Highest PIC Value Research Articles

개의 친자감정을 위한 Microsatellite DNA 다형성 분석

ABSTRACT This study was carried out to investigate a usefulness of the microsatellite DNA markers for individual identification and parentage verification in three dog breeds. A total of 59 random dog (31 Chiwawa, 20 Poongsan, 8 Labrador Retriever) samples were genotyped by using 14 markers (Chiwawa dog), 16 markers (Poongsan dog), and 12 markers (Labrador Retriever dog) among the 17 international standard markers (PEZ1, 3, 5, 6, 8, 10, 11, 12, 13, 15, 16, 17, 20, 21, FHC2010, FHC2054 and FHC2079), respectively. The number of alleles per locus varied from 4 to 14 with a mean value of 6.07 in Chiwawa dog, 2 to 9 with a mean of 4.75 in Poongsan dog, and 3 to 5 with a mean of 4.00 in Labrador Retriever dog. Observed heterozygosity was ranged 0.419q0.968 (mean 0.755), 0.300q0.950 (mean 0.597) and 0.125q0.750 (mean 0.604), and expected heterozygosity was ranged 0.432q0.883 (mean 0.711), 0.262q0.817 (mean 0.559) and 0.425q0.808 (mean 0.660) in these three dog breeds. PIC value was ranged 0.397q0.856 (mean 0.659), 0.222q0.772 (mean 0.503) and 0.354q0.717 (mean 0.563) in these three dog breeds. Of the 17 markers, PEZ1, PEZ3, PEZ6, PEZ10, PEZ12 loci, PEZ1, PEZ6, PEZ13 loci, and PEZ8, PEZ12 loci have relatively high PIC value (
%0.7) in Chiwawa dog, Poongsan dog and Labrador Retriever dog, respectively. The exclusion probability was ranged 0.240q0.741, 0.111q0.616, and 0.198q0.529, and the combination of microsatellite loci was 0.9999, 0.9991, and 0.9968 in Chiwawa dog, Poongsan dog and Labrador Retriever dog, respectively. These results can give basic information for developing parentage verification and individual identification system in these three dog breeds.(

Rapid acid extrusion response triggered by alpha(1) adrenoceptor in CHO cells.

1. Using a microphysiometer with synchronized valve switching, we investigated real-time acid extrusion from Chinese hamster ovary (CHO) cells in which human alpha(1) adrenoceptor (AR) is stably expressed, in response to noradrenaline (NA). 2. In the cells expressing alpha(1a) AR, the time course of extracellular acidification after stimulation had two phases; in the first phase it transiently reached a rate several times greater than the base rate with a peak at around 10 s, and in the second it increased to 2 times the base rate and reached a plateau in 2 min. Both phases showed a concentration-dependent increase of acidification rate in response to NA, but had distinct pEC(50) values; 5.6 for the transient phase and 7.2 for the steady phase. 3. In the cells expressing alpha(1b) AR, the transient phase was not detected but the steady phase was observed. The pEC(50) value was 7.1, although the magnitude of the response was much smaller than that with alpha(1a) AR. 4. Both 5-(N-ethyl-N-isopropyl)amiloride (EIPA) and HOE642 inhibited the acid extrusion response by either AR in a concentration-dependent manner. EIPA and HOE642 had high pIC(50) values (7.4 and 7.3, respectively) for inhibition of the transient phase response via alpha(1a) AR. In the inhibition of the steady phase response via alpha(1a) AR, both drugs revealed the presence of two components in the response; one had high pIC(50) values (8.1 and 8.2 for EIPA and HOE642, respectively) and the other had low pIC(50) values (5.6 and 6.0, respectively). In contrast, the steady phase response via alpha(1b) AR was inhibited by EIPA and HOE642 with low pIC(50) values (5.3 and 5.9, respectively). 5. As Ca2+ was depleted, the alpha(1a) AR-induced transient phase disappeared, while the steady phase was not affected. 6. These results suggest that alpha(1a) AR drives two acid extrusion systems in CHO cells upon stimulation; one elicits the transient response, which is largely mediated by an EIPA/HOE642-sensitive and Ca(2+)-dependent Na(+)-H(+) exchanger (NHE), presumably NHE1, and the other induces the steady acid extrusion that is mediated by NHE1 and another NHE which has low sensitivity to both EIPA and HOE642. alpha(1b) AR drives only the steady phase acid extrusion response, which is mainly mediated by NHEs other than NHE1.

Microsatellite markers from sugarcane ( Saccharum spp.) ESTs cross transferable to erianthus and sorghum

Analysis of a sugarcane ( Saccharum spp.) EST (expressed sequence tag) library of 8678 sequences revealed approximately 250 microsatellite or simple sequence repeats (SSRs) sequences. A diversity of dinucleotide and trinucleotide SSR repeat motifs were present although most were of the (CGG) n trinucleotide motif. Primer sets were designed for 35 sequences and tested on five sugarcane genotypes. Twenty-one primer pairs produced a PCR product and 17 pairs were polymorphic. Primer pairs that produced polymorphisms were mainly located in the coding sequence with only a single pair located within the 5′ untranslated region. No primer pairs producing a polymorphic product were found in the 3′ untranslated region. The level of polymorphism (PIC value) in cultivars detected by these SSRs was low in sugarcane (0.23). However, a subset of these markers showed a significantly higher level of polymorphism when applied to progenitor and related genera ( Erianthus sp. and Sorghum sp.). By contrast, SSRs isolated from sugarcane genomic libraries amplify more readily, show high levels of polymorphism within sugarcane with a higher PIC value (0.72) but do not transfer to related species or genera well.

Large Linkage Analysis in 100 Families with Autosomal Recessive Spinal Muscular Atrophy (SMA) and 11 CEPH Families Using 15 Polymorphic Loci in the Region 5q11.2-q13.3

The autosomal recessive proximal spinal muscular atrophy (SMA) gene was mapped to the region 5q11.2-q13.3 in 1990. Here, we present a large genetic linkage study of 100 SMA families and 11 CEPH families using 14 polymorphic simple sequence repeats (SSRs) and one RFLP in the region 5q11.2-q13.3. The genetic interval between the closest SMA flanking loci D5S435 and D5S557 comprises 1 cM at zmax = 27.94. Two recombinants were identified between the SMA gene and the closest telomeric marker D5S557 (theta = 0.02 at zmax = 8.63). The first places the SMA gene centromeric to this marker; the second suggests a double recombinant at D5S557, which is very unlikely. More likely explanations are discussed in the paper. No recombinant was found between D5S435 and the SMA gene (theta = 0.00 at zmax = 25.36). We localized a recently described polymorphic marker, D5S351 (Hudson et al., 1992), close to the SMA (theta = 0.00 at zmax = 19.01) and the 3'MAP1B gene (theta = 0.01 at zmax = 38.76). Due to its high PIC value of 0.70, it represents a very useful marker for prenatal diagnosis. In addition, we developed a new reverse primer for the nearest centromeric locus D5S435 (Soares et al., 1993), a useful marker for prenatal diagnosis, which has been very difficult to amplify in the past. Three of the markers presented here are newly developed polymorphic SSRs (one tetranucleotide repeat, D5S507/W15CATT, and two dinucleotide repeats, D5S544/C88.2GT and D5S682/C88.3GT). These markers are too far from the SMA gene to be relevant for cloning; nevertheless, as part of the human genome project, they are contributing to the fine genetic mapping of the region 5q11.2-q13.3. The most likely order of the loci based on two-point and multipoint linkage analyses as well as on specific recombination events and physical mapping studies is D5S76-D5S507- D5S6-D5S125-D5S680-D5S435-SMA-D5S557- D5S351-5'MAP1B-3'MAP1B-JK53CA1/2-(D5S127- D5S39)-(D5S544-D5S682). In general, the genetic distances obtained from the SMA and CEPH families are comparable.

Identification and Characterization of Dinucleotide Repeat (CA)n Markers for Genetic Mapping in Dog

A large block of simple sequence repeat (SSR) polymorphisms for the dog genome has been isolated and characterized. Screening of primary libraries by conventional hybridization methods as well as by screening of enriched marker-selected libraries led to the isolation of a large number of genomic clones that contained (CA)n repeats. The sequences of 101 clones showed that the size and complexity of (CA)n repeats in the dog genome were similar to those reported for these markers in the human genome. Detailed analysis of a representative subset of these markers revealed that most markers were moderately to highly polymorphic, with PIC values exceeding 0.70 for 33% of the markers tested. An association between higher PIC values and markers containing longer (CA)n repeats was observed in these studies, as previously noted for similar markers in the human genome. A list of primer sequences that tag each characterized marker is provided, and a comprehensive system of nomenclature for the dog genome is suggested.

Microsatellite based DNA fingerprinting of 28 local rice (<i>Oryza sativa</i> L.) varieties of Bangladesh

A total of 28 local rice (Oryza sativa L.) varieties of Bangladesh were selected for DNA fingerprinting with seven microsatellite DNA markers. Upon PCR amplification the alleles were separated on Agarose gel using a sequencing gel electrophoresis system. The loci were polymorphic (P95) in all of the varieties. Variation was found in number of alleles, allele frequency, observed and expected heterozygosity. The primer, RM335 having motif (CTT)20 also yielded highest number of alleles (15) and highest PIC value (0.909). Genetic differentiation (Fst) values were found in the ranges 0.84 to 1.00 with an average of 0.92 and gene flow (Nm) values ranged from 0.047 to 0.00 with an average of 0.02. High level genetic differentiation and low level gene flow values in 28 rice (Oryza sativa L.) varieties which were indicated of diversity among the varieties as most of these varieties were of landraces. Over all Nei’s genetic distance value (D) ranged from nil to 2.56 among 378 varietals pairs resulting as a means of permutation combination of 28 rice varieties. The UPGMA dendrograme based on Nei's genetic distance placed the varieties into different clusters. All of the varieties were identified with at least one and/or combination of 7 primers. Keywords: Microsatellites; DNA fingerprinting; Oryza sativa; Bangladesh DOI: 10.3329/jbau.v8i1.6391J. Bangladesh Agril. Univ. 8(1): 7-17, 2010

Regional Polymorphism Assessment of Myanmar ‘Sein Ta Lone’ Mango (Mangifera indica Linn) from Sintgaing Township Based on Microsatellite Markers

This study was conducted to explore the genetic diversity and relationship of Sein Ta Lone mango cultivars among 20 commercial orchards in Sintgaing Township, Mandalay region. Nine microsatellite (SSR) markers were used to detect genetic polymorphism in a range from (3 to 6) alleles with (4.33) alleles per marker in average. Six out of nine microsatellite markers gave the PIC values of greater than (0.5). Among them, SSR36 held the highest PIC values of (0.691) while MiSHRS39 and MN85 possessed the least PIC values of (0.368) and (0.387) respectively. The genetic diversity was expressed as unbiased expected heterozygosity (UHe) value with an average of (0.561). The genetic relationship was revealed by (UPGMA) dendrogram in a range of (0.69 to 1.00). Based on UPGMA cluster analysis, three main clusters were classified among three different locations. This study was intended to help cultivar characterization and conservation for proper germplasm management with the estimation of genetic variation and relationship in the existing population of Sein Ta Lone mangoes in Sintgaing Township by microsatellite markers.