Role of domestication in shaping <Emphasis Type="Italic">Castanea sativa</Emphasis> genetic variation in Europe

The genetic structure of sweet chestnut (Castanea sativa Mill.) across Europe was assessed using 73 inter-simple sequence repeat markers to screen 1,768 individuals from 68 stands distributed across 29 sites in five European countries (Italy, France, Spain, Greece, and UK). At each site, trees were sampled from three distinct management types (domestication levels): naturalized stands, managed coppice, and grafted fruit orchards. In more than a third of the orchards, nonlocal genetic material (grafted clones) were evident, showing (as predicted) large differences from the other two domestication levels for most of the within-population genetic diversity parameters estimated. Randomly generated linkage disequilibrium analysis revealed weak though significant differences in two-locus allelic correlations between naturalized stands and coppice, suggesting that long-term management techniques may influence the genetic makeup of the populations. Multivariate analysis revealed the existence of five distinct gene pools across the study area; three were located in Greece, one on the northwestern coast of the Iberian peninsula and a large gene pool covering the rest of the Mediterranean basin. The implications of the results are discussed in relation to developing conservation strategies for chestnut genetic resources in Europe.     

Hydraulic redistribution: limitations for plants in saline soils

Hydraulic redistribution (HR), the movement of water from wet to dry patches in the soil via roots, occurs in different ecosystems and plant species. By extension of the principle that HR is driven by gradients in soil water potential, HR has been proposed to occur for plants in saline soils. Despite the inherent spatial patchiness and salinity gradients in these soils, the lack of direct evidence of HR in response to osmotic gradients prompted us to ask the question: are there physical or physiological constraints to HR for plants in saline environments? We propose that build‐up of ions in the root xylem sap and in the leaf apoplast, with the latter resulting in a large predawn disequilibrium of water potential in shoots compared with roots and soil, would both impede HR. We present a conceptual model that illustrates how processes in root systems in heterogeneous salinity with water potential gradients, even if equal to those in non‐saline soils, will experience a dampened magnitude of water potential gradients in the soil–plant continuum, minimizing or preventing HR. Finally, we provide an outlook for understanding the relevance of HR for plants in saline environments by addressing key research questions on plant salinity tolerance.     

Conditional likelihood score functions for mixed models in linkage analysis

In this paper, we develop a general strategy for linkage analysis, applicable for arbitrary pedigree structures and genetic models with one major gene, polygenes and shared environmental effects. Extending work of Whittemore (1996), McPeek (1999) and Hossjer (2003d), the efficient score statistic is computed from a conditional likelihood of marker data given phenotypes. The resulting semiparametric linkage analysis is very similar to nonparametric linkage based on affected individuals. The efficient score S depends not only on identical-by-descent sharing and phenotypes, but also on a few parameters chosen by the user. We focus on (1) weak penetrance models, where the major gene has a small effect and (2) rare disease models, where the major gene has a possibly strong effect but the disease causing allele is rare. We illustrate our results for a large class of genetic models with a multivariate Gaussian liability. This class incorporates one major gene, polygenes and shared environmental effects in the liability, and allows e.g. binary, Gaussian, Poisson distributed and life-length phenotypes. A detailed simulation study is conducted for Gaussian phenotypes. The performance of the two optimal score functions S(wpairs) and S(normdom) are investigated. The conclusion is that (i) inclusion of polygenic effects into the score function increases overall performance for a wide range of genetic models and (ii) score functions based on the rare disease assumption are slightly more powerful.     

Effective size of populations under partial inbreeding and selection on a set of linked additive genes

The prediction theory of effective population size (Ne) is extended to cover selection on a set of linked additive genes and partial inbreeding (partial selfing or partial full-sib mating). Ne under selection is generally expressed as a function of the cumulative change in frequency of a neutral gene due to the random association between the neutral and selected genes generated by finite sampling. In this study, the association under partial selfing was classified into two types, the association between the neutral and selected genes on the same gamete, and the association between the neutral and selected genes each on the different gametes in the same parent. For partial full-sib mating, an additional association, i.e., the association between the neutral and selected genes each in the different parents in the same family, was included in the model. According to this classification of the association, the coefficient accounting for the cumulative change in frequency of the neutral gene was partitioned into two or three components. A method for computing the partitioned coefficients was obtained from the transition matrix approach, in which the joint effect of linkage, selection and partial inbreeding was taken into account. To assess the joint effects of linkage, selection and partial inbreeding on Ne, numerical computations with the obtained expressions were carried out. The effect of linkage on Ne was generally small, except for an extremely small genome size, while the partial inbreeding resulted in a drastic reduction in Ne. For a given genome size, Ne was essentially independent of the length and number of chromosomes. Some of these results were verified by stochastic simulations.     

Variation and association of fibronectin‐binding protein genes fnbA and fnbB in Staphylococcus aureus Japanese isolates

Fibronectin‐binding proteins A and B (FnBPA and FnBPB) mediate adhesion of Staphylococcus aureus to fibrinogen, elastin and fibronectin. FnBPA and FnBPB are encoded by two closely linked genes, fnbA and fnbB, respectively. With the exception of the N‐terminal regions, the amino acid sequences of FnBPA and FnBPB are highly conserved. To investigate the genetics and evolution of fnbA and fnbB, the most variable regions, which code for the 67th amino acids of the A through B regions (A67–B) of fnbA and fnbB, were focused upon. Eighty isolates of S. aureus in Japan were sequenced and 19 and 18 types in fnbA and fnbB, respectively, identified. Although the phylogeny of fnbA and fnbB were found to be quite different, each fnbA type connected with a specific fnbB type, indicating that fnbA and fnbB mutate independently, whereas the combination of both genes after recombination is stable. Hence those fnbA–fnbB combinations were defined as FnBP sequence types (FnSTs). Representative isolates of each FnST were assigned distinct STs by multilocus sequence typing, suggesting correspondence of FnST with genome lineage. Linkage disequilibrium (LD) analysis of the A67–B region revealed that subdomains N2, N3 and FnBR1 form a LD block in fnbA, whereas N2 and N3 form two independent LD blocks in fnbB. N2–N3 three‐dimensional structural models indicated that not only the variable amino acid residues, but also well‐conserved amino acid residues between FnBPA and FnBPB, are located on the surface of the protein. These results highlight a molecular process of the FnBP that has evolved by mingled mutation and recombination with retention of functions.     

利用与PKD1紧密连锁的微卫星多态性对黑龙江省汉族人群进行ADPKD的症前诊断

目的：利用与PKD1紧密连锁的微卫星的多态性对黑龙江省汉族人群常染色体显性遗传性多裳肾病（autosomal dominant polycystic diseaseADPKD）家系成员进行症状前诊断。方法：扩增PKD1基因内部（KG8）及基因两侧（AC2．5、CW4）共三个微卫星遗传标记,并采用聚丙烯酰胺凝胶电泳进行检测,银染,最后进行家系连锁分析。结果：家系1中一名男孩携带了PKD1突变基因,处于发病前期。结论：通过连锁分析ADPKD进行连锁分析能高效、快捷、准确地进行早期诊断.     

Replicated hybrid zones of Xiphophorus swordtails along an elevational gradient

Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. We show that widespread hybridization has occurred between two neo-tropical stream fishes with partial reproductive isolation. Phylogenetic analyses of mitochondrial sequence data showed that the swordtail fish Xiphophorus birchmanni is monophyletic and that X. malinche is part of an independent monophyletic clade with other species. Using informative single nucleotide polymorphisms in one mitochondrial and three nuclear intron loci, we genotyped 776 specimens collected from twenty-three sites along seven separate stream reaches. Hybrid zones occurred in replicated fashion in all stream reaches along a gradient from high to low elevation. Genotyping revealed substantial variation in parental and hybrid frequencies among localities. Tests of F(IS) and linkage disequilibrium (LD) revealed generally low F(IS) and LD except in five populations where both parental species and hybrids were found suggesting incomplete reproductive isolation. In these locations, heterozygote deficiency and LD were high, which suggests either selection against early generation hybrids or assortative mating. These data lay the foundation to study the adaptive basis of the replicated hybrid zone structure and for future integration of behaviour and genetics to determine the processes that lead to the population genetic patterns observed in these hybrid zones.     

中国汉族apoB基因EcoRI、XbaI、MspI、Ins/Del及3＇端VNTR位点的多态性研究

目的：apo B基因多态性对群体遗传学、心血管疾病等研究领域有着重要的价值,本文分析了中国汉族人群中apoB基因EcoRI、XbaI、MspI、Ins/Del及3＇端VNTR等5个多态性位点的等位基因频率分布,为相关研究提供基础资料。方法：应用PCR-RFLP技术分析EcoRI、XbaI、MspI等3个位点的多态性分布,应用常规PCR方法分析Ins/Del及3＇端VNTR等2个位点的多态性分布。结果：1人群中EcoRI位点有E＋及E-两种等位基因,基因频率分别为87.1%和12.9%;XbaI位点有X＋及X-两种等位基因,基因频率分别为6.1%和93.9%;MspI位点有M＋及M-两种等位基因,基因频率分别为97.1%和2.3%;Ins/Del位点有Ins及Del两种等位基因,基因频率分别为70.7%和29.3%;3＇端VNTR位点有16种等位基因,其中以HVE34与HVE36最为常见,频率分别为33.4%与21%。2连锁不平衡分析表明,5个位点间除XbaI与Ins/Del间存在较弱的连锁不平衡（D＇=0.911,r2=0.175）,其余点位间无显著连锁不平衡。结论：数据比对表明,5个多态性位点的基因型和等位基因频率存在民族、种族差异,因此在apo B基因相关研究中应充分考虑遗传背景造成的影响。