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Cloning of seed dormancy genes (TaSdr) associated with tolerance to pre-harvest sprouting in common wheat and development of a functional marker 总被引:1,自引:0,他引:1
Yingjun Zhang Xilei Miao Xianchun Xia Zhonghu He 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2014,127(4):855-866
Key message
After cloning and mapping of wheat TaSdr genes, both the functional markers for TaSdr - B1 and TaVp - 1B were validated, and the distribution of allelic variations at TaSdr - B1 locus in the wheat cultivars from 19 countries was characterized.Abstract
Seed dormancy is a major factor associated with pre-harvest sprouting (PHS) in common wheat (Triticum aestivum L.). Wheat TaSdr genes, orthologs of OsSdr4 conferring seed dormancy in rice, were cloned by a comparative genomics approach. They were located on homoeologous group 2 chromosomes, and designated as TaSdr-A1, TaSdr-B1 and TaSdr-D1, respectively. Sequence analysis of TaSdr-B1 revealed a SNP at the position -11 upstream of the initiation codon, with bases A and G in cultivars with low and high germination indices (GI), respectively. A cleaved amplified polymorphism sequence marker Sdr2B was developed based on the SNP, and subsequently functional analysis of TaSdr-B1 was conducted by association and linkage mapping. A QTL for GI co-segregating with Sdr2B explained 6.4, 7.8 and 8.7 % of the phenotypic variances in a RIL population derived from Yangxiaomai/Zhongyou 9507 grown in Shijiazhuang, Beijing and the averaged data from those environments, respectively. Two sets of Chinese wheat cultivars were used for association mapping, and results indicated that TaSdr-B1 was significantly associated with GI. Analysis of the allelic distribution at the TaSdr-B1 locus showed that the frequencies of TaSdr-B1a associated with a lower GI were high in cultivars from Japan, Australia, Argentina, and the Middle and Lower Yangtze Valley Winter Wheat Region and Southwest Winter Wheat Region in China. This study provides not only a reliable functional marker for molecular-assisted selection of PHS in wheat breeding programs, but also gives novel information for a comprehensive understanding of seed dormancy. 相似文献2.
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Coralie Barthelemy-Delaux David Marburger Pierre-Marc Delaux Shawn Conley Jean-Michel Ané 《Plant and Soil》2014,382(1-2):165-173
Background and aims
Bradyrhizobium japonicum and soybean (Glycine max (L.) Merr.) form a symbiotic association which allows for biological nitrogen fixation (BNF) to help meet the nitrogen (N) requirement of soybean plants. Rhizobial inoculants are not always used in soybean production in the Midwestern USA because of high naturalized soil populations, but drought conditions experienced in the region during the 2012 growing season may have led to a decline in numbers resulting in the need for inoculation the following growing season. Therefore, the effect of drought on B. japonicum population size was investigated in this study.Methods
Drought conditions, 8 weeks long or 4 weeks long preceded (STOP) or followed (START) by 4 weeks of normal watering, were simulated in two contrasting soil types in a greenhouse setting with soybeans as host plants. Drought conditions were monitored by measuring water content. Population size of B. japonicum was quantified using quantitative real-time polymerase chain reaction (qPCR) and most probable number (MPN) methods and compared to population from non-drought treatment.Results
Using both quantification methods, the response of B. japonicum to drought treatments was minimal.Conclusions
Drought conditions 4 to 8 weeks long did not reduce B. japonicum population size to levels which would affect soybean growth and development. 相似文献5.
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Jonathan R. Gaiero Elizabeth Bent Tandra D. Fraser Leo M. Condron Kari E. Dunfield 《Plant and Soil》2018,427(1-2):39-51
Background and aims
Microbially driven mineralization of organic phosphorus forms is of particular importance in the soil environment, where it becomes available to plants as inorganic orthophosphates. In acidic soils, microbes produce non-specific acid phosphatases (NSAPs; E.C. 3.1.3.2) which act on the most common forms of organic P in the soil. Our understanding of phosphorus turnover in soils would greatly benefit from an improvement in research tools targeting these genes.Methods
Thus, in this study we developed two novel oligonucleotide PCR primer sets, that will enable researchers to target the present and active communities of bacteria with the genetic potential of acid phosphatase production. A total of three primer sets were validated to target the three classes of NSAPs. Utilizing Illumina MiSeq, amplicons from grassland pasture soils were sequenced.Results
The resulting target specificity was high for all three groups; CAAP (97.2%), CBAP (99.5%), and CCAP (94.8%). Quantification of target genes by qPCR indicated measurable differences between classes, ranging from 5 log to 7.5 log for CAAP, 6 log to 8 log for CBAP, and 4 log to 5 log for CCAP.Conclusions
The validated primer sets were specific to the target genes and identified potential quantitative differences between the NSAP classes.7.
Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata 总被引:1,自引:0,他引:1
Jun Zou Harsh Raman Shaomin Guo Dandan Hu Zili Wei Ziliang Luo Yan Long Wenxia Shi Zhong Fu Dezhi Du Jinling Meng 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2014,127(7):1593-1605
Key message
An integrated dense genetic linkage map was constructed in a B. carinata population and used for comparative genome analysis and QTL identification for flowering time.Abstract
An integrated dense linkage map of Brassica carinata (BBCC) was constructed in a doubled haploid population based on DArT-SeqTM markers. A total of 4,031 markers corresponding to 1,366 unique loci were mapped including 639 bins, covering a genetic distance of 2,048 cM. We identified 136 blocks and islands conserved in Brassicaceae, which showed a feature of hexaploidisation representing the suggested ancestral crucifer karyotype. The B and C genome of B. carinata shared 85 % of commonly conserved blocks with the B genome of B. nigra/B. juncea and 80 % of commonly conserved blocks with the C genome of B. napus, and shown frequent structural rearrangements such as insertions and inversions. Up to 24 quantitative trait loci (QTL) for flowering and budding time were identified in the DH population. Of these QTL, one consistent QTL (qFT.B4-2) for flowering time was identified in all of the environments in the J block of the B4 linkage group, where a group of genes for flowering time were aligned in A. thaliana. Another major QTL for flowering time under a winter-cropped environment was detected in the E block of C6, where the BnFT-C6 gene was previously localised in B. napus. This high-density map would be useful not only to reveal the genetic variation in the species with QTL analysis and genome sequencing, but also for other applications such as marker-assisted selection and genomic selection, for the African mustard improvement. 相似文献8.
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Lakshmi Dhevi Nagarajha Selvan Jyothi Embekkat Kaviyil Raja Sekhar Nirujogi Babylakshmi Muthusamy Vinuth N Puttamallesh Tejaswini Subbannayya Nazia Syed Aneesha Radhakrishnan Dhanashree S Kelkar Sartaj Ahmad Sneha M Pinto Praveen Kumar Anil K Madugundu Bipin Nair Aditi Chatterjee Akhilesh Pandey Raju Ravikumar Harsha Gowda Thottethodi Subrahmanya Keshava Prasad 《Clinical proteomics》2014,11(1):1-16
Background
Cryptococcus neoformans, a basidiomycetous fungus of universal occurrence, is a significant opportunistic human pathogen causing meningitis. Owing to an increase in the number of immunosuppressed individuals along with emergence of drug-resistant strains, C. neoformans is gaining importance as a pathogen. Although, whole genome sequencing of three varieties of C. neoformans has been completed recently, no global proteomic studies have yet been reported.Results
We performed a comprehensive proteomic analysis of C. neoformans var. grubii (Serotype A), which is the most virulent variety, in order to provide protein-level evidence for computationally predicted gene models and to refine the existing annotations. We confirmed the protein-coding potential of 3,674 genes from a total of 6,980 predicted protein-coding genes. We also identified 4 novel genes and corrected 104 predicted gene models. In addition, our studies led to the correction of translational start site, splice junctions and reading frame used for translation in a number of proteins. Finally, we validated a subset of our novel findings by RT-PCR and sequencing.Conclusions
Proteogenomic investigation described here facilitated the validation and refinement of computationally derived gene models in the intron-rich genome of C. neoformans, an important fungal pathogen in humans. 相似文献11.
Mustafa Kolukirik Mesut Yılmaz Orhan Ince Canan Ketre Ayşe Istanbullu Tosun Bahar K. Ince 《Annals of clinical microbiology and antimicrobials》2016,15(1):46
Background
Group A streptococci (GAS) are the most common bacterial cause of acute pharyngitis and account for 15–30 % of cases of acute pharyngitis in children and 5–10 % of cases in adults. In this study, a real-time quantitative PCR (qPCR) based GAS detection assay in pharyngeal swab specimens was developed.Methods
The qPCR assay was compared with the gold standard bacterial culture and a rapid antigen detection test (RADT) to evaluate its clinical performance in 687 patients. The analytical sensitivity of the assay was 240 cfu/swab. Forty-five different potential cross-reacting organisms did not react with the test. Four different laboratories for the reproducibility studies were in 100 % (60/60) agreement for the contrived GAS positive and negative swab samples.Results
The relative sensitivities of the RADT and the qPCR test were 55.9 and 100 %; and the relative specificities were 100 and 96.3 %, respectively. Duration of the total assay for 24 samples including pre-analytical processing and analysis changed between 42 and 55 min depending on the type of qPCR instrument used. A simple DNA extraction method and a low qPCR volume made the developed assay an economical alternative for the GAS detection.Conclusion
We showed that the developed qPCR test is rapid, cheap, sensitive and specific and therefore can be used to replace both antigen detection and culture for diagnosis of acute GAS pharyngitis.12.
Guihua Lu Xiping Wang Junhua Liu Kun Yu Yang Gao Haiyan Liu Changgui Wang Wei Wang Guokui Wang Min Liu Guanfan Mao Binfeng Li Jianying Qin Mian Xia Junli Zhou Jingmei Liu Shuqin Jiang Hua Mo Jinteng Cui Nobuhiro Nagasawa Shoba Sivasankar Marc C. Albertsen Hajime Sakai Barbara J. Mazur Michael W. Lassner Richard M. Broglie 《Plant cell reports》2014,33(4):617-631
Key message
A high-quality rice activation tagging population has been developed and screened for drought-tolerant lines using various water stress assays. One drought-tolerant line activated two rice glutamate receptor-like genes. Transgenic overexpression of the rice glutamate receptor-like genes conferred drought tolerance to rice and Arabidopsis.Abstract
Rice (Oryza sativa) is a multi-billion dollar crop grown in more than one hundred countries, as well as a useful functional genetic tool for trait discovery. We have developed a population of more than 200,000 activation-tagged rice lines for use in forward genetic screens to identify genes that improve drought tolerance and other traits that improve yield and agronomic productivity. The population has an expected coverage of more than 90 % of rice genes. About 80 % of the lines have a single T-DNA insertion locus and this molecular feature simplifies gene identification. One of the lines identified in our screens, AH01486, exhibits improved drought tolerance. The AH01486 T-DNA locus is located in a region with two glutamate receptor-like genes. Constitutive overexpression of either glutamate receptor-like gene significantly enhances the drought tolerance of rice and Arabidopsis, thus revealing a novel function of this important gene family in plant biology. 相似文献13.
Mina Jin Soo-Seong Lee Lin Ke Jung Sun Kim Mi-Suk Seo Seong-Han Sohn Beom-Seok Park Guusje Bonnema 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2014,127(2):509-519
Key message
A novel dominant resistance gene, TuRB07, was found to confer resistance to an isolate of TuMV strain C4 in B. rapa line VC1 and mapped on the top of chromosome A06.Abstract
The inheritance of resistance to Turnip mosaic virus in Brassica rapa was investigated by crossing the resistant line, VC1 with the susceptible line, SR5, and genotyping and phenotyping diverse progenies derived from this cross. Both a doubled haploid population, VCS3M-DH, an F2 and two BC1 (F1 × VC1 and F1 × SR5) populations were created. Population tests revealed that the resistance to the TuMV C4 isolate in B. rapa is controlled by a single dominant gene. This resistance gene, TuRB07 was positioned on the top of linkage group A06 of the B. rapa genome through bulk segregation analysis and fine mapping recombinants in three doubled haploid- and one backcross population using microsatellite markers developed from BAC end sequences. Within the region between the two closely linked markers flanking TuRB07, H132A24-s1, and KS10960, in the Chiifu reference genome, two genes encoding nucleotide-binding site and leucine-rich repeat proteins with a coiled-coil motif (CC-NBS-LRR), Bra018862 and Bra018863 were identified as candidate resistance genes. The gene Bra018862 is truncated, but the gene Bra018863 has all the domains to function. Furthermore, the analysis of structural variation using resequencing data of VC1 and SR5 revealed that Bra018863 might be a functional gene because the gene has no structural variation in the resistant line VC1 when compared with Chiifu, whereas at the other NBS-LRR genes large deletions were identified in the resistant line. Allelic differences of Bra018863 were found between VC1 and SR5, supporting the notion that this gene is a putative candidate gene for the virus resistance. 相似文献14.
Alexander Tiong Kah Lord Kavitha Mohandas Sushela Somanath Stephen Ambu 《Annals of clinical microbiology and antimicrobials》2010,9(1):1-5
Background
Pseudomonas aeruginosa is responsible for numerous bloodstream infections associated with severe adverse outcomes in case of inappropriate initial antimicrobial therapy. The present study was aimed to develop a novel quantitative PCR (qPCR) assay, using ecfX as the specific target gene, for the rapid and accurate identification of P. aeruginosa from positive blood cultures (BCs).Methods
Over the period August 2008 to June 2009, 100 BC bottles positive for gram-negative bacilli were tested in order to evaluate performances of the qPCR technique with conventional methods as gold standard (i.e. culture and phenotypic identification).Results
Thirty-three strains of P. aeruginosa, 53 strains of Enterobactericaeae, nine strains of Stenotrophomonas maltophilia and two other gram-negative species were isolated while 3 BCs were polymicrobial including one mixture containing P. aeruginosa. All P. aeruginosa clinical isolates were detected by qPCR except a single strain in mixed culture. Performances of the qPCR technique were: specificity, 100%; positive predictive value, 100%; negative predictive value, 98.5%; and sensitivity, 97%.Conclusions
This reliable technique may offer a rapid (<1.5 h) tool that would help clinicians to initiate an appropriate treatment earlier. Further investigations are needed to assess the clinical benefit of this novel strategy as compared to phenotypic methods. 相似文献15.
Background
Diverse plant and animal species have B chromosomes, also known as accessory, extra or supernumerary chromosomes. Despite being widely distributed among different taxa, the genomic nature and genetic behavior of B chromosomes are still poorly understood.Results
In this study we describe the occurrence of B chromosomes in the African cichlid fish Haplochromis obliquidens. One or two large B chromosome(s) occurring in 39.6% of the analyzed individuals (both male and female) were identified. To better characterize the karyotype and assess the nature of the B chromosomes, fluorescence in situ hybridization (FISH) was performed using probes for telomeric DNA repeats, 18S and 5S rRNA genes, SATA centromeric satellites, and bacterial artificial chromosomes (BACs) enriched in repeated DNA sequences. The B chromosomes are enriched in repeated DNAs, especially non-active 18S rRNA gene-like sequences.Conclusion
Our results suggest that the B chromosome could have originated from rDNA bearing subtelo/acrocentric A chromosomes through formation of an isochromosome, or by accumulation of repeated DNAs and rRNA gene-like sequences in a small proto-B chromosome derived from the A complement. 相似文献16.
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Colin W. Hiebert Brent D. McCallum Julian B. Thomas 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2014,127(9):2005-2009
Key message
KU3198 is a common wheat accession that carries one novel leaf rust resistance (Lr) gene, Lr70 , and another Lr gene which is either novel, Lr52 or an allele of Lr52.Abstract
Leaf rust, caused by Puccinia triticina Eriks. (Pt), is a broadly distributed and economically important disease of wheat. Deploying cultivars carrying effective leaf rust resistance (Lr) genes is a desirable method of disease control. KU3198 is a common wheat (Triticum aestivum L.) accession from the Kyoto collection that was highly resistant to Pt in Canada. An F2 population from the cross HY644/KU3198 showed segregation for two dominant Lr genes when tested with Pt race MBDS which was virulent on HY644. Multiple bulk segregant analysis (MBSA) was employed to find putative chromosome locations of these Lr genes using SSR markers that provided coverage of the genome. MBSA predicted that the Lr genes were located on chromosomes 5B and 5D. A doubled haploid population was generated from the cross of JBT05-714 (HY644*3/KU3198), a line carrying one of the Lr genes from KU3198, to Thatcher. This population segregated for a single Lr gene conferring resistance to Pt race MBDS, which was mapped to the terminal region of the short arm of chromosome 5B with SSR markers and given the temporary designation LrK1. One F3 family derived from the HY644/KU3198 F2 population that segregated only for the second Lr gene from KU3198 was identified. This family was treated as an F2-equivalent population and used for mapping the Lr gene, which was located to the terminal region of chromosome 5DS. As no other Lr gene has been mapped to 5DS, this gene is novel and has been designated as Lr70. 相似文献18.
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