1 pair, CPV???specific probe – JOE/BHQ1, and EV-specific – Cy5/BHQ3. For evaluation of sensitivity and specificity of the method for species-specific detection of CPV, investigated were samples of 68 different strains of orthopoxviruses. Results and conclusions. Implemented was complex approach to species-specific detection of CPV using multiplex real-time PCR variant for simultaneous multilocus detection on the basis of three independent target genes of CPV, to genus-specific detection for the exclusion of false-negative results, and additional oligonucleotide primers and probes, providing for specific detection of EV, aimed at the exclusion of false-positive results.