Quantitative traits in plants: beyond the QTL

Phenotypic variation for quantitative traits results from segregation at multiple quantitative trait loci (QTL), the effects of which are modified by the internal and external environments. Because of their favorable genetic attributes (e.g. short generation time, large families and tolerance to inbreeding), plants are often used to test new concepts in quantitative trait analysis. Thus far, the molecular basis underlying allelic variation at QTL is similar to the identified variation for simple mendelian loci; namely, alterations in gene expression or protein function. Further comprehensive dissection of complex phenotypes will depend on our ability to link genetic components of the QTL variation to genomic databases.     

Genetic architecture of complex traits in plants

Genetic architecture refers to the numbers and genome locations of genes that affect a trait, the magnitude of their effects, and the relative contributions of additive, dominant, and epistatic gene effects. Quantitative trait locus (QTL) mapping techniques are commonly used to investigate genetic architectures, but the scope of inferences drawn from QTL studies are often restricted by the limitations of the experimental designs. Recent advances in experimental and statistical procedures, including the simultaneous analysis of QTL that segregate in diverse germplasm, should improve genetic architecture studies. High-resolution QTL mapping methods are being developed that may define the specific DNA sequence variants underlying QTL. Studies of genetic architecture, combined with improved knowledge of the structure of plant populations, will impact our understanding of plant evolution and the design of crop improvement strategies.     

Association genetics of complex traits in plants

Association mapping is rapidly becoming the main method for dissecting the genetic architecture of complex traits in plants. Currently most association mapping studies in plants are preformed using sets of genes selected to be putative candidates for the trait of interest, but rapid developments in genomics will allow for genome-wide mapping in virtually any plant species in the near future. As the costs for genotyping are decreasing, the focus has shifted towards phenotyping. In plants, clonal replication and/or inbred lines allows for replicated phenotyping under many different environmental conditions. Reduced sequencing costs will increase the number of studies that use RNA sequencing data to perform expression quantitative trait locus (eQTL) mapping, which will increase our knowledge of how gene expression variation contributes to phenotypic variation. Current population sizes used in association mapping studies are modest in size and need to be greatly increased if mutations explaining less than a few per cent of the phenotypic variation are to be detected. Association mapping has started to yield insights into the genetic architecture of complex traits in plants, and future studies with greater genome coverage will help to elucidate how plants have managed to adapt to a wide variety of environmental conditions.     

Inheritance of dermatoglyphic traits in twins: univariate and bivariate variance decomposition analysis

Dermatoglyphic traits in a sample of twins were analyzed to estimate the resemblance between MZ and DZ twins and to evaluate the mode of inheritance by using the maximum likelihood-based Variance decomposition analysis. The additive genetic variance component was significant in both sexes for four traits--PII, AB_RC, RC_HB, and ATD_L. AB RC and RC_HB had significant sex differences in means, whereas PII and ATD_L did not. The results of the Bivariate Variance decomposition analysis revealed that PII and RC_HB have a significant correlation in both genetic and residual components. Significant correlation in the additive genetic variance between AB_RC and ATD_L was observed. The same analysis only for the females sub-sample in the three traits RBL, RBR and AB_DIS shows that the additive genetic RBR component was significant and the AB_DIS sibling component was not significant while others cannot be constrained to zero. The additive variance for AB DIS sibling component was not significant. The three components additive, sibling and residual were significantly correlated between each pair of traits revealed by the Bivariate Variance decomposition analysis.     

Bimodality of stable and plastic traits in plants

Key message

We discovered an unexpected mode of bimodal distribution of stable and plastic traits, which was consistent for homologous traits of 32 varieties of seven species both in well-irrigated fields and dry conditions.

Abstract

We challenged archived genetic mapping data for 36 fruit, seed, flower and yield traits in tomato and found an unexpected bimodal distribution in one measure of trait variability, the mean coefficient of variation, with some traits being consistently more variable than others. To determine the degree of conservation of this distribution among higher plants, we compared 18 homologous phenotypes, including yield and seed production, across different crop species grown in a common ‘crop garden’ experiment. The set included 32 varieties of tomato, eggplant, pepper, melon, watermelon, sunflower and maize. Estimates of canalization were obtained using a ‘canalization replication’ experimental design that generated multiple estimates of the coefficient of variation of traits, as well as their reaction norms in optimal and water-stressed field plots. A common pattern of bimodal distribution of stable and plastic traits was observed for all the varieties and for a wild weed (Solanum nigrum). We propose that canalization profiles of traits in a variety of taxa were ancestrally selected to maximize adaptation and reproductive success.

     

Inheritance of reproductive phenology traits and related QTL identification in apricot

Reproductive phenological traits of great agronomical interest in apricot species, including flowering date, ripening date and fruit development period, were studied during 3 years in two F₁ progenies derived from the crosses ‘Bergeron’ × ‘Currot’ (B × C) and ‘Goldrich’ × ‘Currot’ (G × C). Results showed great variability and segregation in each population, confirming the polygenic nature and quantitative inheritance of all the studied traits. Genetic linkage maps were constructed combining SSR and SNP markers, using 87 markers in the ‘B × C’ population and 89 markers in ‘G × C’. The genetic linkage maps in both progenies show the eight linkage groups (LGs) of apricot, covering a distance of 394.9 cM in ‘Bergeron’ and of 414.3 cM in ‘Currot’. The ‘Goldrich’ and ‘Currot’ maps were of 353.5 and 422.3 cM, respectively. The average distance obtained between markers was thus 7.59 cM in ‘Bergeron’ and 7.53 cM in ‘Currot’, whereas the ‘Goldrich’ and ‘Currot’ averages were 5.6 and 7.5 cM, respectively. According to the polygenic nature of the studied phenology traits, QTLs linked to flowering date, ripening date and the fruit development period were identified during the 3 years of the study in all LGs except for LG 8. Among the QTLs identified, major QTLs for flowering and ripening date and the fruit development period were identified in LG 4, especially important in the ‘G × C’ population.     

Constraints on leaf structural traits in wetland plants

A plant species' ecology is associated with leaf economics, characterized, e.g., by photosynthetic rate, construction costs, and leaf life span. Specific leaf area (SLA, leaf area per leaf dry mass) is often considered to be a key trait in this respect, explaining interspecific variation in leaf economics. To understand factors constraining the specific leaf area, we investigated size-related biomechanical constraints of the traits that determine the SLA-leaf thickness, leaf dry matter content and leaf density-and the constraints these traits exert on each other among 33 herbaceous wetland species of northern Ontario with a wide variety of leaf forms, ranging from wide laminar leaves to long, narrow, and relatively thick columnar leaves. Data from garden experiments were compared with field data. The results agree with biomechanical predictions that lamina thickness and leaf dry matter content are positively and leaf density (fresh mass per volume) negatively associated with leaf length. The traits also constrain each other, but these intertrait relationships are confounded by interspecific variation in leaf length. We conclude that for a full understanding of the adaptive significance of leaf structural design, it is essential to include leaf size in the considerations.     

Engineering novel traits in plants through RNA interference

RNA interference (RNAi) is a homology-dependent gene silencing technology that involves double-stranded RNA directed against a target gene or its promoter region. Using hairpin constructs, double-stranded RNA can be expressed in plants relatively easily, enabling this technology to be applied to a wide range of species to silence the expression of both specific endogenous genes and genes of invading pathogens. RNAi has also been used to engineer metabolic pathways to overproduce secondary products with health, yield or environmental benefits. The application of tissue-specific or inducible gene silencing, with the use of appropriate promoters, and the ability to silence several genes simultaneously should enhance our ability to create novel traits in plants.     

Reinstatement of Ocyroe (Compositae: Astereae)

Nardophyllum armatum, a species from the Puna region of Argentina, Bolivia, and Chile is here transferred to genus Ocyroe, which in turn is resurrected from the synonymy under Nardophyllum. Ocyroe is characterized by thorny branches, discoid capitula, naked receptacles, glandular corollas with a globose swelling at the base, and a profuse 3- to 5-seriate pappus. The new combination Ocyroe armata and a lectotype for Dolichogyne armata are here presented.     

3-Acetonyl-3-hydroxyoxindole: a new inducer of systemic acquired resistance in plants

Systemic acquired resistance (SAR) is an inducible defence mechanism which plays a central role in protecting plants from microbial pathogen attack. Guided by bioassays, a new chemical inducer of SAR was isolated from the extracts of Strobilanthes cusia and identified to be 3-acetonyl-3-hydroxyoxindole (AHO), a derivative of isatin. Tobacco plants treated with AHO exhibited enhanced resistance to tobacco mosaic virus (TMV) and to the fungal pathogen Erysiphe cichoracearum (powdery mildew), accompanied by increased levels of pathogenesis-related gene 1 ( PR-1 ) expression, salicylic acid (SA) accumulation and phenylalanine ammonia-lyase activity. To study the mode of action of AHO, its ability to induce PR-1 expression and TMV resistance in nahG transgenic plants expressing salicylate hydroxylase, which prevents the accumulation of SA, was analysed. AHO treatment did not induce TMV resistance or PR-1 expression in nahG transgenic plants, suggesting that AHO acts upstream of SA in the SAR signalling pathway. In addition, using two-dimensional gel electrophoresis combined with mass spectrometry, five AHO-induced plant proteins were identified which were homologous to the effector proteins with which SA interacts. Our data suggest that AHO may represent a novel class of inducer that stimulates SA-mediated defence responses.     

Polymorphisms for purely cytoplasmically inherited traits in bisexual plants

It is shown that cytoplasm polymorphisms transmitted only by the ovules can be maintained without gene-cytoplasmic interactions. The necessary prerequisites are asymmetry of the plasmotypes in production of ovules and pollen (sexual asymmetry), incomplete and frequency-dependent fertilization efficiency and differential selfing rates. These factors can generate the negative frequency dependence of cytoplasmic fitnesses required for a stable polymorphism. The model considered allows also for facultative fixation of either of two plasmotypes and, thus, may produce all of the dynamical characteristics known for nuclear selection with two alleles at one locus.

Strong sexual asymmetry, which probably occurs frequently in bisexual plants, may facilitate stable cytoplasmic polymorphisms. However, these polymorphisms may also endanger survival of the whole population in the absence of nuclear interactions. Gene-cytoplasmic interactions avoid this risk and, at the same time, utilize the advantages of sexual asymmetry in maintaining genetic polymorphisms.

     

Functional traits and root morphology of alpine plants

Background and Aims

Vegetation has long been recognized to protect the soil from erosion. Understanding species differences in root morphology and functional traits is an important step to assess which species and species mixtures may provide erosion control. Furthermore, extending classification of plant functional types towards root traits may be a useful procedure in understanding important root functions.

Methods

In this study, pioneer data on traits of alpine plant species, i.e. plant height and shoot biomass, root depth, horizontal root spreading, root length, diameter, tensile strength, plant age and root biomass, from a disturbed site in the Swiss Alps are presented. The applicability of three classifications of plant functional types (PFTs), i.e. life form, growth form and root type, was examined for above- and below-ground plant traits.

Key Results

Plant traits differed considerably among species even of the same life form, e.g. in the case of total root length by more than two orders of magnitude. Within the same root diameter, species differed significantly in tensile strength: some species (Geum reptans and Luzula spicata) had roots more than twice as strong as those of other species. Species of different life forms provided different root functions (e.g. root depth and horizontal root spreading) that may be important for soil physical processes. All classifications of PFTs were helpful to categorize plant traits; however, the PFTs according to root type explained total root length far better than the other PFTs.

Conclusions

The results of the study illustrate the remarkable differences between root traits of alpine plants, some of which cannot be assessed from simple morphological inspection, e.g. tensile strength. PFT classification based on root traits seems useful to categorize plant traits, even though some patterns are better explained at the individual species level.     

寄生植物的生物学特性及生态学效应

寄生植物是陆地生态系统的重要组成部分,在多数生态系统中均有分布.寄生植物完全或部分依赖于寄主植物获取有机养分、无机养分和水分等,以满足自身生长发育需求.在生态学效应方面,寄生植物不但直接影响寄主植物的生长发育,也会通过改变寄主植物的竞争力而影响植物群落组成.寄生植物对寄主植物个体水平的影响多是消极的,并能给人类的生产活动造成直接经济损失,故对寄生植物的防治一直是人们关注的热点问题;在群落水平上,寄生植物对促进植物群落的物种多样性有积极的意义,基于此,寄生植物有潜在利用价值.深入了解寄生植物的生理生态学特性,对有害寄生植物的防除和有益寄生植物的利用有重要价值.本文对寄生植物的生物学特性,包括其寄生类型、寄主范围及偏好、寄主识别和吸器的形成与功能,进行了阐述,并就寄生植物对寄主植物和群落结构的影响进行了探讨,对相关研究前景进行了展望.     

Large-scale geographical trends in fruit traits of vertebrate-dispersed temperate plants

Aim  To assess large-scale geographical trends in the character of fleshy, vertebrate-dispersed fruits.
Location  Europe between central Sweden and southern Spain.
Methods  Analyses of fruit of sixty-three plant species from twenty-nine families were compiled from four regional data sets. Four structural and five chemical fruit traits were analysed intraspecifically to control rigorously for phylogenetic lineage effects. Trends were examined in relation to various biological features of the considered species.
Results  Contents of soluble carbohydrate and lipids decreased markedly northwards. Fruit diameter and fresh mass peaked at the wettest site, while the pulp water content remained more constant throughout the gradient than any other fruit trait. Ash content, seed number and seed mass did not change, while the nitrogen content showed conflicting trends. No relation was detected between observed variation in fruit traits and fruit type, fruit colour, ripening season, plant growth form, leaf longevity, or geographical distribution of the considered plant species.
Main conclusions  Considerable intraspecific variability exists in vertebrate-dispersed fruits on large geographical scales. Climate presumably affects particularly those traits related to carbon and water gain and storage. Most research on fruit–frugivore interactions has been carried out on small spatial scales and failed to find matchings between frugivore communities and the character of fleshy fruits. I suggest that explicitly addressed large-scale surveys on the geographical variability of fruits and their disperser assemblages are needed to elucidate their spatial patterns and to determine the extent to which fleshy fruit traits are shaped by animals and/or abiotic factors.