Genetic diversity revealed by EST-SSR markers in carob tree (Ceratonia siliqua L.)

Carob is a caesalpinoid tree species widespread in the Mediterranean. In this paper, carob EST-SSR (Expressed Sequence Tags-Simple Sequence Repeat) markers were used to assess the level of genetic diversity among 71 cultivars and accessions collected in three Mediterranean countries (Italy, Malta and Spain). Starting from 20 microsatellite loci, we identified a set of 9 polymorphic EST-SSRs, with a number of alleles per locus ranging from 2 to 7, and a number of genotypes from 3 to 13. The nine polymorphic EST-SSRs discriminated most of the analyzed genotypes with the exceptions of some cultivated clones having similar phenotypic features and probably belonging to cultivar-populations, and clarified some cases of homonymy.A neighbor joining dendrogram generated three main clusters which did not show a correlation with the distribution areas of the analyzed genotypes. A Bayesian analysis evidenced a high degree of admixture among the gene pools from the three countries. The low level of diversification among geographical areas reveals that the asexual propagation of selected clones played a major role in the diffusion of the species in the western Mediterranean. The work described in this paper represents the first report of carob genotyping achieved through microsatellite markers.     

2′-MeO-RNA Containing Oligodeoxyribonucleotide Primers Can Prevent Template-independent Base Extension on Microarrays

DNA microarrays require tens of thousands of deoxyoligonucleotides to be registered in an addressable fashion through immobilization, so that they have the high-throughput capability of analyzing a large number of samples simultaneously in a minimal volume of each reagent. However, using immobilized DNA molecules on microarrays can impose certain technical problems for some assays. For example, high background noise has been observed in using immobilized oligonucleotide microarrays (DNA chip) for primer extension reactions. This noise may be associated with the reactions of secondary structures formed by the adjacent primers physically constrained on the surface. Single-base extension (SBE) of arrayed primers on a chip has been extensively used in mini-sequencing to examine single nucleotide polymorphisms (SNP). Some primers appeared to be extendable in the absence of any template and thus competed against the base extension directed by the assay target such as genomic DNA. In this article, a method is reported that is capable of reducing template-independent extension by the substitution of a 2′-methoxyribonucleotide in the otherwise oligodeoxyribonucleotide primer. The surrogate compound placed at the 5′-end of the putative secondary structure sequence of a given primer was able to inhibit template-independent extension and to improve data quality of surface-attached primer extension assays.     

Contrasting association of Leptin receptor polymorphisms and haplotypes with polycystic ovary syndrome in Bahraini and Tunisian women: a case–control study

Background: The present study examined the contribution of ethnicity to the association of leptin receptor gene (LEPR) gene variants with polycystic ovary syndrome (PCOS) in Tunisian and Bahraini Arabic-speaking women.Methods: Subjects consisted of 320 women with PCOS, and 446 eumenorrhic women from Tunisia, and 242 women with PCOS and 238 controls from Bahrain. Genotyping of (exonic) rs1137100 and rs1137101 and (intronic) rs2025804 LEPR variants was done by allelic exclusion.Results: The minor allele frequencies (MAFs) of rs1137100 and rs1137101 were significantly different between PCOS cases and control women from Bahrain but not Tunisia, and LEPR rs1137101 was associated with increased PCOS susceptibility only in Bahraini subjects. Furthermore, rs1137100 was associated with decreased PCOS risk among Bahrainis under codominant and recessive models; rs1137100 was negatively associated with PCOS in Tunisians after controlling for testosterone. In addition, rs2025804 was associated with increased PCOS risk among Tunisian but not Bahraini women, after adjusting for key covariates. Negative correlation was seen between rs1137101 and triglycerides in Tunisians, while homeostasis model assessment of insulin resistance (HOMA-IR) and insulin correlated with rs2025804 and rs1137101 among Bahraini subjects, and rs1137101 correlated with estradiol and prolactin. Taking TAG haplotype as common, positive association of TAA and negative association of TGG haplotype with PCOS was seen among Bahraini women; no three-locus PCOS-associated haplotypes were found in Tunisians.Conclusions: The present study is the first to demonstrate the contribution of ethnicity to the association of LEPR gene variants with PCOS, thereby highlighting the significance of controlling for ethnicity in gene association investigations.     

Thiopurine S-Methyltransferase Gene Polymorphisms in a Healthy Slovak Population and Pediatric Patients with Inflammatory Bowel Disease

Thiopurine methyltransferase (TPMT) is a key component in thiopurine metabolism. There is an insufficient evidence about the distribution of the genotype frequencies of TPMT variants and frequencies of TPMT alleles associated with intermediate and deficient activity in a healthy Slovak population and pediatric patients with inflammatory bowel disease (IBD). TPMT variant alleles (*1,*2, *3A, *3B, and *3C) were determined in 114 children treated for IBD and in 281 healthy volunteers. Mutant alleles were present in 9/114 (7.89%) in the IBD patients and in 23/281 (8.19%) of probands. The distribution of the most frequent variants of TPMT gene was similar in a healthy population and patients with IBD.     

Comprehensive genotyping of the USA national maize inbred seed bank

Background

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

Results

The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.

Conclusions

The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.     

幽门螺杆菌基因分型与胃病关系研究进展

幽门螺旋杆菌(Helicobacter pylori,Hp)已被国际癌症组织确认为胃部疾病最主要的致病因子。近年来对于Hp菌株的基因分型、流行病学和致病性等方面的研究逐步深入,越来越多的研究成果证实对Hp基因分型进行细化可为精准医疗提供依据。Hp可依照Cag A羧基末端磷酸化位点、Vac A信号区(s)中间区(m)过渡区(i)缺失区(d)和粘附因子(OMPs)进行基因分型。Hp基因型差异可导致不同毒性作用,从而引起不同临床结果和疗效预后。因此对Hp基因分型可为胃病的防治提供重要依据。本文就Hp基因分型方法、基因分型及其与胃部疾病研究进展进行如下综述。     

Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer

Population size information is critical for managing endangered or harvested populations. Population size can now be estimated from non-invasive genetic sampling. However, pitfalls remain such as genotyping errors (allele dropout and false alleles at microsatellite loci). To evaluate the feasibility of non-invasive sampling (e.g., for population size estimation), a pilot study is required. Here, we present a pilot study consisting of (i) a genetic step to test loci amplification and to estimate allele frequencies and genotyping error rates when using faecal DNA, and (ii) a simulation step to quantify and minimise the effects of errors on estimates of population size. The pilot study was conducted on a population of red deer in a fenced natural area of 5440 ha, in France. Twelve microsatellite loci were tested for amplification and genotyping errors. The genotyping error rates for microsatellite loci were 0–0.83 (mean=0.2) for allele dropout rates and 0–0.14 (mean=0.02) for false allele rates, comparable to rates encountered in other non-invasive studies. Simulation results suggest we must conduct 6 PCR amplifications per sample (per locus) to achieve approximately 97% correct genotypes. The 3% error rate appears to have little influence on the accuracy and precision of population size estimation. This paper illustrates the importance of conducting a pilot study (including genotyping and simulations) when using non-invasive sampling to study threatened or managed populations.     

Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat

Genetic variation present in 64 durum wheat accessions was investigated by using three sources of microsatellite (SSR) markers: EST-derived SSRs (EST-SSRs) and two sources of SSRs isolated from total genomic DNA. Out of 245 SSR primer pairs screened, 22 EST-SSRs and 20 genomic-derived SSRs were polymorphic and used for genotyping. The EST-SSR primers produced high quality markers, but had the lowest level of polymorphism (25%) compared to the other two sources of genomic SSR markers (53%). The 42 SSR markers detected 189 polymorphic alleles with an average number of 4.5 alleles per locus. The coefficient of similarity ranged from 0.28 to 0.70 and the estimates of similarity varied when different sources of SSR markers were used to genotype the accessions. This study showed that EST-derived SSR markers developed in bread wheat are polymorphic in durum wheat when assaying loci of the A and B genomes. A minumum of ten EST-SSRs generated a very low probability of identity (0.36×10⁻¹²) indicating that these SSRs have a very high discriminatory power. EST-SSR markers directly sample variation in transcribed regions of the genome, which may enhance their value in marker-assisted selection, comparative genetic analysis and for exploiting wheat genetic resources by providing a more-direct estimate of functional diversity. Received: 19 December 2000 / Accepted: 17 April 2001     

PCR-SSP技术对广东汉族人HLA-DR基因分型

探索具有高分辨率、高特异性和简捷快速的方法对ＨＬＡ－ＤＲ基因分型,为临床器官移植配型和疾病相关性分析提供实用的方法和基础资料．利用ＤＲ１～ＤＲｗ１８序列特异性的１９组引物及１对内参照引物进行ＰＣＲ扩增即ＰＣＲ－ＳＳＰ对ＨＬＡ－ＤＲ进行基因分型,扩增产物经琼脂糖凝胶电泳,溴乙锭染色,在紫外光下观察分型结果．每个被检个体的ＤＲ型别可由特异引物扩增出现的电泳谱带直接判断．双盲检测２２例的结果１００％正确．在１０２例中国广东地区汉族人中,ＤＲ９和ＤＲ２的基因频率最高,分别为０．２２０５和０．１９１２,ＤＲ１０为最低（０．００９８）．与用ＰＣＲ－ＳＳＯ方法分型获得的结果比较,基因型别分布基本一致,但一些等位基因的频率有差异,表明ＨＬＡ－ＤＲ基因频率的分布在不同地区、不同种族的人群间存在着差异．ＰＣＲ－ＳＳＰ法分辨率和特异性虽不及ＰＣＲ－ＳＳＯ法但比血清学方法精细,分型的全过程只需２～４ｈ能满足临床器官移植配型的要求．基因频率调查结果为器官移植配型和疾病相关性分析提供了基础资料．     

细胞色素P450 2D6缺陷型等位基因的家系分析

利用等位基因特民扩增法(ASA)为基础的基因分型法,对细胞色素P4502D6 (CYP2D6)缺陷型等位基因携带者的9个家庭共38个进行了基因分型,并与用右旋美沙芬为 探针的表型分型法进行对比,发现两种方法的结果是一致的,CYP2D6酶缺陷型等位基因呈常染色体隐性遗传。 Abstract:A genotyping method based on the principle of allele-specific amplification and a phenotyping procedure with dextromethorphan as a probe were employed in familial study of nine families with 38 members for the cytochrome P450 2D6(CYP2D6)deficient alleles——CYP2D6A,CYP2D6B,CYP2D6D and CYP2D6T.The results showed that the CYP2D6 deficient alleles were inherited as an autosomal recessive trait.