The influence of genetic background on resistance to the cabbage aphid (Brevicoryne brassicae) in Kale (Brassica oleracea var. acephala)

Resistance to Brevicoryne brassicae has been identified in the progeny of two selected kale (B. oleracea var. acephala) plants, one from the F1 hybrid cultivar ‘Arsis RS’ and one from the landrace ‘Butzo’. These plants were crossed with susceptible B. oleracea morphotypes that have different periods to flowering. The type of susceptible plant line used had an effect on the resistance phenotypc of the progeny. Tested F2 populations derived from these crosses show that resistance is not under simple genetic control. This, in addition to variation in aphid numbers within accessions, suggests that separation of genetic components of control from environmental ‘noise’ for any accession may only be possible by the production of double haploid plant lines.     

基于激光雷达数据的物种分布模拟: 以美国加州内华达山脉南部区域食鱼貂分布模拟为例

生态位模型通过拟合物种分布与环境变量之间的关系提供物种空间分布预测, 在生物多样性研究中有广泛应用。激光雷达(LiDAR)是一种新兴的主动遥感技术, 已被大量应用于森林三维结构信息的提取, 但其在物种分布模拟的应用研究比较缺乏。本研究以美国加州内华达山脉南部地区的食鱼貂(Martes pennanti)的分布模拟为例, 探索LiDAR技术在物种分布模拟中的有效性。生态位模型采用5种传统多类分类器, 包括神经网络、广义线性模型、广义可加模型、最大熵模型和多元自适应回归样条模型, 并使用正样本-背景学习(presence and background learning, PBL)算法进行模型校正; 同时对这5种模型使用加权平均进行模型集成, 作为第6个模型。此外, 一类最大熵模型也被用于模拟该物种的空间分布。模型的连续输出和二值输出分别使用AUC (area under the receiver operating characteristic curve)以及基于正样本-背景数据的评价指标F_pb进行评价。结果表明, 仅考虑气候因子(温度和降水)时, 7个模型的AUC和F_pb平均值分别为0.779和1.077; 当考虑LiDAR变量(冠层容重、枝下高、叶面积指数、高程、坡度等)后, AUC和F_pb分别为0.800和1.106。该研究表明, LiDAR数据能够提高食鱼貂空间分布的预测精度, 在物种分布模拟方面存在一定的应用价值。     

Genomewide patterns of variation in genetic diversity are shared among populations,species and higher‐order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e. Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST, PBS, d_xy) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.     

Standardized experiments in mutant mice reveal behavioural similarity on 129S5 and C57BL/6J backgrounds

Behavioural analysis of mice carrying engineered mutations is widely used to identify roles of specific genes in components of the mammalian behavioural repertoire. The reproducibility and robustness of phenotypic measures has become a concern that undermines the use of mouse genetic models for translational studies. Contributing factors include low individual study power, non‐standardized behavioural testing, failure to address confounds and differences in genetic background of mutant mice. We have examined the importance of these factors using a statistically robust approach applied to behavioural data obtained from three mouse mutations on 129S5 and C57BL/6J backgrounds generated in a standardized battery of five behavioural assays. The largest confounding effect was sampling variation, which partially masked the genetic background effect. Our observations suggest that strong interaction of mutation with genetic background in mice in innate and learned behaviours is not necessarily to be expected. We found composite measures of innate and learned behaviour were similarly impacted by mutations across backgrounds. We determined that, for frequently used group sizes, a single retest of a significant result conforming to the commonly used P < 0.05 threshold results in a reproducibility of 60% between identical experiments. Reproducibility was reduced in the presence of strain differences. We also identified a P‐value threshold that maximized reproducibility of mutant phenotypes across strains. This study illustrates the value of standardized approaches for quantitative assessment of behavioural phenotypes and highlights approaches that may improve the translational value of mouse behavioural studies.     

Considerations Regarding the Use of Reference Area and Baseline Information in Ecological Risk Assessments

There has been debate in the recent literature as to whether a reference assessment should be included in ecological risk assessments (ERAs) of contaminated sites, and if so, how such an evaluation can be incorporated in a way that aids in decision making. It is our view that an assessment of reference conditions can be useful in the ERA process, for both prospective and retrospective ERAs, given adequate resources and acknowledgement and understanding of the limitations and uncertainties associated with this information. Suggestions and considerations for incorporating reference area information into an ecological risk assessment are discussed.     

rtTA toxicity limits the usefulness of the SP-C-rtTA transgenic mouse

The doxycycline (DOX)-inducible gene expression systems allow tight temporal and spatial control of transgene expression, invaluable in studies of organ development and disease pathogenesis. Transgenic mice using the human Surfactant Protein C promoter to drive the expression of the reverse tetracycline transactivator (SP-C-rtTA) enabled functional analysis of essential gene function during lung development. Here we report that DOX-fed SP-C-rtTA mice during the period in which Type II cells differentiate results in cellular toxicity that may have confounded the interpretation of previous reports using this line. These effects included impaired alveologenesis, loss/reduction in expression of surfactant-associated proteins, and death. Severity was dependent on genetic background: outbred mice or those on a CD1 background are highly susceptible, whereas the C57BL/6 background appeared resistant by morphological criteria. However, quantitative analysis reveled that DOX-fed, SP-C-rtTA C57BL/6 pups had reduced surfactant mRNA accumulation that could contribute to synthetic lethality when combined with other genetic alterations. We conclude that the combination of genetic backgrounds, length of DOX exposure and the presence of the SP-C-rtTA transgene contributed more than previously appreciated to the similarities seen in the phenotypes reported by investigators using the SP-C-rtTA, (tetO)₇-Cre. These studies demonstrate the importance of using appropriate SP-C-rtTA only controls in all experiments.     

A high efficient method of constructing recombinant Bombyx mori (silkworm) multiple nucleopolyhedrovirus based on zero‐background Tn7‐mediated transposition in Escherichia coli

A high efficient way for generation of recombinant Bombyx mori (silkworm) multiple nucleopolyhedrovirus by Tn7‐mediated transposition in Escherichia coli was performed. The new system consists of a conditional replication donor vector pRCDM and an attTn7 site blocked E. coli containing BmNPV‐Bacmid. The donor vector contains a replication origin derived from R6Kγ, which propagated only in host cells with pir gene expression decreased in the transposition background greatly. Compared with original vector derived from pUC, the transposition efficiency increased from 5.7 to 66% (≈10 fold) when using conditional replication vector pRCDM transposition into original BmDH10Bac. A further effort to decrease the transposition background was made by blocking the attTn7 site in host E. coli genome. The resulting attTn7 occupied BmDH10BacΔTn7 resulted in a significant increase from 5.7 to 23% (≈4 fold) in the efficacy of generate recombinant BmNPV Bacmid by transposition. Furthermore, the transposition of BmDH10BacΔTn7 with pRCDM resulted typically in 100% white colonies, and it indicated that a zero transposition background was accomplished. This high efficient and zero background transposition system provides a new simple and rapid method for construction of recombinant BmNPV used to express target genes or produce gene‐delivery virus particles in silkworm. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009