scholarly journals Microsatellite Scan Identifies New Candidate Genes for Susceptibility to Alcoholic Chronic Pancreatitis in Japanese Patients

2008 ◽  
Vol 25 (3) ◽  
pp. 175-180 ◽  
Author(s):  
Kei Kitahara ◽  
Shigeyuki Kawa ◽  
Yoshihiko Katsuyama ◽  
Takeji Umemura ◽  
Yayoi Ozaki ◽  
...  
Keyword(s):  
Chronic Pancreatitis ◽  
Microsatellite Markers ◽  
Candidate Genes ◽  
Disease Susceptibility ◽  
Japanese Patients ◽  
Whole Genome ◽  
Common Risk Factor ◽  
Average Spacing ◽  
Alcoholic Chronic Pancreatitis ◽  
Polymorphic Microsatellite

Alcohol abuse is one of the most common risk factor for chronic pancreatitis, but the underlying pathophysiological mechanisms remain unclear. The aim of this study was to identify genes that contribute to susceptibility or resistance for alcoholic chronic pancreatitis by screening the whole genome. Sixty-five patients with alcoholic chronic pancreatitis (63 men and 2 women, mean age 55.2 years) and 99 healthy Japanese controls were enrolled in this study. This was an association study using 400 polymorphic microsatellite markers with an average spacing of 10.8 cM distributed throughout the whole genome. This search revealed 10 candidate susceptibility regions and 5 candidate resistant regions throughout the genome. No specific microsatellite markers were detected in association with previously reported susceptibility genes for chronic pancreatitis, such asPRSS1, PRSS2, CTRC, SPINK1, CFTR, ALDH2, and CYP2E1. Among the statistically significant markers,D15S1007on chromosome 15q14 showed strong evidence for disease susceptibility (70.8% vs. 35.1%,Pc= 0.0001). Within 500 kb of D15S1007, several genes were candidate genes for susceptibility, includingFMN1, DKFZP686C2281, LOC440268, RYR3, and AVEN, This study identified 10 candidate susceptibility and 5 candidate resistant regions that may contain genes involved in ACP pathogenesis.

scholarly journals Identifying a major locus that regulates spontaneous arthritis in IL-1ra-deficient mice and analysis of potential candidates

2011 ◽  
Vol 93 (2) ◽  
pp. 95-103 ◽  
Author(s):  
YAN JIAO ◽  
FENG JIAO ◽  
JIAN YAN ◽  
QING XIONG ◽  
DANIEL SHRINER ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Candidate Genes ◽  
Microarray Analysis ◽  
Expression Profiles ◽  
Interleukin 1 ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Potential Candidate ◽  
F2 Population ◽  
Deficient Mice

SummaryTo identify genetic loci that regulate spontaneous arthritis in interleukin-1 receptor antagonist (IL-1ra)-deficient mice, an F2 population was created from a cross between Balb/c IL-1ra-deficient mice and DBA/1 IL-1ra-deficient mice. Spontaneous arthritis in the F2 population was examined and recorded. Genotypes of those F2 mice were determined using microsatellite markers. Quantitative trail locus (QTL) analysis was conducted with R/qtlbim. Functions of genes within QTL chromosomal regions were evaluated using a bioinformatics tool, PGMapper, and microarray analysis. Potential candidate genes were further evaluated using GeneNetwork. A total of 137 microsatellite markers with an average of 12 cM spacing along the whole genome were used for determining the correlation of arthritis phenotypes with genotypes of 191 F2 progenies. By whole-genome mapping, we obtained QTLs on chromosomes 1 and 6 that were above the significance threshold for strong Bayesian evidence. The QTL on chromosome 1 had a peak near D1Mit55 and D1Mit425 at 82·6 cM. It may account for as much as 12% of the phenotypic variation in susceptibility to spontaneous arthritis. The QTL region contained 208 known transcripts. According to their functions, Mr1, Pla2g4a and Fasl are outstanding candidate genes. From microarray analysis, 11 genes were selected as favourable candidates based on their function and expression profiles. Three of those 11 genes, Prg4, Ptgs2 and Mr1, correlated with the IL-1ra pathway. Those genes were considered to be the best candidates.

Screening of polymorphic microsatellite markers from the whole-genome sequences of nipa (Nypa fruticans Wurmb.)

2021 ◽  
pp. 1-4
Author(s):  
Junaldo A. Mantiquilla ◽  
Merlene E. Elumba ◽  
Meng-Shin Shiao ◽  
Yu-Chung Chiang
Keyword(s):  
Microsatellite Markers ◽  
Population Studies ◽  
Population Level ◽  
Whole Genome ◽  
Sequencing Technology ◽  
Evolutionary Forces ◽  
Nypa Fruticans ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract Nipa (Nypa fruticans Wurmb.), aside from being part of the mangrove forest ecosystem that has been under assault at an alarming rate, lacks information on its genetic variation at the population level for conservation planning purposes. Microsatellites, or simple sequence repeats (SSRs), are molecular markers employed to detect genetic variations in population studies. Here, the primers for this palm were identified through whole-genome sequencing using the Illumina® Sequencing Technology platform. Over half (52.4%) of SSRs consisted of mononucleotide repeats, whereas the remainder mostly consisted of dinucleotide (22.7%) and trinucleotide (22.4%) repeats. The frequencies of longer repeats (tetranucleotides, pentanucleotides and hexanucleotides) were exceptionally rare (2.5%). At least 18 out of 75 genomic loci were polymorphic, based on 37 randomly selected samples assayed for screening. Polymorphic loci (P) reached a mean of 72% across the Indo-West Pacific region. Estimates of genetic diversity showed a lower mean observed heterozygosity (Ho) (0.195) than expected (He) (0.316), suggesting evolutionary forces were acting across nipa populations. The fixation (F) index (0.388) supported this result, which indicates considerable genetic differentiation among populations in the region. An average of 2.111 alleles (Na) was obtained. In conclusion, these microsatellite markers are promising tools for genetic evaluation of nipa populations to facilitate characterization of this species in its distribution range.

scholarly journals Length of Variable Numbers of Tandem Repeats in the Carboxyl Ester Lipase (CEL) Gene May Confer Susceptibility to Alcoholic Liver Cirrhosis but Not Alcoholic Chronic Pancreatitis

PLoS ONE ◽  
2016 ◽  
Vol 11 (11) ◽  
pp. e0165567 ◽  
Author(s):  
Karianne Fjeld ◽  
Sebastian Beer ◽  
Marianne Johnstone ◽  
Constantin Zimmer ◽  
Joachim Mössner ◽  
...  
Keyword(s):  
Liver Cirrhosis ◽  
Chronic Pancreatitis ◽  
Tandem Repeats ◽  
Alcoholic Liver Cirrhosis ◽  
Alcoholic Chronic Pancreatitis

Development of polymorphic microsatellite markers for the Tertiary relict tree species Taiwania cryptomerioides (Cupressaceae) in East Asia

2021 ◽  
Vol 48 (3) ◽  
pp. 3031-3036
Author(s):  
Mengyun Qin ◽  
Ningning Zhang ◽  
Shixin Zhu ◽  
Caipeng Yue ◽  
Jinyong Huang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
East Asia ◽  
Tree Species ◽  
Polymorphic Microsatellite ◽  
Taiwania Cryptomerioides

Genetic characterization of novel polymorphic microsatellite markers for Epilobium nankotaizanense (Onagraceae), an endemic and threatened herb in Taiwan

2021 ◽  
pp. 1-4
Author(s):  
Yu-Wei Tseng ◽  
Chi-Chun Huang ◽  
Chih-Chiang Wang ◽  
Chiuan-Yu Li ◽  
Kuo-Hsiang Hung
Keyword(s):  
Microsatellite Markers ◽  
Natural Populations ◽  
Conservation Strategy ◽  
Sequencing Data ◽  
Germplasm Collections ◽  
The Family ◽  
Conservation Genetic ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Abstract Epilobium belongs to the family Onagraceae, which consists of approximately 200 species distributed worldwide, and some species have been used as medicinal plants. Epilobium nankotaizanense is an endemic and endangered herb that grows in the high mountains in Taiwan at an elevation of more than 3300 m. Alpine herbs are severely threatened by climate change, which leads to a reduction in their habitats and population sizes. However, only a few studies have addressed genetic diversity and population genetics. In the present study, we developed a new set of microsatellite markers for E. nankotaizanense using high-throughput genome sequencing data. Twenty polymorphic microsatellite markers were developed and tested on 30 individuals collected from three natural populations. These loci were successfully amplified, and polymorphisms were observed in E. nankotaizanense. The number of alleles per locus (A) ranged from 2.000 to 3.000, and the observed (Ho) and expected (He) heterozygosities ranged from 0.000 to 0.929 and from 0.034 to 0.631, respectively. The developed polymorphic microsatellite markers will be useful in future conservation genetic studies of E. nankotaizanense as well as for developing an effective conservation strategy for this species and facilitating germplasm collections and sustainable utilization of other Epilobium species.

Characterization of nine polymorphic microsatellite markers in sprat (Sprattus sprattusL.)

2008 ◽  
Vol 8 (4) ◽  
pp. 861-863 ◽  
Author(s):  
T. DAILIANIS ◽  
M. LIMBORG ◽  
R. HANEL ◽  
D. BEKKEVOLD ◽  
J. LAGNEL ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Microsatellite

scholarly journals Prognosis-Determinant Candidate Genes Identified by Whole Genome Scanning in Eyes with Pterygia

2007 ◽  
Vol 48 (8) ◽  
pp. 3566 ◽  
Author(s):  
Chuan-Hui Kuo ◽  
Dai Miyazaki ◽  
Nobuhiko Nawata ◽  
Takeshi Tominaga ◽  
Atsushi Yamasaki ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Whole Genome ◽  
Genome Scanning
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