Mutagenic oligonucleotide-directed PCR amplification (Mod-PCR): an efficient method for generating random base substitution mutations in a DNA sequence element.

Rice blast is one of the most damaging diseases of rice worldwide. In the present study, we analyzed DNA sequence variation of avirulence (AVR) genes of AVR-Pita1 in field isolates of Magnaporthe oryzae in order to understand the effectiveness of the resistance gene Pi-ta in China. Genomic DNA of 366 isolates of M. oryzae collected from Yunnan province of China were used for polymerase chain reaction (PCR) amplification to examine the existence of AVR-Pita1 using gene-specific PCR markers. Results of PCR products revealed that 218 isolates of M. oryzae carry AVR-Pita1. Among of them, 62.5, 56.3, 58.5, 46.7, 72.4, and 57.4% of M. oryzae carry AVR-Pita1 from northeastern, southeast, western, northwest, southwestern, and central Yunnan province, respectively. The detection rate of AVR-Pita1 was, in order: southwestern > northeastern > western > central > southeastern > northwestern Yunnan province. Moreover, in total, 18 AVR-Pita1 haplotypes encoding 13 novel AVR-Pita1 variants were identified among 60 isolates. Most DNA sequence variation was found to occur in the exon region, resulting in amino acid substitution. Six virulent haplotypes of AVR-Pita1 to Pita were identified among 60 field isolates. The AVR-Pita1 has evolved to virulence from avirulent origins via base substitution. These findings demonstrate that AVR-Pita1 is under positive selection and mutations of AVR-Pita1 are responsible for defeating race-specific resistance in nature.

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A Practical and Efficient Method for The Retrieval of Ancient DNA Sequence*

PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS ◽

10.3724/sp.j.1206.2009.00133 ◽

2009 ◽

Vol 36 (11) ◽

pp. 1495-1502

Author(s):

Ran-Ran LIU ◽

Jing YUAN ◽

Xing-Bo ZHAO ◽

Ning LI

Keyword(s):

Dna Sequence ◽

Ancient Dna ◽

Efficient Method

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A novel method to quantify base substitution mutations at the 10 −6 per bp level in DNA samples

Cancer Letters ◽

10.1016/j.canlet.2017.06.010 ◽

2017 ◽

Vol 403 ◽

pp. 152-158 ◽

Cited By ~ 4

Author(s):

Satoshi Yamashita ◽

Naoko Iida ◽

Hideyuki Takeshima ◽

Naoko Hattori ◽

Masahiro Maeda ◽

...

Keyword(s):

Base Substitution ◽

Novel Method ◽

Substitution Mutations

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The effect of attachment site mutations on strand exchange in bacteriophage lambda site-specific recombination.

Genetics ◽

10.1093/genetics/122.4.727 ◽

1989 ◽

Vol 122 (4) ◽

pp. 727-736

Author(s):

C E Bauer ◽

J F Gardner ◽

R I Gumport ◽

R A Weisberg

Keyword(s):

Attachment Site ◽

Strand Exchange ◽

Segregation Pattern ◽

Base Substitution ◽

Base Pairs ◽

Multiple Mutation ◽

Attachment Sites ◽

Dna Strands ◽

Substitution Mutations ◽

Overlap Region

Abstract Recombination of phage lambda attachment sites occurs by sequential exchange of the DNA strands at two specific locations. The first exchange produces a Holliday structure, and the second resolves it to recombinant products. Heterology for base substitution mutations in the region between the two strand exchange points (the overlap region) reduces recombination; some mutations inhibit the accumulation of Holliday structures, others inhibit their resolution to recombinant products. To see if heterology also alters the location of the strand exchange points, we determined the segregation pattern of three single and one multiple base pair substitution mutations of the overlap region in crosses with wild type sites. The mutations are known to differ in the severity of their recombination defect and in the stage of strand exchange they affect. The three single mutations behaved similarly: each segregated into both products of recombination, and the two products of a single crossover were frequently nonreciprocal in the overlap region. In contrast, the multiple mutation preferentially segregated into one of the two recombinant products, and the two products of a single crossover appeared to be fully reciprocal. The simplest explanation of the segregation pattern of the single mutations is that strand exchanges occur at the normal locations to produce recombinants with mismatched base pairs that are frequently repaired. The segregation pattern of the multiple mutation is consistent with the view that both strand exchanges usually occur to one side of the mutant site. We suggest that the segregation pattern of a particular mutation is determined by which stage of strand exchange it inhibits and by the severity of the inhibition.

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Mapping mutations in genes encoding the two large subunits of Drosophila RNA polymerase II defines domains essential for basic transcription functions and for proper expression of developmental genes

Molecular and Cellular Biology ◽

10.1128/mcb.13.7.4214-4222.1993 ◽

1993 ◽

Vol 13 (7) ◽

pp. 4214-4222

Author(s):

Y Chen ◽

J Weeks ◽

M A Mortin ◽

A L Greenleaf

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Dna Sequence ◽

Pcr Amplification ◽

Single Strand Conformation Polymorphism ◽

Chain Elongation ◽

Developmental Defect ◽

Genes Encoding ◽

Transcript Elongation

We have mapped a number of mutations at the DNA sequence level in genes encoding the largest (RpII215) and second-largest (RpII140) subunits of Drosophila melanogaster RNA polymerase II. Using polymerase chain reaction (PCR) amplification and single-strand conformation polymorphism (SSCP) analysis, we detected 12 mutations from 14 mutant alleles (86%) as mobility shifts in nondenaturing gel electrophoresis, thus localizing the mutations to the corresponding PCR fragments of about 350 bp. We then determined the mutations at the DNA sequence level by directly subcloning the PCR fragments and sequencing them. The five mapped RpII140 mutations clustered in a C-terminal portion of the second-largest subunit, indicating the functional importance of this region of the subunit. The RpII215 mutations were distributed more broadly, although six of eight clustered in a central region of the subunit. One notable mutation that we localized to this region was the alpha-amanitin-resistant mutation RpII215C4, which also affects RNA chain elongation in vitro. RpII215C4 mapped to a position near the sites of corresponding mutations in mouse and in Caenorhabditis elegans genes, reinforcing the idea that this region is involved in amatoxin binding and transcript elongation. We also mapped mutations in both RpII215 and RpII140 that cause a developmental defect known as the Ubx effect. The clustering of these mutations in each gene suggests that they define functional domains in each subunit whose alteration induces the mutant phenotype.

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Randomness of Base Substitution Mutations Induced in the lacl Gene of Escherichia coli by Ionizing Radiation

Radiation Research ◽

10.2307/3576404 ◽

1985 ◽

Vol 101 (2) ◽

pp. 402 ◽

Cited By ~ 15

Author(s):

Takesi Kato ◽

Yoshimitsu Oda ◽

Barry W. Glickman

Keyword(s):

Escherichia Coli ◽

Ionizing Radiation ◽

Base Substitution ◽

Substitution Mutations

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Study on the expression of specific chimeric-orfs of C type cytoplasmic male sterile in maize

Israel Journal of Plant Sciences ◽

10.1080/07929978.2014.945314 ◽

2013 ◽

Vol 61 (1-4) ◽

pp. 25-36 ◽

Cited By ~ 1

Author(s):

Jiyue Wang ◽

Lihua Zeng ◽

Shengqing Wang ◽

Jing Wang ◽

Yanli Lu ◽

...

Keyword(s):

Base Substitution ◽

Pcr Analysis ◽

Male Sterile ◽

Maintainer Line ◽

Cytoplasmic Male Sterile ◽

Real Time Quantitative Pcr ◽

Substitution Mutations ◽

Membrane Spanning ◽

Insertion Mutations ◽

Online Software

In the present study, a mutated chimericorf364, namedorf366-c, was identified in a maize C type cytoplasmic male sterile line (CMS-C) by PCR and RT-PCR. Four base pair adjacent base substitution mutations (CAAA to TTTT) and eight bp insertion mutations were found inorf366-ccompared withorf364. ORF366-C was predicted to contain one membrane-spanning domain using TMHMM online software. Real-time quantitative PCR analysis showed thatorf366-cwas upregulated in the CMS-C line in comparison to its maintainer line at the uninucleate stage. The protokaryotic protein expression oforf366-cinEscherichia colishowed that ORF366-C could be a cytotoxic protein. All the results indicated thatorf366-cmay be associated with maize CMS-C.

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