QTL‐seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker‐assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time‐consuming and labor‐intensive. Here we report the rapid identification of plant QTLs by whole‐genome resequencing of DNAs from two populations each composed of 20–50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL‐seq as applied to plant species. We applied QTL‐seq to rice recombinant inbred lines and F₂ populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL‐seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.     

基于功能性状的常绿阔叶植物防火性能评价

植物功能性状不仅便于评价植物的防火性能,也有利于筛选防火植物。本研究以宁波地区的29个常绿木本植物为对象,在测定植物比叶面积、叶干物质含量、叶片含水量、枝条干物质含量和树皮厚度5个功能性状,以及鲜叶的7个防火性能指标的基础上,通过因子分析将防火性能指标划分为抗燃性f_a(包含抗火性因子f₁和燃烧速度因子f₂2个公因子)与燃烧性f_b 2个防火因子,然后利用Pearson相关和偏相关建立了5个功能性状与各个防火因子的相关性,并对29物种的防火性能进行评价。结果表明：1)比叶面积和树皮厚度与抗火性因子f₁,枝条干物质含量、树皮厚度和当年生叶片含水量与燃烧速度因子f₂,比叶面积与抗燃性因子f_a,叶片干物质含量、比叶面积和当年生叶片含水量与燃烧性因子f_b间存在显著的相关关系;2)偏相关简化植物防火性状后,比叶面积和叶干物质含量分别对抗燃性因子f_a与燃烧性因子f_b的指示性最好;3)分别基于功能性状和燃烧试验的物种抗燃性排序相似度为0.80。本研究证明,基于简易观测的植物功能性状可较好地反映树种的抗火性和燃烧性,可作为植物防火性能有效的评价方法。     

啮齿动物对不同大小和种皮特征种子的取食和搬运

在宁夏六盘山区的辽东栎灌丛,以不同大小的辽东栎种子、野李和华山松种子为材料,研究了种子大小和种皮特征对啮齿动物取食和搬运行为的影响.结果表明:辽东栎小种子和华山松种子的就地取食率均显著高于辽东栎大种子和野李种子;具有厚而坚硬种皮(内果皮)的野李种子被啮齿动物搬运后的取食率和贮藏率均最高.辽东栎大种子被啮齿动物搬运后取食的距离最大(3.10 m),被搬运后贮藏的距离(6.48 m)显著大于其他类型种子.除野李种子外,其他3种类型种子的单个种子取食点都在80％以上,所有种子的单个种子贮藏点都在90％以上,含2个以上种子的取食点和贮藏点较少.较高比例的华山松种子在灌丛基部和洞穴以外的其他环境被取食,其他3种类型种子被啮齿动物搬运后主要集中在灌丛基部和洞穴中取食;种皮(内果皮)厚而坚硬的种子以土壤埋藏方式贮藏的比例偏高.     

Testing of divergent patterns of butterfly niche breadth in a peninsula

The butterfly fauna on the Korean peninsula are comprised of both the Palearctic and Oriental species. We hypothesized that the Oriental species (immigrated across the sea) tend to have a wider niche breadth compared with the Palearctic species (immigrated from the continent) since the former migrates long distances across the sea and has to adapt to new environments. We tested this hypothesis using Korean butterfly data on distribution, habitat, food and life history traits. The distribution and ecological traits such as habitat breadth, overwintering stage, and voltinism of the Oriental species were found to be significantly different from the Palearctic species. However, the diet breadth and food plant type were not different. These results partly confirm the peninsula niche breadth hypothesis, which predicted that Oriental species have a broader niche breadth than Palearctic species.     

Pollen size strongly correlates with stigma depth among Pedicularis species

Darwin proposed that pollen size should be positively correlated with stigma depth rather than style length among species given that pollen tubes first enter the stigma autotrophically, then grow through the style heterotrophically. However, studies often show a positive relationship between pollen size and style length.Five floral traits were observed to be correlated among42 bumblebee-pollinated Pedicularis species(Orobanchaceae) in which stigmas are distinct from styles. The phylogenetic independent contrast analysis revealed that pollen grain volume was more strongly correlated with stigma depth than with style length, consistent with Darwin's functional hypothesis between pollen size and stigma depth.     

Balancing competition for resources with multiple pest regulation in diversified agroecosystems: a process‐based approach to reconcile diversification and productivity

Agroecosystem plant diversification can enhance pest biological regulation and is a promising alternative to pesticide application. However, the costs of competition for resources between plants may exceed the benefits gained by pest regulation. To disentangle the interactions between pest regulation and competition, we developed a generic process‐based approach that accounts for the effects of an associated plant and leaf and root pests on biomass production. We considered three crop–plant associations that differ in competition profiles, and we simulated biomass production under wide ranges of both pest regulation rates and resources’ availability. We analyzed outputs to quantify the pest regulation service level that would be required to attain monoculture yield and other production goals. Results showed that pest regulation requirements were highly dependent on the profile of resource interception of the associated plant and on resources’ availability. Pest regulation and the magnitude of competition between plants interacted in determining the balance between nitrogen and radiation uptake by the crop. Our findings suggest that productivity of diversified agroecosystems relative to monoculture should be optimized by assembling plants whose characteristics balance crops’ resource acquisition. The theoretical insights from our study draw generic rules for vegetation assemblage to optimize trade‐offs between pest regulation and production. Our findings and approach may have implications in understanding, theorizing and implementing agroecosystem diversification. By its generic and adaptable structure, our approach should be useful for studying the effects of diversification in many agroecosystems.     

Linking leaf veins to growth and mortality rates: an example from a subtropical tree community

A fundamental goal in ecology is to link variation in species function to performance, but functional trait–performance investigations have had mixed success. This indicates that less commonly measured functional traits may more clearly elucidate trait–performance relationships. Despite the potential importance of leaf vein traits, which are expected to be related to resource delivery rates and photosynthetic capacity, there are few studies, which examine associations between these traits and demographic performance in communities. Here, we examined the associations between species traits including leaf venation traits and demographic rates (Relative Growth Rate, RGR and mortality) as well as the spatial distributions of traits along soil environment for 54 co‐occurring species in a subtropical forest. Size‐related changes in demographic rates were estimated using a hierarchical Bayesian approach. Next, Kendall's rank correlations were quantified between traits and estimated demographic rates at a given size and between traits and species‐average soil environment. Species with denser venation, smaller areoles, less succulent, or thinner leaves showed higher RGR for a wide range of size classes. Species with leaves of denser veins, larger area, cheaper construction costs or thinner, or low‐density wood were associated with high mortality rates only in small size classes. Lastly, contrary to our expectations, acquisitive traits were not related to resource‐rich edaphic conditions. This study shows that leaf vein traits are weakly, but significantly related to tree demographic performance together with other species traits. Because leaf traits associated with an acquisitive strategy such as denser venation, less succulence, and thinner leaves showed higher growth rate, but similar leaf traits were not associated with mortality, different pathways may shape species growth and survival. This study suggests that we are still not measuring some of key traits related to resource‐use strategies, which dictate the demography and distributions of species.     

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.