Distribution and genetic variability among Campylobacter spp. isolates from different animal species and humans in Switzerland

In Switzerland, a national database with 1028 Campylobacter isolates from poultry, pigs, cats, dogs, cattle, humans, zoo animals and water has been created. The database contains the genetic fingerprint and background information of each Campylobacter isolate. Dominant species could be identified in the different sources with a majority of Campylobacter jejuni in poultry (73%), humans (79%), cattle (95%), zoo animals (40%) and water (100%), of Campylobacter coli in pigs (72%), and of Campylobacter upsaliensis/helveticus in cats and dogs (55%). The comparison of three genotyping methods, amplified fragment length polymorphism (AFLP), pulsed field gel electrophoresis and restriction fragment length polymorphism, revealed that AFLP allows discrimination between the different Campylobacter species and is the most appropriate method to distinguish specific strains within the same species. Genotyping analysis demonstrated that the Campylobacter population is heterogeneous among the different sources and that no dominant clone is spread in the country. Genotyping and the resulting database are useful tools to trace back future Campylobacter infections.     

基于STR技术的4个地方鹅种遗传多样性分析

利用9对高度多态的微卫星引物,运用STR自动化分析技术,对浙东白鹅、皖西白鹅、四川白鹅和太湖鹅等4个地方鹅种的群体遗传多样性进行微卫星分析。根据等位基因频率计算有效等位基因数、群体杂合度等群体遗传参数,分析群体内和群体间的遗传变异,并与上一世代保种群体的遗传信息进行比较。结果表明:在9个座位上共检测到74个等位基因;群体平均期望杂合度为0.605 6,平均多态信息含量为0.553 8。群体间遗传分化差异显著,遗传分化系数为0.043 7。群体间遗传距离为0.033 2~0.111 0,基因流动值为5.820~16.703。两世代遗传多样性无明显差异,表明基因库保种切实保持品种自身的种质特性。     

主要组织相容性复合体在鸟类保护生物学中的应用

在保护生物学研究中,主要组织相容性复合体（major histocompatibility complex,MHC）的遗传多样性越来越受到人们的重视。在研究比较广泛和深入的哺乳动物和鱼类中,MHC被认为与抗病能力、配偶选择和亲缘识别有关。然而,MHC基因对哺乳动物行为产生影响的机制是否适用于鸟类,特别是鸟类野生种群,尚不清楚。文章对MHC多态性机制、MHC基因分型方法及其与鸟类疾病抗性、配偶选择的关系等进行了综述,为研究人员对鸟类保护生物学的深入研究提供参考。     

Characterization of Weissella ceti infections in Brazilian rainbow trout,Oncorhynchus mykiss (Walbaum), farms and development of an oil-adjuvanted vaccine

Weissella ceti is an emerging bacterial pathogen that affects rainbow trout, Oncorhynchus mykiss (Walbaum), farms. The aims of this study were to genotype W. ceti strains isolated from distinct geographical origins and to determine the efficacy of an oil-adjuvanted vaccine against the disease. Between 2010 and 2012, outbreaks were recorded in five Brazilian farms, and 34 W. ceti isolates were genetically characterized by repetitive extragenic palindromic PCR, enterobacterial repetitive intergenic consensus sequences PCR and pulsed-field gel electrophoresis. Two different W. ceti vaccines were tested: an aqueous-based whole-cell inactivated vaccine (bacterin) and oil-adjuvanted vaccine. Their efficacy was evaluated in rainbow trout at 30 and 60 days post-vaccination (d.p.v.). W. ceti was found to be a highly homogeneous population in Brazil, with clonally related genotypes. Oil-adjuvanted vaccine exhibited the best (P < 0.05) protection against disease, reaching relative percentage survival (RPS)values of 92% at 30 and 60 d.p.v. Bacterin resulted in RPS values of 67% and 58% at day 30 and 60, respectively. The oil-adjuvanted vaccine provided effective protection against W. ceti infection in rainbow trout.     

Advances in crop phenotyping and multi-environment trials

Efficient evaluation of crop phenotypes is a prerequisite for breeding, cultivar adoption, genomics and phenomics study. Plant genotyping is developing rapidly through the use of high-throughput sequencing techniques,while plant phenotyping has lagged far behind and it has become the rate-limiting factor in genetics, large-scale breeding and development of new cultivars. In this paper,we consider crop phenotyping technology under three categories. The first is high-throughput phenotyping techniques in controlled environments such as greenhouses or specifically designed platforms. The second is a phenotypic strengthening test in semi-controlled environments, especially for traits that are difficult to be tested in multi-environment trials(MET), such as lodging, drought and disease resistance. The third is MET in uncontrolled environments, in which crop plants are managed according to farmer's cultural practices. Research and application of these phenotyping techniques are reviewed and methods for MET improvement proposed.     

番茄Mi-1基因的SNP分型

SNP分型是SNP分子标记辅助育种,以及分子遗传作图等研究的重要基础技术。试验利用在番茄Mi-1基因中开发出的一个A/T型SNP位点,应用等位基因聚合酶链式反应技术,成功的对438个F2群体进行了SNP分型。结果表明,这一F2群体中有72个纯合T/T基因型,175个杂合A/T基因型,70个纯合A/A基因型,以及121个不明原因缺失的F2单株,已得基因型经卡方测验符合1:2:1分离比例;同时,试验通过在下游引物3′末端第二、三位点引入错配碱基,以及优化PCR反应体系为Mg2+1.875 mmol.L-1,dNTP 100μmol.L-1,提高了反应的准确性,为番茄抗根结线虫辅助育种打下了基础。     

Genotyping by sequencing of 270 Indica rice varieties revealed genetic markers probably related to heavy metal accumulation

Genotyping by sequencing (GBS) has been applied to identify genetic markers in crops for trait association and breeding purposes. Here, we applied GBS technology to study a natural population of 270 Indica rice strains, which resulted in identification of 79,545 genomewide single nucleotide polymorphisms. Using these SNPs, we found the close relationship between the 270 Indica rice strains. Furthermore, we tested the feasibility of using these 270 Indica strains in studying important rice traits by analysing the cadmium and other metal accumulation of these strains and correlating the traits with genetic markers. We identified 32 SNPs to be associated with cadmium (Cd) accumulation, explaining 61.25% of the Cd concentration variances in grains. The genetic markers provided here are valuable resources for future rice studies, and further characterization of the candidate loci identified in this study can also aid the development of low Cd‐accumulating rice varieties.     

A high‐resolution einkorn (Triticum monococcum L.) linkage map involving wild,domesticated and feral einkorn genotypes

A high‐resolution consensus linkage map of Triticum monococcum was assembled from two separate maps involving domesticated, feral and wild einkorn wheat accessions. The genotyping‐by‐sequencing (GBS) approach based on DArTseq markers yielded overstretched maps. Deleting all markers with missing data and then converting dubious singletons to missing data produced two maps of about 1,380 cM, close to the published genome size. The consensus map spanned 1,562 cM, had one bin mapped every 0.92 cM and showed only one gap > 10 cM. Chromosome length varied between 151 cM (chromosome 4) and 270 cM (chromosome 7). The consensus map was compared to other A‐genome maps, and the sequences of genetically mapped DArTseq were used to anchor contigs of the T. monococcum, T. urartu and T. aestivum draft genomes based on sequence homology to assess colinearity and to assign mapped markers to the seven chromosomes of the bread wheat A‐genome. Finally, an in silico functional characterization of the sequences was performed. This high‐resolution map will facilitate QTL and association analysis and assist the genome assembly of the einkorn genome.     

SNP检测方法在动物研究中的应用

单核苷酸多态性(SNP)作为第三代分子标记技术,以其数量丰富、遗传稳定性高、易于快速自动化检测等优点备受关注。该文综述了基于不同原理的SNP分型检测方法,包括几种常见的测序技术、基于酶学及杂交原理的分析检测技术和基于色谱及质谱的相关技术。阐释了方法的原理、分析了方法的优缺点及适用范围。总结了目前在动物遗传育种、亲缘鉴定、动物品种及产品溯源等方面的应用研究现状。为下一步开发更灵敏准确、简便易行、高通量及低成本的SNP检测方法及拓展SNP的应用领域提供参考。     

Founder representation and effective population size in old versus young breeds—genetic diversity of Finnish and Nordic Spitz

Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (f_a) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis () is 168, whereas the genetic effective population size (N_eg) computed the decay of linkage disequilibrium (r²) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had f_a of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz ( = 98 and N_eg = 49). Interestingly, the r² data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed.