Genetic diversity of Campylobacter jejuni isolates from farm animals and the farm environment

The genetic diversity of Campylobacter jejuni isolates from farm animals and their environment was investigated by multilocus sequence typing (MLST). A total of 30 genotypes, defined by allelic profiles (assigned to sequence types [STs]), were found in 112 C. jejuni isolates originating in poultry, cattle, sheep, starlings, and slurry. All but two of these genotypes belonged to one of nine C. jejuni clonal complexes previously identified in isolates from human disease and retail food samples and one clonal complex previously associated with an environmental source. There was some evidence for the association of certain clonal complexes with particular farm animals: isolates belonging to the ST-45 complex predominated among poultry isolates but were absent among sheep isolates, while isolates belonging to the ST-61 and ST-42 complexes were predominant among sheep isolates but were absent from the poultry isolates. In contrast, ST-21 complex isolates were distributed among the different isolation sources. Comparison with MLST data from 91 human disease isolates showed small but significant genetic differentiation between the farm and human isolates; however, representatives of six clonal complexes were found in both samples. These data demonstrate that MLST and the clonal complex model can be used to identify and compare the genotypes of C. jejuni isolates from farm animals and the environment with those from retail food and human disease.     

Genetic dissection of phenotypic diversity in farm animals

Farm animal populations harbour rich collections of mutations with phenotypic effects that have been purposefully enriched by breeding. Most of these mutations do not have pathological phenotypic consequences, in contrast to the collections of deleterious mutations in model organisms or those causing inherited disorders in humans. Farm animals are of particular interest for identifying genes that control growth, energy metabolism, development, appetite, reproduction and behaviour, as well as other traits that have been manipulated by breeding. Genome research in farm animals will add to our basic understanding of the genetic control of these traits and the results will be applied in breeding programmes to reduce the incidence of disease and to improve product quality and production efficiency.     

Genetic diversity of Poa annua in western Oregon grass seed crops

The genetic diversity of Poa annua L.populations collected from western Oregon grass-seed fields was surveyed using 18 randomly amplified polymorphic DNA (RAPD) markers. Markers from 1357 individual plants from 47 populations collected at three sampling dates (fall, winter, and spring) for 16 sites were used to measure genetic diversity within and among populations. Site histories varied from low to high herbicide selection pressure, and some sites were subdivided by 3 years of differing post-harvest residue management. Gene diversity statistics, simple frequency of haplotype occurrence, and analysis of molecular variance (AMOVA) revealed the presence of significant variability in P. annua among sites, among collection dates within sites, and within collection dates. Nei gene-diversity statistics and population-differentiation parameters indicated that P. annua populations were highly diverse. Mean Nei gene diversity (h) for all 47 populations was 0.241 and total diversity (H_T) was 0.245. A greater proportion of this diversity, however, was within (H_S=0.209) rather than among (G_ST=0.146) populations. When populations were grouped by season of collection, within-group diversity was H_S=0.241, while among-group diversity was G_ST=0.017. When populations were grouped by site, within-group diversity was H_S=0.224, while among-group diversity was G_ST=0.087. The diversity among populations within season for fall, winter, and spring collections was G_ST=0.121, 0.142, and 0.133, respectively. Populations collected from fields with histories of high herbicide selection pressure showed low differentiation among collection dates, with G_ST as low as 0.016, whereas those collected from fields with low herbicide selection pressure showed greater differentiation among collection dates, with G_ST as high as 0.125. At high selection-pressure sites, populations were also lower in gene diversity (as low as h=0.155), while at low selection-pressure sites there was higher gene diversity (as high as h=0.286). The site to site variability was greater for the high selection-pressure sites (G_ST=0.107 or 69% of the total among-population variance), while the season of germination variability was greater at sites of low herbicide-selection pressure (G_ST=0.067, or 70% of the total among-population variance). High initial diversity coupled with a long-term re-supply of genotypes from the seed bank must have been factors in maintaining the genetic diversity of this weed despite the intensive use of herbicides. Knowledge of the genetic diversity of Willamette Valley P. annua should help in formulating more effective strategies for managing this weed. Received: 24 July 1999 / 11 November 1999     

Genetic diversity of the European bison herd from the Prioksko-Terrasny nature reserve

Maintaining the existing genetic diversity in populations is one of the most important measures for species conservation. Some components of this diversity in the bison population of the Prioksko-Terrasny Nature Reserve, including the level of preservation of the founder genetic diversity or the founder genomic equivalent (fge) of the current bison stock and the indices of similarity (mk) and genome uniqueness (gu), as well as their effects on viability of the animals from 1950-1995 were studied. The data obtained were treated and the diversity parameters were calculated with the use of the SPARKS software package. This was performed in collaboration with the Institute for Zoo Biology and Wildlife Research (Berlin, Germany). The results of the analysis indicated that, in breeding groups of the European bison, the fge, mk, and gu values should be maintained at levels higher than 1.30, lower than 40%, and higher than 10%, respectively. When selecting males for specific groups of females, the male gu should be at least 20%, and mk should be lower than 40%.     

A genome-wide analysis of single nucleotide polymorphism diversity in the world's major cereal crops

Over 3.5 million expressed sequence tags from the major cereal taxa were used to electronically mine over 176 000 putative single nucleotide polymorphisms (SNPs). The density, distribution and degree of linkage between these SNPs were compared among the different taxa. The frequency of sequence polymorphism was lowest in diploid taxa (rice, barley and sorghum), intermediate in tetraploid maize and highest in allohexaploid wheat and octoploid sugarcane. SNPs were further categorized as either intravarietal (differences between gene family members and homoeologues) or varietal (differences between two varieties), and as either co-segregating or non-co-segregating with neighbouring polymorphisms. Varietal co-segregating SNPs represent the best candidates for molecular markers as they show variation between varieties and have a high probability of being validated, as sequencing errors are unlikely to co-segregate with one another. This elite class of SNPs was most abundant in barley and least abundant in wheat and rice. Despite the large number of observed sequence polymorphisms in allohexaploid wheat, only a fraction of those available are likely to make good molecular markers. In addition, we found that rice SNPs up to 10 kb apart were in linkage disequilibrium (LD), but that high levels of LD attributable to population structure confounded the tracking of LD over greater distances.     

Genetic diversity of Listeria monocytogenes strains from a high-prevalence dairy farm

Listeria monocytogenes is a significant food-borne human and veterinary pathogen. Contaminated silage commonly leads to disease in livestock, but the pervasive nature of the bacterium can make it difficult to identify the source of infection. An investigation of bovine listeriosis that occurred on a Pacific Northwest dairy farm ("farm A") revealed that the clinical strain was closely related to fecal strains from asymptomatic cows, and that farm environment was heavily contaminated with a diversity of L. monocytogenes strains. In addition, the farm A clinical strain was closely related to clinical and environmental strains obtained 1 year prior from a second Northwest dairy farm ("farm B"). To investigate the source(s) of contamination on farm A, environmental samples were collected from farm A at two time points. Pulsed-field gel electrophoresis characterization of 538 isolates obtained from that farm identified 57 different AscI pulsovars. Fecal isolates obtained from individual cows were the most genetically diverse, with up to 94% of fecal samples containing more than one pulsovar. The maximum numbers of pulsovars and serotypes isolated from a fecal sample of one cow were 6 and 4, respectively. Serotype 1/2a was isolated most frequently at both time points. Microarray genotyping of bovine listeriosis, fecal, and silage strains from both farms identified four probes that differentiated listeriosis strains from environmental strains; however, no probe was common to both bovine listeriosis strains.     

Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design

Little consideration has been given to the genetic composition of populations associated with marine reserves, as reserve designation is generally to protect specific species, communities or habitats. Nevertheless, it is important to conserve genetic diversity since it provides the raw material for the maintenance of species diversity over longer, evolutionary time-scales and may also confer the basis for adaptation to environmental change. Many current marine reserves are small in size and isolated to some degree (e.g. sea loughs and offshore islands). While such features enable easier management, they may have important implications for the genetic structure of protected populations, the ability of populations to recover from local catastrophes and the potential for marine reserves to act as sources of propagules for surrounding areas. Here, we present a case study demonstrating genetic differentiation, isolation, inbreeding and reduced genetic diversity in populations of the dogwhelk Nucella lapillus in Lough Hyne Marine Nature Reserve (an isolated sea lough in southern Ireland), compared with populations on the local adjacent open coast and populations in England, Wales and France. Our study demonstrates that this sea lough is isolated from open coast populations, and highlights that there may be long-term genetic consequences of selecting reserves on the basis of isolation and ease of protection.     

Genetic diversity and population structure of Pepino mosaic virus in tomato crops of Spain and Morocco

Pepino mosaic virus (PepMV, genus Potexvirus) is an emergent and highly infectious pathogen responsible for economically important diseases in tomato crops. An extensive survey of tomato plants showing PepMV‐like symptoms was carried out in 2017 to study the PepMV genetic diversity and populations structure in different tomato‐producing areas of Spain and Morocco. Molecular dot‐blot hybridization analysis showed that virus populations from Spain and Morocco were mainly composed of isolates belonging to the Chilean 2 (CH2) strain, although isolates of the European (EU) strain were detected in significant proportions in Spanish populations, mainly in mixed infections. A few isolates of the American (US1) strain were also detected in Tenerife (Canary Islands, Spain) crops. Eighty‐five isolates were randomly selected and sequenced in the genomic region that encodes the triple gene block and capsid protein genes. Our phylogenetic and population genetics analyses confirmed the presence of the CH2, EU and US1 PepMV strains. Despite the high genetic similarity observed within populations, variants were maintained at low frequency under purifying selection, and differentiation among more geographically distant locations was identified, with potential gene flow contributing to the shaping of the PepMV populations structure.     

中国香菇主栽品种遗传多样性的SSR分析及指纹图谱构建

【目的】香菇(Lentinulaedodes)是世界第二大食用菌,研究我国现有栽培种群体的遗传多样性和遗传构成以及准确鉴定品种是新品种开发和产业健康发展的基础。【方法】采用多态性的SSR(Simple sequence repeat)分子标记对中国历年来使用主栽品种进行遗传多样性及群体结构分析,比较其谱系来源,解析中国主栽品种的群体多样性构成,并构建指纹图谱用于品种鉴定。【结果】24对多态性SSR引物对51份香菇菌株都具有多态性。聚类分析在相似系数0.69处可将栽培种群体分为4个类群,野生种驯化或参与杂交获得的菌株位于类群Ⅲ和Ⅳ,其他菌株位于另外两个类群Ⅰ和Ⅱ。群体结构分析可将栽培群体分为6个遗传构成,显示L808、L135等代表性菌株在各自的构成中参与了其他菌株的选育过程,解释了以其为亲本的部分品种的谱系来源。依据筛选出的9对条带清晰的SSR引物组合构建了多位点SSR指纹图谱,可对45个香菇商业菌种进行辨识。【结论】我国香菇主栽品种亲缘关系较近,育种多围绕L808、L135、9015等核心代表性品种进行,本研究可为选育具有自主知识产权、适应不同栽培模式的新品种提供依据;指纹图谱的构建也能为香菇品种的准确鉴定提供保证。     

真鲷自然群体和人工繁殖群体的遗传多样性

采用RAPD技术对真鲷野生群体及人工繁殖群体各23个个体进行了DNA多态性检测。实验选取OPK组16个10 bp随机引物用于两群体的遗传多样性分析。在野生群体和人工繁殖群体中分别获得131和123条扩增片段,两群体的多态片段比例分别为62.60%和54.47%,平均杂合度分别为0.4786和0.3633,可见真鲷野生群体及人工繁殖群体的遗传多样性较为丰富,在选择育种和遗传改良方面具有较大的潜力。人工繁殖群体的多态片段比例和平均杂合度都低于野生群体,意味着在生产过程中要采取行之有效的管理保护措施以避免或减少遗传多样性水平的降低,确保真鲷增养殖业的可持续发展。     

四川省草莓主产区灰葡萄孢菌的遗传多样性

为明确四川省草莓灰葡萄孢Botrytis cinerea群体遗传结构及其多样性水平,采用ISSR分子标记技术对分离自四川省10个县（市）的195株灰葡萄孢菌进行了遗传多态性分析。结果表明,四川省灰葡萄孢菌多态性丰富,6条ISSR引物共产生了63个多态性位点,应用Popgene32软件计算四川省不同主产区域（除德阳广汉种群外）种群的Nei’s基因多样性指数（H）和Shannon信息指数（I）均达到了H>0.2、I>0.3的水平,表明四川省的灰葡萄孢菌具有丰富的遗传多样性;灰葡萄孢菌群体的遗传多样性（Ht）均值为0.2976,种群内遗传多样性（Hs=0.2458）远远高于种群间（Dst=0.0518）的遗传多样性;遗传分化系数（Gst）均值0.1742,基因流（Nm）均值2.3696,说明该地区灰葡萄孢菌种群间遗传分化不明显,群体内基因交流频繁。通过UPGMA法和Omishare Tools热图软件均可将10个采集点分为3个类群,来自绵阳江油的菌株单独构成一个类群,来自成都崇州和德阳广汉的菌株构成一个类群,其余的菌株构成另外一个类群;利用Structure 2.3软件对195份灰葡萄孢菌进行群体结构分析,可将134份菌株划分成21个群,另外61个菌株被列为混合群体。     

The impact of the EU regulatory constraint of transgenic crops on farm income

World population and the need for nutritious food continue to grow. For 14 years farmers from a range of countries across the globe have been accessing transgenic technologies either to reduce crop production costs, increase yield and/or to exploit a range of rotational benefits. In 2009 134 Mha of transgenic crops was grown. The arable area of the EU 27 is approximately 102 Mha; however, only about 0.1 Mha of transgenic crops, mainly maize in Spain, is grown in the EU. This is in part due to limited approvals before the establishment of a moratorium on the cultivation of transgenic crops. In this paper we estimate the revenue foregone by EU farmers, based on the potential hectarages of IR and HT transgenic crops that have been economically successful elsewhere if they were to be grown in areas of the EU where farmers could expect an overall financial benefit. This benefit would accrue primarily from reduced input costs. We estimate that if the areas of transgenic maize, cotton, soya, oil seed rape and sugar beet were to be grown where there is agronomic need or benefit then farmer margins would increase by between €443 and €929 M/year. It is noted that this margin of revenue foregone is likely to increase if the current level of approval and growth remains low, as new transgenic events come to market and are rapidly taken up by farmers in other parts of the world.     

Assessing the genetic diversity in small farm animal populations

Genetic variation is vital for the populations to adapt to varying environments and to respond to artificial selection; therefore, any conservation and development scheme should start from assessing the state of variation in the population. There are several marker-based and pedigree-based parameters to describe genetic variation. The most suitable ones are rate of inbreeding and effective population size, because they are not dependent on the amount of pedigree records. The acceptable level for effective population size can be considered from different angles leading to a conclusion that it should be at least 50 to 100. The estimates for the effective population size can be computed from the genealogical records or from demographic and marker information when pedigree data are not available. Marker information could also be used for paternity analysis and for estimation of coancestries. The sufficient accuracy in marker-based parameters would require typing thousands of markers. Across breeds, diversity is an important source of variation to rescue problematic populations and to introgress new variants. Consideration of adaptive variation brings new aspects to the estimation of the variation between populations.     

Bacterial diversity in organically-enriched fish farm sediments

The bacterial diversity and community structure within both organically enriched and adjacent, unimpacted, near-shore marine sediments at two fish farms in southern Tasmania, Australia, was examined using 16S rRNA gene clone library construction and analysis. Sediments at both caged and reference sites at both farms showed a very high level of microbial diversity. Over 900 clones were analysed and grouped into 631 unique phylotypes. Reference sites were dominated by Delta- and Gammaproteobacteria and the Cytophaga-Flavobacteria-Bacteroides group. Cage site sediments were also dominated by these phylotypes, as well as members of the Alpha- and Epsilonproteobacteria. Diversity and coverage indices indicated that the actual diversity of the sediments was much greater than that detected, despite a large sampling effort. All libraries were shown to be statistically different from one another (P < 0.05). Many phylotypes did not group with cultured bacteria, but grouped with other environmental clones from a wide array of marine benthic environments. Diversity and evenness indices suggested that although both parameters changed after farming, diverse communities were present in all sediments. The response of the microbial community to organic load suggested that random, rather than predictable, succession events determine community composition and diversity, and that sediment type may influence bacterial community and sediment response to organic perturbation.     

Begomovirus diversity in tomato crops in Costa Rica

Begomoviruses (Geminiviridae family) are characterized by their high recombination rate and a wide range of hosts, making their control difficult. In Costa Rica, various species of bipartite begomoviruses have been reported, which are Pepper golden mosaic virus (PepGMV), Tomato yellow mottle virus (ToYMoV), Tomato leaf curl Sinaloa virus (ToLCSiV) and the monopartite begomovirus Tomato yellow leaf curl virus (TYLCV). Since the TYLCV first report in Costa Rica, neither additional knowledge has been produced on how this begomovirus has spread in the country's territory nor on the distribution of the other bipartite species. A total of 429 tomato samples collected during the years 2015–2016 were used to study these aspects. Each sample was georeferenced and analysed with various techniques such as nucleic acid hybridization, polymerase chain reaction (PCR) and sequencing for the begomoviruses previously reported in Costa Rica. It was found that the presence/absence of the different species can vary, depending on the province. TYLCV is present in the six provinces analysed in this work, with a proportion from 3.7 to 86.6 per cent. Alajuela, Cartago, and Heredia are the provinces most affected by tomato-infecting begomoviruses. Fourteen different haplotypes of TYLCV were detected, but all were identified as TYLCV-IL. The distribution of TYLCV was related to the presence of the whitefly Bemisia tabaci MED, especially in the country's main tomato production areas. This information allows the phytosanitary surveillance services to develop strategies for the integrated management of the disease and to contribute data to the genetic improvement programmes of the crop.     

猕猴桃属(Actinidia)植物的遗传多样性

猕猴桃属（Ａｃｔｉｎｉｄｉａ）植物全世界有６６个种、约１１８个种下分类单位（变种、变型）。中国有猕猴桃属６２个种,猕猴桃遗传资源极为丰富。本文就猕猴桃的遗传资源多样性主要特点作概要综述：１）形态性状多样性（重要的园艺及经济性状）;２）营养成分及风味多样性;３）性别变异;４）染色体倍性变异;５）同工酶水平遗传多样性;６）ＤＮＡ水平遗传多样性。     

Genetic diversity and introgression in the Scottish wildcat

This paper describes a genetic analysis of wild-living cats in Scotland. Samples from 230 wild-living Scottish cats (including 13 museum skins) and 74 house cats from England and Scotland were surveyed for nine microsatellite loci. Pelage characteristics of the wild-living cats were recorded, and the cats were then grouped into five separate categories depending on the degree to which they conformed to the characteristics attributed to Felis silvestris Schreber, 1775. Allele frequency differences between the morphological groups are greater than those among the three house cat samples. Analysis of genetic distances suggests that more of the differences between individuals can be explained by pelage than geographical proximity, and that pelage and geographical location are not confounded. Ordination of the genetic distances suggests two main groups of wild-living cats, with intermediates, and one group is genetically very similar to the house cats, while the other group contains all cats taxonomically identified as wildcat based on morphology. A genetic mixture analysis gives similar results to the ordination, but also suggests that the genotypes of a substantial number of cats in the wildcat group are drawn from a gene pool with genotypes in approximately equilibrium proportions. We argue that this is evidence that these cats do not have very recent domestic ancestry. However, from the morphological data it is highly likely that this gene pool also contains a contribution from earlier introgression of domestic cat genes.