Meiotic parthenogenesis in a root-knot nematode results in rapid genomic homozygosity

Many isolates of the plant-parasitic nematode Meloidogyne hapla reproduce by facultative meiotic parthenogenesis. Sexual crosses can occur, but, in the absence of males, the diploid state appears to be restored by reuniting sister chromosomes of a single meiosis. We have crossed inbred strains of M. hapla that differ in DNA markers and produced hybrids and F(2) lines. Here we show that heterozygous M. hapla females, upon parthenogenetic reproduction, produce progeny that segregate 1:1 for the presence or absence of dominant DNA markers, as would be expected if sister chromosomes are rejoined, rather than the 3:1 ratio typical of a Mendelian cross. Codominant markers also segregate 1:1 and heterozygotes are present at low frequency (<3%). Segregation patterns and recombinant analysis indicate that a homozygous condition is prevalent for markers flanking recombination events, suggesting that recombination occurs preferentially as four-strand exchanges at similar locations between both pairs of non-sister chromatids. With this mechanism, meiotic parthenogenesis would be expected to result in rapid genomic homozygosity. This type of high negative crossover interference coupled with positive chromatid interference has not been observed in fungal or other animal systems in which it is possible to examine the sister products of a single meiosis and may indicate that meiotic recombination in this nematode has novel features.     

Functional genomic approaches using the nematode Caenorhabditis elegans as a model system

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.     

Genetic-physiological compatibility and karyotypes of stem nematode]

The paper presents literary and the authors own data. The potato stem eelworm Ditylenchus destructor has a set of chromosomes 2n=44-48 and does not cross with the close species D. dipsaci from onion, garlic, parsley and parsnip. Most stem eelworms of the collective species D. dipsaci have n=12 and cross with each other producing fertile progeny. Some forms of stem eelworms, e.g. those of broad beans, plantain, dandelion and falcaria are polyploid. Intraspecies and intrapopulation polymorphism according to the number of chromosomes was recorded. Some races do not cross, some cross but unilaterally, some races produce sterile, non-viable or little viable hybrids. The species D. dipsaci should be regarded not only as a complex of species but as a group of forms at different stages of intraspecies differentiation.     

Whole-genome comparison between Photorhabdus strains to identify genomic regions involved in the specificity of nematode interaction

The bacterium Photorhabdus establishes a highly specific association with Heterorhabditis, its nematode host. Photorhabdus strains associated with Heterorhabditis bacteriophora or Heterorhabditis megidis were compared using a Photorhabdus DNA microarray. We describe 31 regions belonging to the Photorhabdus flexible gene pool. Distribution analysis of regions among the Photorhabdus genus identified loci possibly involved in nematode specificity.     

Methodologic aspects of genomic fingerprinting in population studies]

Use of DNA fingerprinting in population studies is complicated by a number of methodical problems caused by the necessity to work with a large amount of experimental data and insufficient reproducibility of the results. In this work, possible approaches to overcome methodical difficulties faced by the authors during elaboration of the experimental technique are discussed.     

Importance of the matriline for genomic imprinting,brain development and behaviour

Mammalian brain development commences during foeto-placental development and is strongly influenced by the epigenetic regulation of imprinted genes. The foetal placenta exerts considerable influence over the functioning of the adult maternal hypothalamus, and this occurs at the same time as the foetus itself is developing a hypothalamus. Thus, the action and interaction of two genomes in one individual, the mother, has provided a template for co-adaptive functions across generations that are important for maternal care and resource transfer, while co-adaptively shaping the mothering capabilities of each subsequent generation. The neocortex is complex, enabling behavioural diversity and cultural learning such that human individuals are behaviourally unique. Retrotransposons may, in part, be epigenetic mediators of such brain diversity. Interestingly some imprinted genes are themselves retrotransposon-derived, and retrotransposon silencing by DNA methylation is thought to have contributed to the evolutionary origins of imprint control regions. The neocortex has evolved to be adaptable and sustain both short-term and long-term synaptic connections that underpin learning and memory. The adapted changes are not themselves inherited, but the predisposing mechanisms for such epigenetic changes are heritable. This provides each generation with the same ability to make new adaptations while constrained by a transgenerational knowledge-based predisposition to preserve others.     

Accuracy of genomic prediction within and across populations for nematode resistance and body weight traits in sheep

Genomic prediction utilizes single nucleotide polymorphism (SNP) chip data to predict animal genetic merit. It has the advantage of potentially capturing the effects of the majority of loci that contribute to genetic variation in a trait, even when the effects of the individual loci are very small. To implement genomic prediction, marker effects are estimated with a training set, including individuals with marker genotypes and trait phenotypes; subsequently, genomic estimated breeding values (GEBV) for any genotyped individual in the population can be calculated using the estimated marker effects. In this study, we aimed to: (i) evaluate the potential of genomic prediction to predict GEBV for nematode resistance traits and BW in sheep, within and across populations; (ii) evaluate the accuracy of these predictions through within-population cross-validation; and (iii) explore the impact of population structure on the accuracy of prediction. Four data sets comprising 752 lambs from a Scottish Blackface population, 2371 from a Sarda×Lacaune backcross population, 1000 from a Martinik Black-Belly×Romane backcross population and 64 from a British Texel population were used in this study. Traits available for the analysis were faecal egg count for Nematodirus and Strongyles and BW at different ages or as average effect, depending on the population. Moreover, immunoglobulin A was also available for the Scottish Blackface population. Results show that GEBV had moderate to good within-population predictive accuracy, whereas across-population predictions had accuracies close to zero. This can be explained by our finding that in most cases the accuracy estimates were mostly because of additive genetic relatedness between animals, rather than linkage disequilibrium between SNP and quantitative trait loci. Therefore, our results suggest that genomic prediction for nematode resistance and BW may be of value in closely related animals, but that with the current SNP chip genomic predictions are unlikely to work across breeds.     

Estimation of genomic variation between British populations of the potato cyst nematode Globodera pallida using RAPD-PCR

Random amplified polymorphic DNA (RAPD) has been used to investigate the interrelationships of 20 populations of Globodera pallida collected originally from field soils around the UK. RAPD analysis revealed a high level of relative genomic diversity within British G. pallida but there was no general correlation of genomic similarity with geographic distribution. Two populations of pathotype Pa1 were clearly divergent from the bulk of G. pallida and might represent a distinct introduction. Two other populations, from Scotland and Wales, were also dissimilar from each other and from the rest of the G. pallida populations.     

Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation

Determining what factors affect the structuring of genetic variation is key to deciphering the relative roles of different evolutionary processes in species differentiation. Such information is especially critical to understanding how the frequent shifts and fragmentation of species distributions during the Pleistocene translates into species differences, and why the effect of such rapid climate change on patterns of species diversity varies among taxa. Studies of mitochondrial DNA (mtDNA) have detected significant population structure in many species, including those directly impacted by the glacial cycles. Yet, understanding the ultimate consequence of such structure, as it relates to how species divergence occurs, requires demonstration that such patterns are also shared with genomic patterns of differentiation. Here we present analyses of amplified fragment length polymorphisms (AFLPs) in the montane grasshopper Melanoplus oregonensis to assess the evolutionary significance of past demographic events and associated drift-induced divergence as inferred from mtDNA. As an inhabitant of the sky islands of the northern Rocky Mountains, this species was subject to repeated and frequent shifts in species distribution in response to the many glacial cycles. Nevertheless, significant genetic structuring of M. oregonensis is evident at two different geographic and temporal scales: recent divergence associated with the recolonization of the montane meadows in individual sky islands, as well as older divergence associated with displacements into regional glacial refugia. The genomic analyses indicate that drift-induced divergence, despite the lack of long-standing geographic barriers, has significantly contributed to species divergence during the Pleistocene. Moreover, the finding that divergence associated with past demographic events involves the repartitioning of ancestral variation without significant reductions of genomic diversity has intriguing implications - namely, the further amplification of drift-induced divergence by selection.     

Ethanol-response genes and their regulation analyzed by a microarray and comparative genomic approach in the nematode Caenorhabditis elegans

The nematode shows responses to acute ethanol exposure that are similar to those observed in humans, mice, and Drosophila, namely hyperactivity followed by uncoordination and sedation. We used in this report the nematode Caenorhabditis elegans as a model system to identify and characterize the genes that are affected by ethanol exposure and to link those genes functionally into an ethanol-induced gene network. By analyzing the expression profiles of all C. elegans ORFs using microarrays, we identified 230 genes affected by ethanol. While the ethanol response of some of the identified genes was significant at early time points, that of the majority was at late time points, indicating that the genes in the latter case might represent the physiological consequence of the ethanol exposure. We further characterized the early response genes that may represent those involved directly in the ethanol response. These genes included many heat shock protein genes, indicating that high concentration of ethanol acts as a strong stress to the animal. Interestingly, we identified two non-heat-shock protein genes that were specifically responsive to ethanol. glr-2 was the only glutamate receptor gene to be induced by ethanol. T28C12.4, which encodes a protein with limited homology to human neuroligin, was also specific to ethanol stress. Finally, by analyzing the promoter regions of the early response genes, we identified a regulatory element, TCTGCGTCTCT, that was necessary for the expression of subsets of ethanol response genes.     

高通量测序技术在线虫多样性研究中的应用

土壤线虫多样性是土壤生态学研究的热点之一, 然而对土壤线虫群落组成及多样性的研究通常受到分类学和方法学的限制。当前, 分子生物学技术的快速发展丰富了我们对土壤线虫多样性的认识, 但也存在一定的局限性。本文综述了常用分子生物学技术如变性梯度凝胶电泳(denaturing gradient gel electrophoresis, DGGE)、末端限制性片段长度多态性分析(terminal restriction fragment length polymorphism, T-RFLP)、实时荧光定量PCR (quantitative real-time PCR, qPCR)和高通量测序(high-throughput sequencing, HTS)技术近年来在线虫多样性研究中的应用, 重点从土壤线虫DNA提取方法、引物和数据库的选择、高通量测序技术和形态学鉴定结果的比较等方面阐述了高通量测序技术在线虫多样性研究中的优势与不足, 并提出选择合适的线虫DNA提取方法结合特定引物和数据库进行注释分析, 仍是今后使用高通量测序技术开展线虫多样性研究的重点。当研究目标是土壤线虫多样性时, 优先推荐富集线虫悬液提取DNA的方法, 因此, 研究人员应根据具体目标选择最优组合开展实验研究。     

RAPD linkage map of the genomic region encompassing the root-knot nematode (Meloidogyne javanica) resistance locus in carrot

Inheritance studies have indicated that resistance to the root-knot nematode (Meloidogyne javanica) in carrot inbred line ’Brasilia-1252’ is controlled by the action of one or two (duplicated) dominant gene(s) located at a single genomic region (designated the Mj-1 locus). A systematic search for randomly amplified polymorphic DNA (RAPD) markers linked to Mj-1 was carried out using bulked segregant analysis (BSA). Altogether 1000 ten-mer primers were screened with 69.1% displaying scorable amplicons. A total of approximately 2400 RAPD bands were examined. Four reproducible markers (OP-C2₁₇₀₀, OP-Q6₅₀₀, OP-U12₇₀₀, and OP-AL15₅₀₀) were identified, in coupling-phase linkage, flanking the Mj-1 region. The genetic distances between RAPD markers and the Mj-1 locus, estimated using an F₂ progeny of 412 individuals from ’Brasilia 1252’×’B6274’, ranged from 0.8 to 5.7 cM . The two closest flanking markers (OP-Q6₅₀₀ and OP-AL15₅₀₀) encompassed a region of 2.7 cM . The frequency of these RAPD loci was evaluated in 121 accessions of a broad-based carrot germplasm collection. Only five entries (all resistant to M. javanica and genetically related to ’Brasilia 1252’) exhibited the simultaneous presence of all four markers. An advanced line derived from the same cross, susceptible to M. javanica but relatively resistant to another root-knot nematode species (M. incognita), did not share three of the closest markers. These results suggest that at least some genes controlling resistance to M. incognita and M. javanica in ’Brasilia 1252’ reside at distinct loci. The low number of markers suggests a reduced amount of genetic divergence between the parental lines at the region surrounding the target locus. Nevertheless, the low rate of recombination indicated these markers could be useful landmarks for positional cloning of the resistance gene(s). These RAPD markers could also be used to increase the Mj-1 frequency during recurrent selection cycles and in backcrossing programs to minimize ’linkage drag’ in elite lines employed for the development of resistant F₁ hybrids. Received: 22 June 1999 / Accepted: 6 July 1999     

New species of spiral nematode from the mountain tundra of Kamchatka]

A new species of nematodes, Rotylenchus alpinus sp. n., is described. The species was found in the rhizosphere of Vaccinum uliginosum and Arctous alpina from the mountain tundra of Kamchatka. It differs from the close species R. orientalis in having a higher place of entering of the oesophagal dorsal gland duct, well developed hind ovary and in having males. From R. goodeyi the species differs by a lower place of entering of the dorsal gland duct, smaller sizes of the body and gubernaculum.