Role of interleukin-4 genetic polymorphisms and environmental factors in the risk of asthma in children.

Asthma is an allergic disease characterized by hyperresponsiveness and chronic inflammation of the airway. The interleukin-4 (IL-4) gene and its single nucleotide polymorphisms are associated with asthma susceptibility in children. A case-control study was performed to evaluate the relationship between asthma risk and the IL-4 rs2243250 (589 C/T) and rs2070874 (107 T/C), and IL-4 receptor (IL-4R) rs1801275 (576 Q/R) polymorphisms in 317 childhood asthma patients and 351 healthy children as controls. Polymerase chain reaction amplification and sequencing was performed. The effects of interactions between the genes of interest and environmental factors were also analyzed. IL-4 rs2243250 and rs2070874 allele and genotype frequencies did not significantly differ between the asthma and control groups (P > 0.05), but those of IL-4R rs1801275 did (P < 0.05). The RR genotype and R allele of this IL-4R variant were significantly associated with asthma risk, with odds ratios (ORs; and 95% confidence intervals) of 2.97 (2.08-4.25) and 2.99 (2.32-3.85), respectively. Logistic regression analysis showed that the IL-4R 576 Q/R RR genotype demonstrated a positive interaction with environments associated with smoking or pets in its effect on asthma risk, with ORs of 2.18 (P = 0.02) and 2.29 (P = 0.01), respectively. Our results suggest that the IL-4R rs1801275 polymorphism is associated with childhood asthma, and the RR genotype confers a high risk of developing this condition. This variant exhibited positive interactions with environments in which smoking or pets were present in increasing the risk of childhood asthma.

Phylogenetic analysis of the Mongolian gerbil (Meriones unguiculatus) from China based on mitochondrial genome.

Meriones unguiculatus (Gerbillinae, Rodentia) is widely used as an animal model of human disease. Here, we provide the first report of the complete mitochondrial genome sequence of M. unguiculatus (GenBank accession Nos. KF425526 and NC_023263). The sequence contained the conserved vertebrate pattern of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 major noncoding region. We identified one extended termination-associated sequence and one conserved sequence block in the non-coding region. The putative origin of replication for the light strand (OL) was 35 bp long. The OL stem and adjacent sequences were highly conserved, but the loop region differed from those of other rodent species. Base composition and codon usage of the 13 protein-coding genes in M. unguiculatus were compared with those of 23 rodent species with previously sequenced mitochondrial genomes. An A+T content of 63.0% was present in M. unguiculatus; this is similar to the Murinae average (62.4 ± 0.8%) and falls between the average for Mus musculus (63.1 ± 0.1%) and Rattus sp (61.7 ± 0.4%). The AT and GC skew values of M. unguiculatus were 0.035 and -0.28, respectively, similar to those of Cricetinae species (0.057 ± 0.05 and -0.31 ± 0.05). The codon families exhibited similar abundance in all 24 species. Analysis of phylogenetic relationships with 23 other rodent species using neighbor-joining and maximum likelihood protocols and the 12 protein-coding regions on the H strand showed that M. unguiculatus should be classified as genus Meriones, sub-family Gerbillinae, family Muridae.

Development of novel DNA markers for genetic analysis of grey hamsters by cross-species amplification of microsatellites.

The grey hamster has been used in biomedical research for decades. However, effective molecular methods for evaluating the genetic structure of this species are lacking, which hinders its wider usage. In this study, we employed cross-amplification of microsatellite loci of species within the same genus by polymerase chain reaction. Loci screened included 107 from the Mongolian gerbil (MG) and 60 from the Chinese hamster (CH); of these, 15 polymorphic loci were identified for the grey hamster. Of the 167 loci screened, 95 (56.9%) with clear bands on agarose gel were initially identified. After sequencing, 74 (77.9%) of these matched the criteria for microsatellite characteristics, including 41 from MG and 33 from CH. Lastly, 15 (20.3%) loci with more than two alleles for each locus were identified through capillary electrophoresis scanning. To justify the applicability of the 15 grey hamster loci, genetic indexes of grey hamsters were evaluated using 46 generations of outbred stock, established 20 years ago, from Xinjiang, China. Mean effective allele numbers and expected heterozygosity of stock were as low as, respectively, 1.2 and 0.14; these were 2.8 and 4.0 times inferior, respectively, to wild grey hamsters. This finding suggests that the genetic structure of the stock-bred population is too weak to resist artificial and natural selection, mutation and genetic drifting. In conclusion, we have developed de novo microsatellite markers for genetic analysis of the grey hamster, providing data and methodology for the enrichment of a genetic library for this species.

Selection of an effective microsatellite marker system for genetic control and analysis of gerbil populations in China.

Although gerbils have been widely used in many areas of biological research over many years, there is currently no effective genetic quality control system available. In the present study, we sought to establish a microsatellite marker system for quality control and conducted an optimized analysis of 137 microsatellite loci in two laboratory gerbil populations and one wild population. Independent sample t-tests on the mean effective allele number, mean of Shannon's information index, and mean HE suggested that 28 of the 137 microsatellite markers were informative for gerbil genetic control. Analysis of 4 laboratory gerbil populations and 1 wild population using the 28 microsatellite loci indicated that allele numbers varied from 1.9639 (Guangzhou, GZ) to 6.6071 (North-West wild, NW). The average of HO versus HE was 0.6236/0.3802, 0.6671/0.4159, 0.4185/0.3464, 0.4592/0.3821, and 0.3972/0.4167 for the Beijing, NW, Hangzhou, Dalian, and GZ populations, respectively. The GZ population showed the greatest differentiation, having higher RST and Nei's standard genetic distances. An AMO-VA revealed high genetic differentiation among the five populations (FST = 0.296). The microsatellite system established here is effective and will be important in future studies for genetic quality control and monitoring of gerbil breeds.

Selected representative microsatellite loci for genetic monitoring and population structure analysis of miniature swine.

To optimize the combination of microsatellite loci for genetic control of outbred swine stocks, 32 of 100 loci distributed among almost all chromosomes (except 12) were screened out by 1.5% agarose, 8% polyacrylamide gel and capillary electrophoresis scanning among 3 miniature swine outbred stocks, namely Bama (BM), Guizhou (GZ) and Tibeta (TB). The mean total and effective allele numbers among these stocks were 12.1 and 5.9, respectively. The mean heterozygosity for these breeds was 0.5428, 0.6978 and 0.7646, and polymorphism information content was 0.5469, 0.7296 and 0.7663, respectively. Accordingly, hereditary variation from low to high was BM < GZ < TB. This showed that the genetic relationship between BM and GZ pigs was closer, and both were distant from TB. Additionally, the effectiveness of the 32-locus combination for evaluation of genetic quality was demonstrated in Changchun-junmo-1 (CJ-1), a standard outbred Chinese pig stock, in which the mean total and effective allele numbers and mean heterozygosity were 6.1613, 3.8483 and 0.6903, respectively. Since our results were consistent with the breeding pedigrees, the 32 loci could be used for both genetic monitoring within the individual outbred miniature swine stocks and population structure analysis between them.

Selecting representative microsatellite loci for genetic monitoring and analyzing genetic structure of an outbred population of orange tabby cats in China.

We optimized a panel of microsatellite markers from cat and tiger genetic data for efficient genetic monitoring and used it to analyze the genetic structure of an outbred cat stock in China. We selected a set of rich polymorphic microsatellite loci from 131 cat microsatellite loci and 3 Sumatran tiger microsatellite loci using agarose gel electrophoresis. Next, the set of optimized genetic markers was used to analyze the genetic variation in an outbred population of orange tabby cats in China by simple-tandem repeat scanning. Thirty-one loci rich in polymorphisms were selected and the highest allele number in a single locus was 8. Analysis of the orange tabby cat population illustrated that the average observed number of alleles, mean effective allele number, mean Shannon's information index, mean expected heterozygosity, and observed heterozygosity were 3.8387, 2.4027, 0.9787, 0.5565, and 0.5528, respectively. The 31 microsatellite markers used were polymorphic and suitable for analyzing the genetic structure of cats. The population of orange tabby cats was confirmed to be a well-outbred stock.

Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species.

Retrotransposon-based molecular markers are powerful molecular tools. However, these markers are not readily available due to the difficulty in obtaining species-specific retrotransposon primers. Although recent techniques enabling the rapid isolation of retrotransposon sequences have facilitated primer development, this process nonetheless remains time-consuming and costly. Therefore, research into the transferability of retrotransposon primers developed from one plant species onto others would be of great value. The present study investigated the transferability of retrotransposon primers derived from 'Luotian-tianshi' persimmon (Diospyros kaki Thunb.) across other fruit crops, as well as within the genus using inter-retrotransposon amplified polymorphism molecular marker. Fourteen of the 26 retrotransposon primers tested (53.85%) produced robust and reproducible amplification products across all fruit crops tested, indicating their applicability across plant species. Four of the 13 fruit crops showed the best transferability performances: persimmon, grape, citrus, and peach. Furthermore, similarity coefficients and UPGMA clustering indicated that these primers could further offer a potential tool for germplasm differentiation, parentage identification, genetic diversity assessment, classification, and phylogenetic studies across a variety of plant species. Transferability was further confirmed by examining published primers derived from Rosaceae, Gramineae, and Solanaceae. This study is one of the few currently available studies concerning the transferability of retrotransposon primers across plant species in general, and is the first successful study of the transferability of retrotransposon primers derived from persimmon. The primers presented here will help reduce costs for future retrotransposon primer development and therefore contribute to the popularization of retrotransposon molecular markers.