Multilocus microsatellite analysis reveals extensive genetic diversity in Neospora caninum

Neospora caninum is a world-wide parasite that causes neuromuscular disorders in dogs and bovine abortion. Biological diversity among isolates has been proved in both in vivo and in vitro studies. In contrast, little is known about the genetic diversity of this parasite. Microsatellite sequence analysis constitutes a suitable tool that has been used for the genetic analysis of other apicomplexan parasites. In this report, we describe the identification and analysis of 13 microsatellite loci from N. caninum DNA sequences deposited in public databases, which were evaluated with the use of 9 isolates grown in vitro. One microsatellite was monomorphic, and the remaining 12 loci exhibited 3 to 9 separate alleles. Multilocus analysis showed that each of the 9 isolates investigated here displayed a unique profile and revealed no association between the genetic similarity and host or geographic origin. The multilocus analysis approach described here might nevertheless provide the powerful tool needed to study the genetic complexity of N. caninum and the molecular epidemiology of neosporosis.     

An extensive study of the genetic diversity within seven French wine grape variety collections

The process of vegetative propagation used to multiply grapevine varieties produces, in most cases, clones genetically identical to the parental plant. Nevertheless, spontaneous somatic mutations can occur in the regenerative cells that give rise to the clones, leading to consider varieties as populations of clones that conform to a panel of phenotypic traits. Using two sets of nuclear microsatellite markers, the present work aimed at evaluating and comparing the intravarietal genetic diversity within seven wine grape varieties: Cabernet franc, Cabernet Sauvignon, Chenin blanc, Grolleau, Pinot noir, Riesling, Savagnin, comprising a total number of 344 accessions of certified clones and introductions preserved in French repositories. Ten accessions resulted in being either self-progeny, possible offspring of the expected variety or misclassified varieties. Out of the 334 remaining accessions, 83 displayed genotypes different from the varietal reference, i.e., the microsatellite profile shared by the larger number of accessions. They showed a similarity value ranging from 0.923 to 0.992, and thus were considered as polymorphic monozygotic clones. The fraction of polymorphic clones ranged from 2 to 75% depending on the variety and the set of markers, the widest clonal diversity being observed within the Savagnin. Among the 83 polymorphic clones, 29 had unique genotype making them distinguishable; others were classified in 21 groups sharing the same genotype. All microsatellite markers were not equally efficient to show diversity within clone collections and a standard set of five microsatellite markers (VMC3a9, VMC5g7, VVS2, VVMD30, and VVMD 32) relevant to reveal clonal polymorphism is proposed.     

Utilizing the genetic diversity within rice cultivars

Plant breeding of rice emphasizes improvement in yield, disease resistance, and milling quality. Numerous other traits (e.g., bran carotenoids) that historically have not been selected for could provide added value in expanding niche markets, as well as be useful tools for understanding the genetic control of these traits. Residual heterozygosity is present in many rice cultivars; therefore, it is possible to select for different alleles within an existing cultivar. By identifying and using cultivars with high levels of variability for a trait, we were able to develop separate lines from single cultivars that showed high and low levels of that trait. The rice cultivar RU9101001 and the warm- and cold-sprouting lines that were derived from it were used to demonstrate that residual heterozygosity was present within a cultivar and that the original heterozygosity was separated in the derived lines. Rice simple sequence repeat markers were heterozygous in the parent RU9101001 cultivar, but the cold-sprouting lines were homozygous for one set of alleles and the warm-sprouting lines were homozygous for the other set. Through detailed phenotypic screening, we developed lines that exhibited low and high levels of the following traits in the specified cultivars: cold-sprouting from RU9101001 and Bonnet 73, postharvest yellowing from Tominishiki, early tillering from Hei Jaio and Tominishiki, and bran carotenoid levels from Spring. If variability exists in a cultivar, then utilization of residual heterozygosity may provide a quicker and more efficient means to develop lines with special characteristics using cultivars that are already agronomically valuable or to develop near isogenic lines for genetic and biochemical investigations.     

Cryoconservation of South African plant genetic diversity

South Africa has a rich flora which exhibits among the highest species density in the world, distributed across nine biomes that support an impressive diversity of animal life. However, a variety of human actions, invasion by alien species, natural disturbances and climate change collectively impact negatively on the great diversity of both plant and animal species. In situ conservation has long been practised, primarily in nature reserves, complemented by ex situ conservation in national botanic gardens, but in vitro plant conservation is not common. In the context of animal biodiversity conservation, the Wildlife Biological Resource Centre of the National Zoological Gardens utilises cryobanking as one of its major focuses and is now poised to expand as the repository for the cryoconservation of plant germplasm, particularly for indigenous recalcitrant-seeded and poor-seeding species. However, there are particular problems associated with successful germplasm cryostorage of such tropical and subtropical plants. As we see the science and application of cryobiology and cryoconservation as cross-cutting and transdisciplinary, we have entrained formal networking among scientists offering a range of specialisations aimed at a deeper understanding of common problems and practical outcomes to facilitate both plant and animal biobanking. The endeavours are aimed at elucidating the basis of both successes and failures in our efforts to attain optimal outcomes. With focus on best practices, standard operating procedures, validation and risk management for cryopreserved and cold-stored plant and animal material, our ultimate aim is to facilitate restoration by the safe reintroduction of indigenous species.     

An analysis of genetic diversity across the maize genome using microsatellites

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.     

Pan-genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption

Thermococcales has a strong adaptability to extreme environments, which is of profound interest in explaining how complex life forms emerge on earth. However, their gene composition, thermal stability and evolution in hyperthermal environments are still little known. Here, we characterized the pan-genome architecture of 30 Thermococcales species to gain insight into their genetic properties, evolutionary patterns and specific metabolisms adapted to niches. We revealed an open pan-genome of Thermococcales comprising 6070 gene families that tend to increase with the availability of additional genomes. The genome contents of Thermococcales were flexible, with a series of genes experienced gene duplication, progressive divergence, or gene gain and loss events exhibiting distinct functional features. These archaea had concise types of heat shock proteins, such as HSP20, HSP60 and prefoldin, which were constrained by strong purifying selection that governed their conservative evolution. Furthermore, purifying selection forced genes involved in enzyme, motility, secretion system, defence system and chaperones to differ in functional constraints and their disparity in the rate of evolution may be related to adaptation to specific niche. These results deepened our understanding of genetic diversity and adaptation patterns of Thermococcales, and provided valuable research models for studying the metabolic traits of early life forms.     

Extremely low genetic diversity and extensive genetic admixture at the northern range margins of Bombax ceiba

Understanding the evolutionary processes in species at the margins of their range is of great significance, because marginal populations may harbor local adaptations and will initiate further expansion in response to changes in the environment. Here we examined genetic variation in two nuclear genes and one chloroplast intergenic spacer in 13 northern marginal populations and one geographically central population of Bombax ceiba, a tree distributed mainly in tropical regions. Our results revealed an extremely low level of genetic diversity in each population at the northern margin of its range and strong genetic differentiation between southern China and South Asia. Cultivated and natural populations showed no significant differences in genetic variability. Genetic admixture in a nuclear gene was detected in 10 of the 13 populations at the northern margin of their range. The founder effect, in which a small number of individuals colonize the northern margins of its range, may explain the extremely low genetic diversity. During the establishment of new populations, different source populations may mix and undergo further genetic drift and differentiation. This study indicates that patterns of genetic diversity in tropical species at the margin of their range may also be severely influenced by founder effects.     

Australia as a global sink for the genetic diversity of avian influenza A virus

Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.     

Polymorphic Alu insertions and genetic diversity among African populations

Thorough assessment of modern genetic diversity and interpopulation affinities within the African continent is essential for understanding the processes that have been at work during the course of worldwide human evolution. Regardless of whether autosomal, Y-chromosome, or mtDNA markers are used, allele- or haplotype-frequency data from African populations are necessary in setting the framework for the construction of global population phylogenies. In the present study we analyze genetic differentiation and population structure in a data set of nine African populations using 12 polymorphic Alu insertions (PAls). Furthermore, to place our findings within a global context, we also examined an equal number of non-African groups. Frequency data from 456 individuals presented for the first time in this work plus additional data obtained from the literature indicate an overall pattern of higher intrapopulation diversity in sub-Saharan populations than in northern Africa, a prominent differentiation between these two locations, an appreciably high degree of transcontinental admixture in Egypt, and significant discontinuity between Morocco and the Iberian peninsula. Moreover, the topologies of our phylogenetic analyses suggest that out of the studied sub-Saharan groups, the southern Bantu population of Sotho/ Tswana presents the highest level of antiquity, perhaps as a result of ancestral or acquired Khoisan genetic signals. Close affinities of eastern sub-Saharan populations with Egypt in the phylogenetic trees may indicate the existence of gene flow along the Nile River.     

The evolution of reproductive diversity in Afrobatrachia: A phylogenetic comparative analysis of an extensive radiation of African frogs

The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co‐evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (～400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift toward using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans.     

Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa

Genetic diversity in nine African buffalo (Syncerus caffer) populations throughout Africa was analysed with 14 microsatellites to study the effects of rinderpest epidemics and habitat fragmentation during the 20th century. A gradient of declining expected heterozygosity was observed among populations in Save Valley Conservancy (Zimbabwe), and northern and southern Kruger National Park (South Africa). This was explained by a high mortality in northern Kruger National Park during the rinderpest pandemic at the end of the 19th century followed by recolonization from neighbouring populations, resulting in intermediate heterozygosity levels in northern Kruger National Park. In other populations expected heterozygosity was very high, indicating that rinderpest and recent habitat fragmentation had a limited effect on genetic diversity. From expected heterozygosity, estimates of long-term effective population size were derived. Migration rates among populations in eastern and southern Africa were very high, as shown by a weak isolation by distance and significant correlation in allele frequencies between populations. However, there were indications that dry habitats could limit migration. Genetic distances within buffalo in central Africa were relatively large, supporting their status as distinct subspecies. Finally, it was observed that the higher polymorphic microsatellites were less sensitive at detecting isolation by distance and differences in Ne, which may be a result of the high mutation pressure at these loci.     

孑遗植物银杏群体遗传多样性的ISSR分析

采用ISSR分子标记技术,对江苏泰兴、美国纽约的栽培银杏(Ginkgo biloba)群体和中国3个可能为野生的银杏自然群体(浙江西天目山、贵州务川、湖北大洪山区)的遗传多样性水平和群体遗传结构进行了研究。用13个引物对5个群体共66个样品进行扩增,共得到88个清晰的扩增位点,其中多态性位点62个,多态位点百分率(PPB)为70．45％。POPGENE分析结果表明：与其他裸子植物相比,银杏具有丰富的遗传变异(He=0．2408;Ho=0．3599)。贵州务川群体的遗传多样性水平最高(PPB=56．82％,He=0．2089,Ho=0．3087),江苏泰兴栽培群体(PPB=34．09％,,Ho=0．1269,Ho=0．1858)和美国纽约的栽培群体(PPB=23．86％,,He=0．0884,Ho=0．1312)的遗传多样性水平较低。Nei′s遗传多样性分析和AMOVA分析表明,3个可能的自然群体间出现了一定程度的遗传分化(Gst=0．1476,Φst=14．26％)。群体间一定程度的遗传分化可能是人为选择压力和基因流障碍引起的。根据Nei′s遗传距离矩阵分别构建了群体间和个体间的遗传关系树状图。由UPGMA聚类分析可知,贵州务川群体与浙江西天目山群体优先聚类;美国纽约群体与湖北大洪山群体具有较近的亲缘关系,它们可能为同一野生群体的后裔。通过对银杏群体遗传结构的分析并结合群落学调查研究,结果表明：贵州务川银杏群体很可能为野生自然群体。基于银杏群体遗传学和生态学的研究结果,建议在自然银杏群体最适生境和遗传多样性最高的贵州务川建立银杏保护区。由于银杏群体间出现了一定程度的分化,建议3个自然群体间可进行植株和幼苗相互移栽,以提高群体间的基因交流,以最大限度地保护银杏的遗传多样性。     

Genome-wide genetic diversity,population structure and admixture analysis in African and Asian cattle breeds

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.     

SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato

Background

The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.

Results

With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties.

Conclusions

Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.     

Assembling global maps of cellular function through integrative analysis of physical and genetic networks

To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies 'modules' as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 and 30 min, depending on the size of the data set being analyzed.     

Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin

The geographical distribution of single nucleotide polymorphism (SNP) in the mitochondrial genome of the human malaria parasite Plasmodium falciparum was investigated. We identified 88 SNPs in 516 isolates from seven parasite populations in Africa, Southeast Asia and Oceania. Analysis of the SNPs postulated a sub-Saharan African origin and recovered a strong negative correlation between within-population SNP diversity and geographic distance from the putative African origin over Southeast Asia and Oceania. These results are consistent with those previously obtained for nuclear genome-encoded housekeeping genes, indicating that the pattern of inheritance does not substantially affect the geographical distribution of SNPs.     

不同国家水稻品种的遗传多样性分析

探讨世界不同国家水稻品种的遗传多样性,旨在为各国品种资源的有效利用提供理论依据。本研究利用63对引物对36份来源于不同国家的水稻品种进行遗传多样性分析。共检测到269个等位基因,每个位点的等位基因数(Na)平均为4.54个,有效等位基因数(Ne)平均为3.22,基因多样性指数(H)平均为0.64,Shannon’s信息指数(I)平均为1.21,引物RM206、RM257、RM410、RM235、RM266的等位基因数较多在7条以上。所处纬度相近的国家或地区的水稻品种之间的遗传距离较近,被聚为同一类群,而所处纬度较远的国家或地区的水稻品种被分到了不同类群。结果表明,水稻品种之间的遗传差异与纬度和地理距离有很大的关系。