How to Use Genetic Data to Distinguish Between Natural and Human-Mediated Introduction of <Emphasis Type="Italic">Littorina littorea</Emphasis> to North America

The rapid range southward expansion of the periwinkle Littorina littorea from the Canadian maritimes has fueled a long-running debate over whether this species was introduced to North America by human activity. A reappraisal of the mitochondrial DNA sequence evidence finds considerable endemic allelic diversity in the American population. The degree of endemic genetic diversity is higher than expected from human-mediated colonization, but not so much to suggest that it survived the last glacial maximum in America. Coalescent estimates of population divergence agree that colonization of America preceded European contact. A reappraisal of the ITS nuclear sequence data finds extensive recombination. Taking this recombination into account strengthens the genetic case against human-mediated introduction. Finally, a reappraisal of conflicting allozyme studies from the 1970’s supports a claim of limited divergence between American and European populations. This is consistent with post-glacial colonization, but the allozyme data cannot distinguish between natural or human-mediated colonization. Taken as a whole, the DNA sequence data supports the many sub-fossil reports of an American L. littorea population in the Canadian maritimes that preceded even the first visits by the Vikings.     

Modelling the genetic architecture of flowering time control in barley through nested association mapping

Background

Barley, globally the fourth most important cereal, provides food and beverages for humans and feed for animal husbandry. Maximizing grain yield under varying climate conditions largely depends on the optimal timing of flowering. Therefore, regulation of flowering time is of extraordinary importance to meet future food and feed demands. We developed the first barley nested association mapping (NAM) population, HEB-25, by crossing 25 wild barleys with one elite barley cultivar, and used it to dissect the genetic architecture of flowering time.

Results

Upon cultivation of 1,420 lines in multi-field trials and applying a genome-wide association study, eight major quantitative trait loci (QTL) were identified as main determinants to control flowering time in barley. These QTL accounted for 64% of the cross-validated proportion of explained genotypic variance (p_G). The strongest single QTL effect corresponded to the known photoperiod response gene Ppd-H1. After sequencing the causative part of Ppd-H1, we differentiated twelve haplotypes in HEB-25, whereof the strongest exotic haplotype accelerated flowering time by 11 days compared to the elite barley haplotype. Applying a whole genome prediction model including main effects and epistatic interactions allowed predicting flowering time with an unmatched accuracy of 77% of cross-validated p_G.

Conclusions

The elaborated causal models represent a fundamental step to explain flowering time in barley. In addition, our study confirms that the exotic biodiversity present in HEB-25 is a valuable toolbox to dissect the genetic architecture of important agronomic traits and to replenish the elite barley breeding pool with favorable, trait-improving exotic alleles.

     

基于COⅠ基因对温州沿海岛屿疣荔枝螺遗传多样性研究

温州沿海岛屿众多,水文环境复杂,疣荔枝螺（Reishia clavigera）是岩相潮间带常见种,对其群体间遗传多样性的分析,有助于合理保护和开发利用种质资源。本实验对温州沿海14个典型岛屿的158个疣荔枝螺个体,进行细胞色素氧化酶亚基Ⅰ（COⅠ）基因片段序列测定,得到158 条长度为672 bp的序列,A、T、C、G 四种碱基含量分别为23.0%、38.4%、17.4%和21.2%。共检测到保守位点562个,变异位点108 个,其中包括简约信息位点57 个,单突变位点51 个。所有个体的核苷酸多样性指数Pi为0.008 0 ± 0.029 7,单倍型多样性为指数Hd为0.978 ± 0.006,平均核苷酸差异度为5.328。群体间遗传距离在0.005 7 ~ 0.011 1之间,群体内遗传距离在0.005 7 ~ 0.010 8之间,不同疣荔枝螺群体之间的遗传距离处于同一水平。霓屿岛和大竹峙岛群体内遗传距离最小,洞头岛群体内遗传距离最大。共检测到102 个单倍型,大部分单倍型聚合为一支,没有形成明显的区系结构,各个岛屿的疣荔枝螺存在基因交流。     

Variation in chloroplast single-sequence repeats in Portuguese maritime pine (Pinus pinaster Ait.)

Genetic variation in 12 Pinus pinaster (maritime pine) populations spanning most of the distribution range of the species in Portugal was evaluated using six polymorphic chloroplast microsatellite (cpSSR) loci. Thirty-two haplotypes were found. There were indications of very weak differentiation among populations (Weir’s θcoefficient, 0.023), and the R _ST value, derived from the stepwise mutation model (SMM), was not significantly different from zero. The pattern, in which similarities in allele size, in base pairs, do not contribute to the genetic structure, may be due to the recent mixing of genetic material from different stands through plantations. Overall, a high level of haplotypic variation within populations was detected. Using the SMM estimator (mean genetic distance of individuals within populations, D ² _sh –––) we divided the populations into two groups, with above and below average values. The first group contained 5 populations, mainly from the central part of the country, which possess, in general, high levels of haplotypic diversity. Among them, 2 populations were divergent from the others based on the pair-wise Nei’s distance. The results indicate that there is no discernible geographic genetic pattern for the Portuguese populations of P. pinaster investigated. The history of expansion of the species range in Portugal during the twentieth century (mainly due to human activity) and extensive gene flow among populations associated with the expansion could explain this finding. Received: 15 February 2000 / Accepted: 14 April 2000     

The association between HLA-A alleles and an Alu dimorphism near HLA-G

The AluYb8 sequences are a subfamily of short interspersed Alu retroelements that have been amplified within the human genome during recent evolutionary time and are useful polymorphic markers for studies on the origin of human populations. We have identified a new member of the Yb8 subfamily, AluyHG, located between the HLA-H and -G genes and 88-kb telomeric of the highly polymorphic HLA-A gene within the alpha block of the major histocompatibility complex (MHC). The AluyHG element was characterised with a view to examining the association between AluyHG and HLA-A polymorphism and reconstructing the history of the MHC alpha block. A specific primer pair was designed for a simple PCR assay to detect the absence or presence (dimorphism) of the AluyHG element within the DNA samples prepared from a panel of 46 homozygous cell-lines containing complete or recombinant ancestral haplotypes (AH) of diverse ethnic origin and 92 Caucasoid and Asian subjects on which HLA-A typing was available. The AluyHG insertion was most strongly associated with HLA-A2 and, to a lesser degree with HLA-A1, -A3, -A11, and A-19. The gene frequency of the AluyHG insertion for 146 Caucasians and 94 Chinese-Han was 0.30 and 0.32 and there was no significant difference between the observed and expected frequencies. The results of the association studies and the phylogenetic analysis of HLA-A alleles suggest that the AluyHG sequence was integrated within the progenitor of HLA-A2, but has been transferred by recombination to other human ancestral populations. In this regard, the dimorphic AluyHG element is an important diagnostic marker for HLA association studies and could help in elucidating the evolution and functions of the MHC alpha block and polymorphism within and between ancestral haplotypes. Received: 7 December 2000 / Accepted: 28 February 2001     

p53 polymorphisms in Russia and Belarus: correlation of the 2-1-1 haplotype frequency with longitude

Four different polymorphisms in the human p53 gene (a 16-bp duplication in intron 3, and three RFLPs: for Bsh1236I at codon 72, for MspI in intron 6 and for BamHI in the 3 flanking region) and extended haplotypes were studied in nine geographically diverse populations from Russia and Belarus. The Yakuts differed from all other populations, as they had a significantly higher frequency of the BamHI A1 allele. Most populations did not differ significantly from each other in the frequency of the Bsh1236I polymorphism. The 16-bp duplication A1 allele and MspI A2 allele frequencies were significantly higher in the Yakut and Khant populations. Linkage disequilibrium values (D) between BamHI and other polymorphic sites were not significant in many cases; for this reason we have used the 16 bp–Bsh1236I–MspI haplotype frequencies only. Of eight possible haplotypes, five were observed in the populations investigated. Haplotype 1-2-2 was the most frequent in all populations. The next most common haplotype, 1-1-2, was present at very similar frequencies among the Byelorussians and Russians from Smolensk, but was more frequent in other populations. The frequency of haplotype 2-1-1 showed a nearly continuous decrease from West to East (from 17.857% among the Byelorussians to 0.685% in the Yakuts from the Verkhoyansk) and correlated with longitude (Spearmans r=–0.8667, P=0.0025), which may be due to natural selection and adaptation. The relationships among populations were evaluated by means of Neis D_A distances for the 16 bp–Bsh1236I–MspI haplotype frequencies. Based on the multidimensional scaling analysis a correlation between p53 haplotype frequencies and ethnicity is supposed.     

Endothelial nitric oxide synthase genotype and haplotype are not associated with diabetic retinopathy in diabetes type 2 patients

Polymorphisms in the endothelial nitric oxide synthase (eNOS) gene have been associated with the development of diabetic retinopathy (DR) in patients with type 1 diabetes mellitus (T1DM), but not with T2DM. However, no previous study has analyzed combinations of genetic markers (haplotypes), which can be more informative. We studied three eNOS genetic polymorphisms: a single nucleotide polymorphism in the promoter region (T(-786)C), in exon 7 (Glu298Asp), and a variable number of tandem repeats in intron 4 (b/a) in 103 healthy controls, and in 170 patients with T2DM (without DR, N=114; with DR, N=56). We also examined the association of eNOS gene haplotypes with T2DM and with DR. No differences were found in the frequencies of genotypes and alleles of the three polymorphisms among the three groups of subjects. However, the "C-Glu-b" haplotype was more common in healthy controls (24%) than in T2DM patients (7%) (P=0.0001). Finally, no significant difference in the distribution of eNOS haplotypes frequencies was found when T2DM patients with or without DR were compared (P=0.7372). These findings suggest no association between DR and individual eNOS haplotypes in T2DM patients. The "C-Glu-b" haplotype, however, may have a protective effect against T2DM. Further studies should be conducted to address the molecular basis for such an effect.     

广东汉族健康人载脂蛋白AⅠ-CⅢl-AⅣ基因簇DNA多态性及其单倍型分布

本文研究了中国广东汉族健康人群apoAI-CⅢ-AIV基因簇DNA限制性内切酶PstI、SstI和EcoRI片段长度多态性。其中等位基因P_1,P_2,S_1,S_2,R_1和R_2的频率分别为0.98,0.02,0.96,0.04,0.90和0.10。经卡方检验符合Hardy-Weinbery氏遗传平衡,与其他种族比较,本文结果显示中国广东汉族人P_2等位基因频率低于日本人、亚洲印第安人和高加索人,S_2等位基因频率低于日本人、菲律宾人、沙特阿拉伯人和亚洲印第安人,而与高加索人相近,R_2等位基因频率稍高于高加索人。不同种族间apoAI-CⅢ-AIV基因簇DNA多态频率无疑存在差异,这种差异可能是由于遗传漂变和自然选择单独或联合作用所致。对P_1、P_2,S_1、S_2和R_1、R_2构成的单倍型和连锁平衡程度进行了分析,结果显示这些单倍型处于连锁不平衡状态。     

Differential promoter activities of functional haplotypes in the 5′‐flanking region of human Sulfotransferase 1A1

Previously, we reported five common single nucleotide polymorphisms (SNPs), ?624G>C, ?396G>A, ?358A>C, ?341C>G, and ?294T>C, and six common haplotypes (CGACT, GAACT, GGAGC, GGACC, CAACT, and GAACC) in the 5′‐flanking region of the SULT1A1 gene that were associated with altered enzymatic activity. In the present study, we performed in vitro assays to determine the functional impact of these genetic variations on the promoter activity. Dual luciferase reporter assays revealed that these SNPs are located in a negative regulatory fragment of the SULT1A1 gene. Further experiments demonstrated that these SNPs and haplotypes affected promoter activities of SULT1A1. Electrophoretic mobility shift assays showed distinctive binding patterns for the SNPs ‐396G>A and ‐294T>C, due to differential binding affinities of the G/A alleles and the T/C alleles to nuclear proteins extracted from the liver carcinoma cell lines, HepG2 and Huh7. © 2012 Wiley Periodicals, Inc. J Biochem Mol Toxicol 26:422–428, 2012; View this article online at wileyonlinelibrary.com . DOI 10:1002/jbt.21437     

Influences of rare copy-number variation on human complex traits

1. Download : Download high-res image (239KB)
2. Download : Download full-size image