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1.
Kenta Shirasawa Hideki Hirakawa Tsukasa Nunome Satoshi Tabata Sachiko Isobe 《Plant biotechnology journal》2016,14(1):51-60
Genome‐wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro‐Tom genome were identified by a whole‐genome shotgun sequencing analysis to estimate the spectrum and distribution of whole‐genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired‐end reads for four EMS‐induced mutants and three gamma‐ray‐irradiated lines as well as a wild‐type line were obtained by next‐generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma‐ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1 140 687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild‐type Micro‐Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild‐type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse‐genetic approaches. 相似文献
2.
Vikas K. Singh Aamir W. Khan Rachit K. Saxena Vinay Kumar Sandip M. Kale Pallavi Sinha Annapurna Chitikineni Lekha T. Pazhamala Vanika Garg Mamta Sharma Chanda Venkata Sameer Kumar Swathi Parupalli Suryanarayana Vechalapu Suyash Patil Sonnappa Muniswamy Anuradha Ghanta Kalinati Narasimhan Yamini Rajeev K. Varshney 《Plant biotechnology journal》2016,14(5):1183-1194
To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing‐based bulked segregant analysis (Seq‐BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R‐ and S‐bulks with the help of draft genome sequence and reference‐guided assembly of ICPL 20096 (resistant parent). Seq‐BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re‐sequenced and their combined analysis with R‐ and S‐bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2‐Mb flanking regions of seven candidate SNPs identified through Seq‐BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re‐sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan_01839 for SMD resistance and C.cajan_03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics‐assisted breeding in pigeonpea. 相似文献
3.
Sandip M. Kale Swathi Parupalli Vinay Kumar Annapurna Chitikineni Suryanarayana Vechalapu Chanda Venkata Sameer Kumar Mamta Sharma Anuradha Ghanta Kalinati Narasimhan Yamini Sonnappa Muniswamy Rajeev K. Varshney 《Plant biotechnology journal》2017,15(7):906-914
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time‐consuming. In recent years, a number of single nucleotide polymorphism (SNP)‐based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion–deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel‐seq approach, which is a combination of whole‐genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel‐seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW‐ and SMD‐resistant and FW‐ and SMD‐susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel‐seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel‐seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species. 相似文献
4.
莴苣胚囊发育为蓼型,减数分裂形成的4个大孢子中只有合点端的一个大孢子可继续发育,其余3个大孢子从珠孔端依次退化.大孢子母细胞中的钙沉淀颗粒很少,减数分裂后的四分体中的钙沉淀颗粒稍有增加.以后,4个大孢子中的钙沉淀颗粒在数量上有明显差异:即将退化的大孢子中钙明显减少,而未退化大孢子细胞质中则保持有较多的细小钙沉淀颗粒.大孢子的退化是一种细胞程序死亡现象,细胞中的钙浓度降低时可能启动了大孢子细胞的程序性死亡过程,而细胞中的钙浓度高时则保持大孢子细胞的继续发育.文章首次揭示了大孢子发生过程中钙的分布特征. 相似文献
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M. R. BROADLEY A. J. ESCOBAR-GUTIÉRREZ A. BURNS & I. G. BURNS 《The New phytologist》2000,147(3):519-526
Relationships between nitrogen (N) content and growth are routinely measured in plants. This study determined the effects of N on the separate morphological and physiological components of plant growth, to assess how N-limited growth is effected through these components. Lettuce ( Lactuca sativa ) plants were grown hydroponically under contrasting N-supply regimes, with the external N supply either maintained continuously throughout the period of study, or withdrawn for up to 14 d. Richards' growth functions, selected using an objective curve-fitting technique, accounted for 99.0 and 99.1% of the variation in plant dry weight for control and N-limited plants respectively. Sublinear relationships occurred between N and relative growth rates under restricted N-supply conditions, consistent with previous observations. There were effects of treatment on morphological and physiological components of growth. Leaf weight ratio increased over time in control plants and decreased in N- limited plants. Shoot:root ratio followed a similar pattern. On a whole-plant basis, assimilation of carbon decreased in N-limited plants, a response paralleled by differences in stomatal conductance between treatments. Changes in C assimilation, expressed as a function of stomatal conductance to water vapour, suggest that the effects of N limitation on growth did not result directly from a lack of photosynthetic enzymes. Relationships between plant N content and components of growth will depend on the availability of different N pools for remobilization and use within the plant. 相似文献
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Screening of RAPD Markers Linked to the Photoperiod-Sensitivity Gene in Rice Chromosome 6 Using Bulked Segregant Analysis 总被引:2,自引:0,他引:2
Bulked segregant analysis was used to determine randomly amplifiedpolymorphic DNA (RAPD) markers in a specific interval in themiddle of chromosome 6 of rice for tagging the photoperiod sensitivitygene.Two pools of F2 individuals (japonica cv. Nipponbare and indicacv. Kasalath) were constructed according to the genotypes ofthree restriction fragment length polymorphism (RFLP) markerslocated at both ends and the middle of the targeted interval.Then another pair of pools were constructed based on the "graphicalgenotype," which was made with our high density linkage map.RAPD analysis was performed using these DNA pools as templates,and polymorphic fragments were detected and mapped. Using 80primers, either singlyor pairwise, we tested 2,404 primer pairsand established 14 markers tightly linked to the photoperiodsensitivitygene. The obtained RAPD markers were converted intosequence-tagged sites bycloning and sequencing of the polymorphicfragments and they can be used directlyfor construction of physicalmaps. This bulked segregant method can be applied for any speciesand any region of interest in which detailed linkage maps orphysical maps are needed. 相似文献
9.
Kiehne Kristine Neale David B. 《Molecular breeding : new strategies in plant improvement》1998,4(3):179-185
We present a method to identify molecular markers linked to a genomic interval in outbred pedigrees. Using information from fully informative RFLP markers on a single linkage group containing a quantitative trait locus for wood specific gravity, we constructed four DNA pools from nonrecombinant progeny of a three-generation outbred pedigree. The four pools were screened to identify linked RAPD markers. The phase and zygosity of a linked RAPD marker could be determined directly from the array of RAPD bands present or absent in the four pools. Two hundred fifty-six primers were tested on the four DNA pools, revealing 61 putatively linked loci. Nine RAPD loci were linked to the genomic interval. The approach developed here could be generally applied to saturation mapping in outbred pedigrees where fully informative markers have previously been mapped. 相似文献
10.
Caroline A. Dowling;Jiaqi Shi;Jacob A. Toth;Michael A. Quade;Lawrence B. Smart;Paul F. McCabe;Susanne Schilling;Rainer Melzer; 《The Plant journal : for cell and molecular biology》2024,119(1):383-403
Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is highly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive (“autoflower”) cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. We identified extensive sequence divergence between alleles of CsFT1 from photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences, especially in introns. Furthermore, we observed higher expression of one of the CsFT1 copies found in the photoperiod-insensitive cultivar. Genotyping of several mapping populations and a diversity panel confirmed a correlation between CsFT1 alleles and photoperiod response, affirming that at least two independent loci involved in the photoperiodic control of flowering, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached. 相似文献
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《Bioscience, biotechnology, and biochemistry》2013,77(3):672-676
Stored cut lettuce gradually turns brown on the cut section after several days of storage, because cutting induces phenylalanine ammonia-lyase (PAL) activity, the biosynthesis of polyphenol is promoted, and the polyphenols are oxidized by polyphenol oxidase. In this study, we screened for inhibitors of PAL derived from fermented broths of microbes and from foods and found that a cinnamon extract definitely inhibited PLA of cut lettuce. An active component was isolated by chromatographic procedures and was identified as trans-cinnamaldehyde. Browning of cut lettuce immersed in a solution containing trans-cinnamaldehyde was definitely repressed. 相似文献
13.
BACKGROUND AND AIMS: The objective of this research was to examine the effects of differences in light spectrum on the stomatal conductance (Gs) and dry matter production of lettuce plants grown under a day/night cycle with different spectra, and also the effects on Gs of short-term exposure to different spectra. METHODS: Lettuce (Lactuca sativa) plants were grown with 6 h dark and 18 h light under four different spectra, red-blue (RB), red-blue-green (RBG), green (GF) and white (CWF), and Gs and plant growth were measured. KEY RESULTS AND CONCLUSIONS: Conductance of plants grown for 23 d under CWF rose rapidly on illumination to a maximum in the middle of the light period, then decreased again before the dark period when it was minimal. However, the maximum was smaller in plants grown under RB, RGB and GF. This demonstrates that spectral quality during growth affects the diurnal pattern of stomatal conductance. Although Gs was smaller in plants grown under RGB than CWF, dry mass accumulation was greater, suggesting that Gs did not limit carbon assimilation under these spectral conditions. Temporarily changing the spectral quality of the plants grown for 23 d under CWF, affected stomatal responses reversibly, confirming studies on epidermal strips. This study provides new information showing that Gs is responsive to spectral quality during growth and, in the short-term, is not directly coupled to dry matter accumulation. 相似文献
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Mark D. Burow Charles E. Simpson Andrew H. Paterson James L. Starr 《Molecular breeding : new strategies in plant improvement》1996,2(4):369-379
DNA markers linked to a root-knot nematode resistance gene derived from wild peanut species have been identified. The wild diploid peanut accessions K9484 (Arachis batizocoi Krapov. & W. C. Gregory), GKP10017, (A. cardenasii Krapov & W. C. Gregory), and GKP10602 (A. diogoi Hoehne) possess genes for ressitance to Meloidogyne arenaria. These three accessions and A. hypogaea cv. Florunner were crossed to generate the hybrid resistant breeding line TxAg-7. This line was used as donor parent to develop a BC4F2 population segregating for resistance. Three RAPD markers associated with nematode resistance were identified in this population by bulked segregant analysis. Linkage was confirmed by screening 21 segregatingh BC4F2 and 63 BC5F2 single plants. Recombination between marker RKN410 and resistance, and between marker RKN440 and resistance, was estimated to be 5.4±1.9% and 5.8±2.1%, respectively, on a per-generation basis. These two markers identified a resistance gene derived from either A. cardenasii or A. diogoi, and were closely linked to each other. Recombination between a third marker, RKN229, inherited from A. cardenasii or A. diogoi, and resistance was 9.0±3.2% per generation. Markers RKN410 and RKN229 appeared to be linked genetically and flank the same resistance gene. All markers were confirmed by hybridization of cloned or gel-purified marker DNA to blots of PCR-amplified DNA. Pooled data on the segregation of BC5F2 plants was consistent with the presence of one resistance gene in the advanced breeding lines. Different distributions of resistance in the BC5F2 progeny and TxAG-7 suggest the presence of additional resistance genes in TxAG-7. 相似文献
16.
Takahiro Noda Kazuhiko Iimure Shunsuke Okamoto Akira Saito 《Bioscience, biotechnology, and biochemistry》2017,81(8):1484-1488
Browning of plant tissue is generally considered attributable to enzymatic oxidation by polyphenol oxidase (PPO). Electrophoresis followed by activity staining has been used as an effective procedure to visually detect and isolate isozymes; however, it has not been applied for examination of various PPO isozymes in lettuce. Our study demonstrated that different lettuce PPO isozymes could be detected at different pH in active staining, and multiple isozymes were detected only under alkaline conditions. As a result, we concluded that activity staining with approximately pH 8 enabled to detect various PPO isozymes in lettuce. By expression analysis of the PPO isozymes after wounding, PPO isozymes that correlated with time-course of tissue browning were detected. The wound-induced PPO may play a key role in enzymatic browning. 相似文献
17.
Seo Y. W. Johnson J. W. Jarret R. L. 《Molecular breeding : new strategies in plant improvement》1997,3(3):177-181
Near-isogenic lines in conjunction with bulked segregant analysis were used to identify a DNA marker in wheat (Triticum aestivum L.) associated with the H21 gene conferring resistance to biotype L of Hessian fly [Mayetiola destructor (Say)] larvae. Near-isogenic lines were developed by backcross introgression BC3F3:4 (Coker 797 * 4 / Hamlet) and differed by the presence or absence of H21 (on 2RL) derived from Chaupon rye (Secale cereale L.). Bulked DNA samples were prepared from near-isogenic lines and BC3F2 population individuals segregating for reaction to Hessian fly biotype L and screened for random amplified polymorphic DNA markers using 46 10mer primers. Random-amplified polymorphic DNA markers from resistant and susceptible individuals and parental lines were scored and these data were used to identify a 3 kb DNA fragment that was related to the occurrence of H21. This fragment was amplified from DNA isolated from Hamlet, a near-isogenic line carrying 2RL, and bulked DNA from resistant BC3F2 individuals, but not from the recurrent parent Coker 797 or DNA bulks from susceptible BC3F2 plants. Analysis of 111 BC3F2 segregating individuals and BC3F2:3 segregants confirmed the co-segregation of the 3 kb DNA marker with the H21 resistance gene to Hessian fly. Use of this marker could facilitate more rapid screening of plant populations for Hessian fly resistance and monitoring the introgression of H21. 相似文献
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Garratt LC Linforth R Taylor AJ Lowe KC Power JB Davey MR 《Plant biotechnology journal》2005,3(2):165-174
Metabolite fingerprinting has been achieved using direct atmospheric pressure chemical ionization-mass spectrometry (APCI-MS) and linked gas chromatography (GC-APCI/EI-MS) for transgenic lettuce (Lactuca sativa L. cv. Evola) plants expressing an IPT gene under the control of the senescence-specific SAG12 promoter from Arabidopsis thaliana (P(SAG12)-IPT). Mature heads of transgenic lettuce and their azygous controls were maintained under defined conditions to assess their shelf life. Transgenic lettuce plants exhibited delayed senescence and significant increases (up to a maximum of threefold) in the concentrations of three volatile organic compounds (VOCs), corresponding to molecular masses of 45, 47 and 63, when compared with heads from azygous plants. These VOCs were identified as acetaldehyde (45), ethanol (47) and dimethyl sulphide (63). The increase in dimethyl sulphide was paralleled by an accumulation of reactive oxygen species (ROS) in the heads of transgenic plants. These results demonstrate the applicability of metabolic fingerprinting techniques to elucidate the underlying pleiotropic responses of plants to transgene expression. 相似文献
20.
The pigment and auxotrophic mutants of Rhodobacter sphaeroides Y6 were obtained by treatment with ethyl methanesulfonate (EMS) followed by lithium chloride (LiCl). Treatment with 0.081
MEMS and subsequent treatment with 0.071 M LiCl resulted in 12% higher frequency og than that by 0.081 mol/L EMS alone, and
the same frequency of pigment mutations than application of 0.081 M EMS alone; the frequency of auxotrophic mutations increased
2.5-fold when treatment with lithium chloride was applied. A blue shift by 10 nm was recorded in the absorption spectrum of
carotenoids form YM5-3 green mutant; considerable accumulation of neurosporine was revealed by HPLC and mass spectrometry.
The method is efficient for isolating the mutants of photosynthetic bacteria.
Published in Russian in Mikrobiologiya, 2006, Vol. 75, No. 6, pp. 758–764.
The text was submitted by the authors in English. 相似文献