Genetic Mapping and Genomic Selection Using Recombination Breakpoint Data

The correct models for quantitative trait locus mapping are the ones that simultaneously include all significant genetic effects. Such models are difficult to handle for high marker density. Improving statistical methods for high-dimensional data appears to have reached a plateau. Alternative approaches must be explored to break the bottleneck of genomic data analysis. The fact that all markers are located in a few chromosomes of the genome leads to linkage disequilibrium among markers. This suggests that dimension reduction can also be achieved through data manipulation. High-density markers are used to infer recombination breakpoints, which then facilitate construction of bins. The bins are treated as new synthetic markers. The number of bins is always a manageable number, on the order of a few thousand. Using the bin data of a recombinant inbred line population of rice, we demonstrated genetic mapping, using all bins in a simultaneous manner. To facilitate genomic selection, we developed a method to create user-defined (artificial) bins, in which breakpoints are allowed within bins. Using eight traits of rice, we showed that artificial bin data analysis often improves the predictability compared with natural bin data analysis. Of the eight traits, three showed high predictability, two had intermediate predictability, and two had low predictability. A binary trait with a known gene had predictability near perfect. Genetic mapping using bin data points to a new direction of genomic data analysis.     

ZmGA3ox2, a candidate gene for a major QTL,qPH3.1, for plant height in maize

Maize plant height is closely associated with biomass, lodging resistance and grain yield. Determining the genetic basis of plant height by characterizing and cloning plant height genes will guide the genetic improvement of crops. In this study, a quantitative trait locus (QTL) for plant height, qPH3.1, was identified on chromosome 3 using populations derived from a cross between Zong3 and its chromosome segment substitution line, SL15. The plant height of the two lines was obviously different, and application of exogenous gibberellin A₃ removed this difference. QTL mapping placed qPH3.1 within a 4.0 cM interval, explaining 32.3% of the phenotypic variance. Furthermore, eight homozygous segmental isolines (SILs) developed from two larger F₂ populations further narrowed down qPH3.1 to within a 12.6 kb interval. ZmGA3ox2, an ortholog of OsGA3ox2, which encodes a GA3 β‐hydroxylase, was positionally cloned. Association mapping identified two polymorphisms in ZmGA3ox2 that were significantly associated with plant height across two experiments. Quantitative RT‐PCR showed that SL15 had higher ZmGA3ox2 expression relative to Zong3. The resultant higher GA₁ accumulation led to longer internodes in SL15 because of increased cell lengths. Moreover, a large deletion in the coding region of ZmGA3ox2 is responsible for the dwarf mutant d1‐6016. The successfully isolated qPH3.1 enriches our knowledge on the genetic basis of plant height in maize, and provides an opportunity for improvement of plant architecture in maize breeding.     

兴安落叶松针叶解剖结构变化及其光合能力对气候变化的适应性

叶片易受环境因子影响,其形态解剖结构特征不但与叶片的生理功能密切相关,而且反映树木对环境变化的响应和适应。叶片结构的改变势必会改变树木的生理功能。同一树种长期生长在异质环境条件下,经过自然选择和适应,会在形态和生理特性等方面产生变异,形成特定的地理种群。另外,母体所经受的环境胁迫也会影响到其子代的生长、发育和生理等特征。因此,了解植物叶片形态结构对环境变化的响应与适应是探索植物对环境变化的响应适应机制的基础。兴安落叶松(Larix gmelinii Rupr.)是我国北方森林的优势树种,主要分布在我国东北地区,但日益加剧的气候变化可能会改变其现有的分布区。为了区分叶片对气候变化的可塑性和适应性,本研究采用同质园法比较测定了6个不同气候条件下的兴安落叶松种源的32年生树木的针叶解剖结构和光合生理相关因子,利用石蜡切片方法分析了针叶的解剖结构特征、光合能力（Pmax-a）、水分利用效率（WUE）之间的关系及其对气候变化的适应性。结果表明：表皮细胞厚度、叶肉细胞厚度、传输组织厚度、维管束厚度、内皮层厚度以及叶片总厚度均存在显著的种源间差异（P < 0.05）。叶肉细胞厚度与Pmax-a、气孔导度和WUE之间均存在显著的正相关关系（P < 0.05）。叶肉细胞厚度、表皮细胞厚度、叶片总厚度以及叶肉细胞厚度和表皮细胞厚度在叶片总厚度中所占比例均与种源地的干燥度指数（即年蒸发量与年降水量之比）呈正线性关系。这些结果说明：不同种源兴安落叶松针叶解剖结构因对种源原地气候条件的长期适应而产生显著的差异,从而引起其针叶光合作用、水分利用等生理功能发生相应的变化,从而有利于该树种在气候变化的情景下得以生存和繁衍。     

Conversion of L-Galactono-1,4-lactone to L-Ascorbate Is Regulated by the Photosynthetic Electron Transport Chain in Arabidopsis

In this study we focused on the effects of light irradiation and the addition of L-galactono-1,4-lactone (L-GalL) on the conversion of exogenous L-GalL to L-ascorbate (AsA) and the total AsA pool size in detached leaves of Arabidopsis plants and transgenic plants expressing the rat L-gulono-1,4-lactone oxidase gene. Increases in the total AsA level in L-GalL-treated leaves depended entirely on light irradiation. Treatment with an inhibitor of photosynthetic electron transport together with L-GalL reduced the increase in total AsA under light. Light, particularly the redox state of photosynthetic electron transport, appeared to play an important role in the regulation of the conversion of L-GalL to AsA in the mitochondria, reflecting the cellular level of AsA in plants.     

Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect communities

The assumption that traits and phylogenies can be used as proxies of species niche has faced criticisms. Evidence suggested that phylogenic relatedness is a weak proxy of trait similarity. Moreover, different processes can select different traits, giving opposing signals in null model analyses. To circumvent these criticisms, we separated traits of stream insects based on the concept of α and β niches, which should give clues about assembling pressures expected to act independently of each other. We investigated the congruence between the phylogenetic structure and trait structure of communities using all available traits and all possible combinations of traits (4095 combinations). To account for hierarchical assembling processes, we analyzed patterns on two spatial scales with three pools of genera. Beta niche traits selected a priori – i.e., traits related to environmental variation (e.g., respiration type) – were consistently clustered on the smaller scale, suggesting environmental filtering, while α niche traits – i.e., traits related to resource use (e.g., trophic position) – did not display the expected overdispersion, suggesting a weak role of competition. Using all traits together provided random patterns and the analysis of all possible combinations of traits provided scenarios ranging from strong clustering to overdispersion. Communities were phylogenetically overdispersed, a pattern previously interpreted as phylogenetic limiting similarity. However, our results likely reflect the co‐occurrence of ancient clades due to the stability of stream habitats along the evolutionary scale. We advise ecologists to avoid using combinations of all available traits but rather carefully traits based on the objective under consideration. Both trait and phylogenetic approaches should be kept in the ecologist toolbox, but phylogenetic distances should not be used as proxies of traits differences. Although the phylogenetic structure revealed processes operating at the evolutionary scale, only specific traits explained local processes operating in our communities.     

Lemna minor tolerance to metal‐working fluid residues: implications for rhizoremediation

For the first time in the literature, duckweed (Lemna minor) tolerance (alone or in combination with a consortium of bacteria) to spent metal‐working fluid (MWF) was assessed, together with its capacity to reduce the chemical oxygen demand (COD) of this residue. In a preliminary study, L. minor response to pre‐treated MWF residue (ptMWF) and vacuum‐distilled MWF water (MWFw) was tested. Plants were able to grow in both residues at different COD levels tested (up to 2300 mg·l^?1), showing few toxicity symptoms (mainly growth inhibition). Plant response to MWFw was more regular and dose responsive than when exposed to ptMWF. Moreover, COD reduction was less significant in ptMWF. Thus, based on these preliminary results, a second study was conducted using MWFw to test the effectiveness of inoculation with a bacterial consortium isolated from a membrane bioreactor fed with the same residue. After 5 days of exposure, COD in solutions containing inoculated plants was significantly lower than in non‐inoculated ones. Moreover, inoculation reduced β+γ‐tocopherol levels in MWFw‐exposed plants, suggesting pollutant imposed stress was reduced. We therefore conclude from that L. minor is highly tolerant to spent MWF residues and that this species can be very useful, together with the appropriate bacterial consortium, in reducing COD of this residue under local legislation limits and thus minimise its potential environmental impact. Interestingly, the lipophilic antioxidant tocopherol (especially the sum of β+γ isomers) proved to be an effective plant biomarker of pollution.