Detection Of Sequence Polymorphisms Research Articles

Appraisal of genetic variability and detection of sequence polymorphism in the Rc and Rd loci among the pigmented and non-pigmented genotypes of rice

Appraisal of genetic variability and detection of sequence polymorphism in the Rc and Rd loci among the pigmented and non-pigmented genotypes of rice

Ontogenetic sequence reconstruction and sequence polymorphism in extinct taxa: an example using early tetrapods (Tetrapoda: Lepospondyli)

Ontogenetic sequence reconstruction is challenging particularly for extinct taxa because of when, where, and how fossils preserve. Different methods of reconstruction exist, but the effects of preservational bias, the applicability of size-independent methods, and the prevalence of sequence polymorphism (intraspecific variation) remain unexplored for paleontological data. Here I compare five different methods of ontogenetic sequence reconstruction and their effects on the detection of sequence polymorphism, using a large collection of the extinct vertebrates Microbrachis pelikani and Hyloplesion longicostatum. The postcranial ossification sequences presented here for those taxa are the first examples known for extinct lepospondyls. Sequences were reconstructed according to skull length, trunk length, increasing number of ontogenetic events, majority-rule consensus, and Ontogenetic Sequence Analysis (OSA). Results generally were in agreement, demonstrating that paleontological data may be used to robustly reconstruct developmental patterns. When reconstructing sequences based on fossils, size-based methods and OSA are more objective and less dependent on preservational bias than other techniques. Apart from the other methods, OSA also allows for statistical analysis of observed and predicted polymorphism. However, OSA requires a large sample size to yield meaningful results, and size-based methods are justified in paleontological studies when sample size is limited by poor preservation. Different methods of reconstruction detected different patterns of sequence polymorphism, although across all methods the magnitude of sequence variation for M. pelikani and H. longicostatum (1.3−3.4%) was within the lower range of values reported for extant vertebrates. Compared with other extinct and extant tetrapods, all sequence reconstruction methods consistently showed that M. pelikani and H. longicostatum exhibit advanced ossification of the pubis and delayed ossification of the scapula. However, the postcranial ossification sequences of these two taxa largely are congruent with those of other tetrapods, suggesting an underlying conservative ancestral pattern that evolved early in tetrapod history.

SAMPL: A technique for somaclonal variation fingerprinting inMusa

SAMPL primers designed for genomic profiling in chickpea (Cicer arietinum L.) were tested for their applicability to fingerprinting of DNA of banana cultivars and soma-clonal variants. Most of the chickpea primers allowed amplification of genomic DNA of banana and detection of sequence polymorphisms within theMusa acuminata genome (A). Our results demonstrate that the highly resolving SAMPL technique is useful in banana genomics, especially for the distinction and characterization of commercially important cultivars and promising somaclonal variants containing the A genome.

Cloning of porcine IGF1 receptor cDNA and detection of sequence polymorphisms using RT-PCR.

A cDNA encoding the porcine type 1 insulin-like growth factor receptor (IGF1R) was amplified by reverse transcriptase-polymerase chain reaction (RT-PCR). The sequence of a 4.2-kb product was determined and had an open reading frame, encoding 1367 amino acids with 98.1 and 95.2% sequence similarity to the human and rat IGF1R, respectively. In the comparison of RT-PCR derived IGF1R sequences from 12 unrelated pigs, 12 silent sequence variants were found.

Significance of the HLA‐DQB matching in one‐haplotype identical kidney transplant pairs and the matching analysis by the polymerase chain reaction (PCR) — heteroduplex — polymorphism method

Sixty-five living related kidney transplant pairs were analyzed for matching at HLA class II loci by the polymerase chain reaction (PCR)--sequence specific oligonucleotide probe (SSOP) method. The retrospective HLA matching study revealed that there were many early graft loss cases despite the DQB compatibility, contrary to our expectation. There were 54 DRB1 one-mismatched cases, in which 7 of the 11 (64%) DQB zero-mismatched cases had lost their grafts, while the graft loss cases were only 10 of the 43 (23%) DQB one-mismatched pairs (P value = 0.0006). The DQB matching of these cases was studied in detail, because the PCR-SSOP methods are based on the detection of sequence polymorphisms in a relatively narrow range, i.e., recognized sequences by SSOPs. The PCR--heteroduplex--polymorphism analysis method was developed to analyze the polymorphism in exon 2 of the DQB1 gene. However, all the pairs proved to be compatible for the DQB, demonstrating that the DQB compatibility was associated with a harmful influence on the graft outcome. These observations suggested that the DQB1 incompatibility might exert the low responsiveness to HLA haplo-identical allogeneic transplants.

44 ASPECTS OF PRENATAL DIAGNOSIS IN HEMOPHILIA A (HA) AND B (HB)

Prenatal diagnosis (PD) of genetic diseases is the accepted preventive medical application of clinical genetics in many severe diseases such as HA and HB. We observed 408 women at risk for HA and 77 for HB coming respectively from 223 and 58 families. From 1987 we performed 72 PD out of 60 women on chorionic villus sampling (CVS) by transabdominal approach, free hand under continuous ultrasound guidance, at 10 weeks gestation. Even if earlier sampling is possible, a delaied procedure allowed to cut down the risks of miscarriage and of fetal limb abnormalities. In our hands the fetal loss risk is about 1.5%. We diagnosed 12 affected males, 24 healthy males and 28 female fetuses. At the beginning in 3 cases the sample was not sufficient for DNA analysis and, after CVS, in 2 cases the mother was uninformative and in 3 cases the mother was diagnosed as non carrier. We did not observe any malformation or pregnancy loss in the patients analyzed for hemophilia, probably related to the absence of other risk factors. The use of PCR for DNA analysis, allowed us to improve the carrier detection and PD of HA and HB reducing the time of analysis, increasing the informativity with the detection of sequence polymorphisms and using less chorionic tissue. The last 15 PD were performed by PCR. We gave a genetic counselling to 13 pregnant women at risk, avoiding the CVS in non carrier females. Therefore the acceptance of antenatal diagnosis increased: 8/60 women performed more then one PD (5/8 two CVS and 3/8 three CVS). On 10 pregnancies we analyzed the fetal sex by PCR obtaining the sex diagnosis in few hours. In 9/10 the result was confirmed by chromosomal analysis and only in 1 case we missed the diagnosis.