染色体加倍对忍冬生物学性状及其生态适应性的影响

忍冬（Lonicera japonica Thunb.）属忍冬科忍冬属，是一种重要的药用植物，其花蕾称为金银花（Flos Lonicerae），在我国已有1000多年的药用历史，具有清热解毒、凉散风热等功效。我们利用秋水仙素诱导二倍体“大毛花”品种茎尖选育出同源四倍体“九丰一号”品种，并在生产中发现花蕾产量显著提高，而药效成份含量是否发生变化了呢？四倍体忍冬表现出典型的器官巨大性，这些变化是否与其较强生态适应性之间存在联系呢？染色体加倍增强了忍冬的生态适应性，其生态修复功能如何呢？在本研究中，主要从以下几个方面进行了探讨：（1）染色体加倍对其叶片，茎、花蕾和花蕾产量及其药效成份等生物学性状的影响;（2）染色体加倍后植物对水分胁迫的响应;（3）染色体加倍后植物对热胁迫的响应;（4）除上述两个品种外，增加一个变异品种“红银花”，探讨3个忍冬品种对退化生态系统的修复功能。主要结果如下： 1. 通过测定根尖细胞染色体数目和使用流式细胞仪分析茎尖细胞DNA含量，表明四倍体忍冬（2n = 4x = 36）确实来自二倍体忍冬（2n = 2x = 18）的染色体加倍。四倍体忍冬气孔细胞大小显著大于二倍体，而气孔密度显著低于二倍体。四倍体忍冬没有光合“午休”，而二倍体存在明显的光合“午休”，这可能与其存在抗高温的叶片解剖结构特性有关。四倍体忍冬叶片较二倍体变大、变厚、变浓绿（较高叶绿素含量）。与二倍体相比，四倍体忍冬单位叶面积重量显著增高，表明其具有较强的生态适应性。四倍体忍冬单个花蕾的鲜重和干重均显著大于二倍体。连续3年的花蕾产量调查表明，四倍体显著高于二倍体。染色体加倍使其茎干粗壮、节间变短、新梢上着生花蕾数目增多及单个花蕾变大，这是其花蕾高产的生物学基础。对金银花的药效成份而言，染色体加倍不影响绿原酸的含量，但增加了木犀草苷的含量。结果表明，染色体加倍能增加金银花的产量和药效成份的含量，建议四倍体忍冬在药材生产中推广应用。 2. 水分胁迫显著降低二倍体和四倍体忍冬叶片的净光合速率、气孔导度和蒸腾速率。水分胁迫也降低电子传递速率、光系统II实际量子产量和光化学猝灭，而增加非光化学猝灭、总可溶性糖、脯氨酸和丙二醛的含量。四倍体忍冬对水分胁迫的响应表现为其叶片水势、气体交换、叶绿素荧光和有关代谢物含量的变化程度低于二倍体，并且复水后其恢复能力快于二倍体，表明染色体加倍增强了忍冬的抗旱能力。分析其主要原因，可能是由于四倍体植株总叶面积减少、单位叶面积重量增加、叶片表皮细胞和栅栏组织增大以及叶片表皮毛较浓密等形态解剖结构特性有关。结果表明，染色体加倍能增加忍冬植物的抗旱能力，而使其具有较强的生态适应性。 3. 二倍体和四倍体忍冬受48 ºC热胁迫处理6 h和恢复10 h，以及离体叶片45 ºC，50 ºC，55 ºC 水浴热胁迫3 min，应用叶绿素荧光成像系统研究了它们对热胁迫的响应。热胁迫显著降低了两个品种叶片的最大光化学效率、电子传递速率、光系统II实际量子产量和光化学猝灭，降低了四倍体的非光化学猝灭，而增加了二倍体的非光化学猝灭。热胁迫增加了两个品种叶片的总可溶性糖、脯氨酸和丙二醛的含量。四倍体受热胁迫的叶绿素荧光参数和有关代谢物的响应程度低于二倍体，以及其恢复程度快于二倍体，表明染色体加倍提高了抗热性。此外，叶绿素荧光成像的异质性也表明，四倍体的抗热能力大于二倍体。进一步的叶片解剖结构分析表明，四倍体叶片的表皮细胞变大、栅栏组织增厚、表皮毛较浓密等特点，是其抗热性强的主要原因。 4.根据以上的研究结果，通过四倍体忍冬生态修复功能的野外试验证明染色体加倍后其生态适应性变化。在本研究中，针对北京市门头沟区大面积不同类型的废弃地急需恢复植被和景观的问题，在恢复生态学理念的指导下，综合运用集成技术，将3个忍冬品种植物用于这些退化生态系统的恢复。在王平镇的公路下边坡（以碎石和矿渣为主）、煤矿、石灰窑和采石场4种类型废弃地建立生态修复的试验示范区。结果表明，在4个废弃地类型上引进的3个金银花品种，具有使示范区快速复绿、当年成景和群落快速形成的潜力，并具有对不同退化迹地的适应能力和恢复效果，其中四倍体忍冬效果更好些，这主要与其形态解剖结构和较强的生态适应性有关。

Epithelial mesenchymal transition traits in human breast cancer cell lines parallel the CD44HI/CD24lO/-stem cell phenotype in human breast cancer

We review here the recently emerging relationship between epithelial-mesenchymal transition (EMT) and breast cancer stem cells (BCSC), and provide analyses of published data on human breast cancer cell lines, supporting their utility as a model for the EMT/BCSC state. Genome-wide transcriptional profiling of these cell lines has confirmed the existence of a subgroup with mesenchymal tendencies and enhanced invasive properties ('Basal B'/Mesenchymal), distinct from subgroups with either predominantly luminal ('Luminal') or mixed basal/luminal ('Basal A') features (Neve et al. Cancer Cell, 2006). A literature-derived EMT gene signature has shown specific enrichment within the Basal B subgroup of cell lines, consistent with their over-expression of various EMT transcriptional drivers. Basal B cell lines are found to resemble BCSC, being CD44highCD24low. Moreover, gene products that distinguish Basal B from Basal A and Luminal cell lines (Basal B Discriminators) showed close concordance with those that define BCSC isolated from clinical material, as reported by Shipitsin et al. (Cancer Cell, 2007). CD24 mRNA levels varied across Basal B cell lines, correlating with other Basal B Discriminators. Many gene products correlating with CD24 status in Basal B cell lines were also differentially expressed in isolated BCSC. These findings confirm and extend the importance of the cellular product of the EMT with Basal B cell lines, and illustrate the value of analysing these cell lines for new leads that may improve breast cancer outcomes. Gene products specific to Basal B cell lines may serve as tools for the detection, quantification, and analysis of BCSC/EMT attributes.

Coordination and plasticity in leaf anatomical traits of invasive and native vine species

Premise of the study: Plant invasiveness can be promoted by higher values of adaptive traits (e.g., photosynthetic capacity, biomass accumulation), greater plasticity and coordination of these traits, and by higher and positive relative influence of these functionalities on fitness, such as increasing reproductive output. However, the dataset for this premise rarely include linkages between epidermal-stomatal traits, leaf internal anatomy, and physiological performance. Methods: Three ecological pairs of invasive vs non-invasive (native) woody vine species of South-East Queensland, Australia were investigated for trait differences in leaf morphology and anatomy under varying light intensity. The linkages of these traits with physiological performance (e.g. water use efficiency, photosynthesis, and leaf construction cost) and plant adaptive traits of specific leaf area, biomass, and relative growth rates were also explored. Key results: Mean leaf anatomical trait differed significantly between the two groups, except for stomatal size. Plasticity of traits, and to a very limited extent, their phenotypic integration were higher in the invasive relative to the native species. ANOVA, ordination, and analysis of similarity suggest that for leaf morphology and anatomy, the three functional strategies contribute to the differences between the two groups in the order phenotypic plasticity > trait means > phenotypic integration. Conclusions: The linkages demonstrated in the study between stomatal complex/gross anatomy and physiology are scarce in the ecological literature of plant invasiveness, but the findings suggest that leaf anatomical traits need to be considered routinely as part of weed species assessment and in the worldwide leaf economic spectrum.

Genetics of rheumatoid arthritis contributes to biology and drug discovery

A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA)1. Here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating ~10 million single-nucleotide polymorphisms. We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2, 3, 4). We devised an in silico pipeline using established bioinformatics methods based on functional annotation5, cis-acting expression quantitative trait loci6 and pathway analyses7, 8, 9—as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes—to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Background: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

Using morphological traits to identify persistent lucernes for dryland agriculture in NSW, Australia

This paper reports on several studies conducted to better understand the variability between lucerne cultivars and lines, and use this to predict persistence in dryland grazing pastures in eastern Australia. Morphological traits of 20 cultivars/lines were measured in irrigated and dryland spaced plant experiments. Studies were also conducted to describe variation among lucernes in their utilisation of starch and responses to water deficit, pests and diseases. Multiple regression analyses were used to develop simple models where the measured traits could be used to predict persistence of lucerne lines in dryland evaluation experiments. Although there was significant variation among cultivars/lines in most measured traits, no single trait reliably predicted persistence of cultivars/lines in dryland evaluation experiments. However, variation in persistence at both sites could be explained by models developed by multiple regression using differences in the mean lengths of the longest stems at 10% flower in summer and winter. Persistent lucernes were those that had relatively long stems in summer and short stems in winter. Water use efficiencies, starch utilisation patterns and resistances to pests and diseases of different lucernes provided some improvement to this simple model, but these improvements were not consistent.

The role of root architectural traits in adaptation of wheat to water-limited environments

Better understanding of root system structure and function is critical to crop improvement in water-limited environments. The aims of this study were to examine root system characteristics of two wheat genotypes contrasting in tolerance to water limitation and to assess the functional implications on adaptation to water-limited environments of any differences found. The drought tolerant barley variety, Mackay, was also included to allow inter-species comparison. Single plants were grown in large, soil-filled root-observation chambers. Root growth was monitored by digital imaging and water extraction was measured. Root architecture differed markedly among the genotypes. The drought-tolerant wheat (cv. SeriM82) had a compact root system, while roots of barley cv. Mackay occupied the largest soil volume. Relative to the standard wheat variety (Hartog), SeriM82 had a more uniform rooting pattern and greater root length at depth. Despite the more compact root architecture of SeriM82, total water extracted did not differ between wheat genotypes. To quantify the value of these adaptive traits, a simulation analysis was conducted with the cropping system model APSIM, for a wide range of environments in southern Queensland, Australia. The analysis indicated a mean relative yield benefit of 14.5% in water-deficit seasons. Each additional millimetre of water extracted during grain filling generated an extra 55 kg ha-1 of grain yield. The functional implications of root traits on temporal patterns and total amount of water capture, and their importance in crop adaptation to specific water-limited environments, are discussed.

Detection and use of QTL for complex traits in multiple environments.

QTL mapping methods for complex traits are challenged by new developments in marker technology, phenotyping platforms, and breeding methods. In meeting these challenges, QTL mapping approaches will need to also acknowledge the central roles of QTL by environment interactions (QEI) and QTL by trait interactions in the expression of complex traits like yield. This paper presents an overview of mixed model QTL methodology that is suitable for many types of populations and that allows predictive modeling of QEI, both for environmental and developmental gradients. Attention is also given to multi-trait QTL models which are essential to interpret the genetic basis of trait correlations. Biophysical (crop growth) model simulations are proposed as a complement to statistical QTL mapping for the interpretation of the nature of QEI and to investigate better methods for the dissection of complex traits into component traits and their genetic controls.

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10−8). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

A review of the biology, ecology, distribution and control of Mozambique tilapia, Oreochromis mossambicus (Peters 1852) (Pisces: Cichlidae) with particular emphasis on invasive Australian populations

Oreochromis mossambicus (Peters 1852) are native to the eastward flowing rivers of central and southern Africa but from the early 1930s they have been widely distributed around the world for aquaculture and for biological control of weeds and insects. While O. mossambicus are now not commonly used as an aquaculture species, the biological traits that made them a popular culture species including tolerance to wide ranging ecological conditions, generalist dietary requirements and rapid reproduction with maternal care have also made them a 'model' invader. Self-sustaining populations now exist in almost every region to which they have been imported. In Australia, since their introduction in the 1970s, O. mossambicus have become established in catchments along the east and west coasts and have the potential to colonise other adjacent drainages. It is thought that intentional translocations are likely to be the most significant factor in their spread in Australia. The ecological and physical tolerances and preferences, reproductive behaviour, hybridization and the high degree of plasticity in the life history traits of O. mossambicus are reviewed. Impacts of O. mossambicus on natural ecosystems including competitive displacement of native species, habitat alteration, predation and as a vector in the spread of diseases are discussed. Potential methods for eradicating or controlling invasive populations of O. mossambicus including physical removal, piscicides, screens, environmental management and genetic technologies are outlined.

Phenotyping novel stay-green traits to capture genetic variation in senescence dynamics

Stay-green plants retain green leaves longer after anthesis and can have improved yield, particularly under water limitation. As senescence is a dynamic process, genotypes with different senescence patterns may exhibit similar final normalised difference vegetative index (NDVI). By monitoring NDVI from as early as awn emergence to maturity, we demonstrate that analysing senescence dynamics improves insight into genotypic stay-green variation. A senescence evaluation tool was developed to fit a logistic function to NDVI data and used to analyse data from three environments for a wheat (Triticum aestivum L.) population whose lines contrast for stay-green. Key stay-green traits were estimated including, maximum NDVI, senescence rate and a trait integrating NDVI variation after anthesis, as well as the timing from anthesis to onset, midpoint and conclusion of senescence. The integrative trait and the timing to onset and mid-senescence exhibited high positive correlations with yield and a high heritability in the three studied environments. Senescence rate was correlated with yield in some environments, whereas maximum NDVI was associated with yield in a drought-stressed environment. Where resources preclude frequent measurements, we found that NDVI measurements may be restricted to the period of rapid senescence, but caution is required when dealing with lines of different phenology. In contrast, regular monitoring during the whole period after flowering allows the estimation of senescence dynamics traits that may be reliably compared across genotypes and environments. We anticipate that selection for stay-green traits will enhance genetic progress towards high-yielding, stay-green germplasm.

Modelling the effect of plant water use traits on yield and stay-green expression in sorghum

Post-rainy sorghum (Sorghum bicolor (L.) Moench) production underpins the livelihood of millions in the semiarid tropics, where the crop is affected by drought. Drought scenarios have been classified and quantified using crop simulation. In this report, variation in traits that hypothetically contribute to drought adaptation (plant growth dynamics, canopy and root water conducting capacity, drought stress responses) were virtually introgressed into the most common post-rainy sorghum genotype, and the influence of these traits on plant growth, development, and grain and stover yield were simulated across different scenarios. Limited transpiration rates under high vapour pressure deficit had the highest positive effect on production, especially combined with enhanced water extraction capacity at the root level. Variability in leaf development (smaller canopy size, later plant vigour or increased leaf appearance rate) also increased grain yield under severe drought, although it caused a stover yield trade-off under milder stress. Although the leaf development response to soil drying varied, this trait had only a modest benefit on crop production across all stress scenarios. Closer dissection of the model outputs showed that under water limitation, grain yield was largely determined by the amount of water availability after anthesis, and this relationship became closer with stress severity. All traits investigated increased water availability after anthesis and caused a delay in leaf senescence and led to a ‘stay-green’ phenotype. In conclusion, we showed that breeding success remained highly probabilistic; maximum resilience and economic benefits depended on drought frequency. Maximum potential could be explored by specific combinations of traits.

Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.

Germination Biology and Occurrence of Polyembryony in Two Forms of Cats Claw Creeper Vine, Dolichandra unguis-cati (Bignoniaceae): Implications for Its Invasiveness and Management

Cat’s claw creeper vine, Dolichandra unguis-cati (L.) Lohmann (syn. Macfadyena unguis-cati (L.) Gentry), is a major environmental weed in Australia. Two forms of the weed with distinctive leaf morphology and reproductive traits, including varying fruit size, occur in Queensland, Australia. The long pod form occurs in a few localities in Queensland, while the short pod form is widely distributed in Queensland and northern part of New South Wales. This investigation aimed to evaluate germination behavior and occurrence of polyembryony (production of multiple seedlings from a single seed) in the two forms of the weed. Seeds were germinated in growth chambers set to 10/20°C, 15/25°C, 20/30°C, 30/45°C and 25°C, representing ambient temperature conditions of the region. Germination and polyembryony were monitored over a period of 12 weeks. For all the treatments in this study, seeds from short pod plants exhibited significantly higher germination rates and higher occurrence of polyembryony than those from long pod plants. Seeds from long pod plants did not germinate at the lowest temperature of 10/20°C; in contrast, those of the short pod form germinated under this condition, albeit at a lower rate (reaching a maximum 45% germination at week 12). Results from this study could explain why the short pod form of D. unguis-cati is the more widely distributed plants in Australia, while the long pod is confined to a few localities. The results have implication in predicting future range of both forms of the invasive D. unguis-cati, as well as inform management decisions for control of the weed.