Development of a STS marker assay for detecting loss of heterozygosity in rice hybrids

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 23-26
Author(s):  
Xiaomei Li ◽  
Richard R-C Wang ◽  
Steve R Larson ◽  
N Jerry Chatterton
Keyword(s):  
Loss Of Heterozygosity ◽  
Dna Sequence ◽  
Random Amplified Polymorphic Dna ◽  
Rice Chromosome ◽  
Agarose Gel ◽  
Chromosome 2 ◽  
Sts Marker ◽  
Cross Hybridization ◽  
Pcr Products ◽  
Marker Assay

The RAPD (random amplified polymorphic DNA) markers OPE15750 and OPE15300 were affected by loss of heterozygosity (LOH) in rice hybrids AMR × 'M202' and AMR × 'L202'. The markers were mapped to the same locus at or near the centromere of rice chromosome 2. The two RAPD products were cloned, sequenced, and found to have lengths of 734 bp and 297 bp, respectively. The 297-bp sequence shares a 98% homology with one end of the 734-bp sequence, accounting for the cross-hybridization previously observed between the two clones. Based on the DNA sequence of the 734-bp fragment, a pair of STS (sequence-tagged site) primers was designed and tested. Rice plants homozygous for either OPE15734 or OPE15297 all produced PCR fragments of the same length, 482 bp. However, the two PCR products were discernible by digestion with the restriction enzyme XbaI prior to gel electrophoresis. The STS product from plants homozygous for OPE15734 was cut into two fragments of 239 and 240 bp, which appeared as one single band in an agarose gel; whereas the STS product from plants homozygous for OPE15297 was not cut by XbaI and was characterized by a 482-bp band in the agarose gel. These STS primers were tested in rice hybrids and F2 progenies derived from the hybrids of AMR × 'M202' and AMR × 'L202'. Homozygosity for OPE15297 was confirmed for all F2 panicle rows derived from AMR × 'M202'. In contrast, F2 panicle rows of AMR × 'L202' exhibited two different segregation patterns (genotypes), i.e., either uniformly homozygous for the 240-bp marker (OPE15734/OPE15734) or segregating for the 482- and 240-bp markers (OPE15734/OPE15297). This STS-marker system provides a robust assay for detecting the occurrence of LOH in rice hybrid progenies.Key words: DNA sequence, homology, PCR, RAPD.

Loss of heterozygosity and accelerated genotype fixation in rice hybrids

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 789-796 ◽  
Author(s):  
RR -C Wang ◽  
X -M Li ◽  
N J Chatterton
Keyword(s):  
Loss Of Heterozygosity ◽  
Random Amplified Polymorphic Dna ◽  
Somatic Cells ◽  
Rice Cultivar ◽  
Molecular Data ◽  
Breeding Cycle ◽  
Chromosome 2 ◽  
Somatic Variation ◽  
Daughter Cells

Loss of heterozygosity is reported in rice hybrids of a particular heritage. Hybrids derived from a plant selected from the Chinese rice cultivar 'Zhongxin No. 1' exhibited somatic variations as evidenced by having both segregating and uniform panicle rows in F2 progenies. F3 plants from uniform F2 rows were found to be homozygous for all 14 RAPD (random amplified polymorphic DNA) markers, of which two co-dominant markers were located on chromosome 2 and five other markers were on five different chromosomes. RAPD markers unique to either parent were present or absent in all F2 plants within some panicle rows, yet segregated in a Mendelian manner in other panicle rows. The molecular data suggest that somatic cells in these hybrids do not always contain both parental homologues of some chromosomes. These findings support the hypothesis that somatic chromosome pairing and recombination lead to loss of heterozygosity and non-identical daughter cells following mitosis. Sequential mitotic assortment of chromosome homologues of a plant's genome can lead to homozygous or nearly homozygous somatic cells that eventually develop into reproductive cells. As a result of this unique mechanism in rice hybrids derived from Zhongxin No. 1, uniform or less-segregating progenies can be identified from F2 or F3 panicle rows at a much higher frequency than normally expected. This phenomenon can be utilized to shorten the breeding cycle of rice, or other crops when plants containing gene(s) for mitotic pairing are identified, or when the genes are isolated from rice and effectively transferred into other crops.Key words: LOH, in vivo somatic variation, homozygous F2, RAPD, apomixis.

scholarly journals Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran

2015 ◽  
Vol 8 (8) ◽  
pp. 185 ◽  
Author(s):  
Sina Mobasherizadeh ◽  
Hasan Shojaei ◽  
Seyed Asghar Havaei ◽  
Kamyar Mostafavizadeh ◽  
Fazollah Davoodabadi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Laboratory Tests ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Cost Effective ◽  
Agarose Gel ◽  
Healthy Children ◽  
Rapd Fingerprinting ◽  
Pcr Products

<p>The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates.</p><p>The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program.<strong></strong></p><p>The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), “RT1” (12, 48%), “RT2” (8, 32%), “RT3” (3, 12%), and “RT4 and RT5”, (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types.</p><p>This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests.</p>

Development of a STS marker assay for detecting loss of heterozygosity in rice hybrids

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 23-26
Author(s):  
Xiaomei Li ◽  
Richard R.-C. Wang ◽  
Steve R. Larson ◽  
N. Jerry Chatterton
Keyword(s):  
Loss Of Heterozygosity ◽  
Sts Marker ◽  
Marker Assay

scholarly journals Isolation and mapping of a polymorphic DNA sequence pHHH133 on chromosome 2 (D2S45)

1987 ◽  
Vol 15 (23) ◽  
pp. 10075-10075
Author(s):  
M. Hoff ◽  
Y. Nakamura ◽  
L. Ballard ◽  
P. O'Connell ◽  
M. Leppert ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Chromosome 2

scholarly journals Isolation and mapping of a polymorphic DNA sequence pYNZ9.1 on chromosome 2 (D2S46)

1987 ◽  
Vol 15 (23) ◽  
pp. 10074-10074 ◽  
Author(s):  
M. Culver ◽  
Y. Nakamura ◽  
L. Ballard ◽  
P. O'Connell ◽  
M. Leppert ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Chromosome 2

A cDNA from Drosophila melanogaster encodes a lamin C-like intermediate filament protein

1993 ◽  
Vol 104 (4) ◽  
pp. 1263-1272 ◽  
Author(s):  
C.A. Bossie ◽  
M.M. Sanders
Keyword(s):  
Drosophila Melanogaster ◽  
Intermediate Filament ◽  
Blot Analysis ◽  
Polytene Chromosomes ◽  
Intermediate Filament Protein ◽  
Chromosome 2 ◽  
Cross Hybridization ◽  
Intermediate Filament Proteins ◽  
Nuclear Lamins ◽  
Filament Protein

A novel intermediate filament cDNA, pG-IF, has been isolated from a Drosophila melanogaster embryonic expression library screened with a polyclonal antiserum produced against a 46 kDa cytoskeletal protein isolated from Kc cells. This 46 kDa protein is known to be immunologically related to vertebrate intermediate filament proteins. The screen resulted in the isolation of four different cDNA groups. Of these, one has been identified as the previously characterized Drosophila nuclear lamin cDNA, Dm0, and a second, pG-IF, demonstrates homology to Dm0 by cross hybridization on Southern blots. DNA sequence analysis reveals that pG-IF encodes a newly identified intermediate filament protein in Drosophila. Its nucleotide sequence is highly homologous to nuclear lamins with lower homology to cytoplasmic intermediate filament proteins. pG-IF predicts a protein of 621 amino acids with a predicted molecular mass of 69,855 daltons. In vitro transcription and translation of pG-IF yielded a protein with a SDS-PAGE estimated molecular weight of approximately 70 kDa. It contains sequence principles characteristic of class V intermediate filament proteins. Its near neutral pI (6.83) and the lack of a terminal CaaX motif suggests that it may represent a lamin C subtype in Drosophila. In situ hybridization to polytene chromosomes detects one band of hybridization on the right arm of chromosome 2 at or near 51A. This in conjunction with Southern blot analysis of various genomic digests suggests one or more closely placed genes while Northern blot analysis detects two messages in Kc cells.

scholarly journals Analysis of the genetic polymorphism of Paracoccidioides brasiliensis and Paracoccidioides cerebriformis "Moore" by random amplified polymorphic DNA (RAPD) and 28S ribosomal DNA sequencing: Paracoccidioides cerebriformis revisited

2005 ◽  
Vol 47 (3) ◽  
pp. 119-123 ◽  
Author(s):  
Sarah Desirée Barbosa Cavalcanti ◽  
José Eduardo Levi ◽  
Kátia Cristina Dantas ◽  
José Eduardo Costa Martins
Keyword(s):  
Genetic Polymorphism ◽  
Dna Sequence ◽  
Ribosomal Dna ◽  
Dna Analysis ◽  
Paracoccidioides Brasiliensis ◽  
Random Amplified Polymorphic Dna ◽  
Distinct Species ◽  
De Medicina ◽  
28S Ribosomal Dna ◽  
Mycological Laboratory

Our purpose was to compare the genetic polymorphism of six samples of P. brasiliensis (113, 339, BAT, T1F1, T3B6, T5LN1), with four samples of P. cerebriformis (735, 741, 750, 361) from the Mycological Laboratory of the Instituto de Medicina Tropical de São Paulo, using Random Amplified Polymorphic DNA Analysis (RAPD). RAPD profiles clearly segregated P. brasiliensis and P. cerebriformis isolates. However, the variation on band patterns among P. cerebriformis isolates was high. Sequencing of the 28S rDNA gene showed nucleotide conservancy among P. cerebriformis isolates, providing basis for taxonomical grouping, and disclosing high divergence to P. brasiliensis supporting that they are in fact two distinct species. Moreover, DNA sequence suggests that P. cerebriformis belongs in fact to the Aspergillus genus.

scholarly journals Isolation and mapping of a polymorphic DNA sequence pHHH122 on chromosome 2 (D2S54)

1987 ◽  
Vol 15 (23) ◽  
pp. 10078-10078 ◽  
Author(s):  
E. Fujimoto ◽  
Y. Nakamura ◽  
P. O'Connell ◽  
M. Leppert ◽  
G.M. Lathrop ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Chromosome 2

scholarly journals Isolation of a polymorphic DNA sequence (λEMBL3.303, D2S14) from chromosome 2

1987 ◽  
Vol 15 (3) ◽  
pp. 1341-1341
Author(s):  
J. Brennan ◽  
N.K. Spurr ◽  
W.F. Bodmer
Keyword(s):  
Dna Sequence ◽  
Chromosome 2

scholarly journals Genetic diversity of fruit borer, Helicoverpa armigera (Lepidoptera: Noctuidae) based on random amplified polymorphic DNA- polymerase chain reaction

2014 ◽  
Vol 39 (2) ◽  
pp. 263-271
Author(s):  
AKMZ Rahman ◽  
MA Haque ◽  
SN Alam ◽  
P Yasodha ◽  
V Balasubramani
Keyword(s):  
Genetic Variability ◽  
Helicoverpa Armigera ◽  
Indian Population ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Taq Polymerase ◽  
Agroecological Zones ◽  
Pcr Products ◽  
Helicoverpa Armígera ◽  
Fruit Borer

The genetic variability of Helicoverpa armigera (Hübner) at different agroecological zones of Bangladesh in comparison with Indian population was conducted in India during September 2008 to February 2009. A total of 12 H. armigera populations of which 10 populations collected from different agroecological zones of Bangladesh and two populations from India were tested for their genetic variability. Eight out of the ten primers produced scorable PCR products by amplifying the template DNA with taq polymerase and were subjected for analysis. Those eight primers got amplified to a total of 138 markers which produced polymorphic markers. The similarity coefficient based on 138 RAPD markers ranged from 0.000 to 0.777 of the pair-wise combination among twelve samples of H. armigera. An UPGMA dendrogram based on Jaccard’s similarity coefficient was constructed for the 12 samples of H. armigera. The dendrogram showed that H. armigera population from Bangladesh had 25 to 45 percent similarity, and in its Indian population the similarity remained within this range. DOI: http://dx.doi.org/10.3329/bjar.v39i2.20428 Bangladesh J. Agril. Res. 39(2): 263-271, June 2014

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