Mapping of the bs5 and bs6 non-race-specific recessive resistances against bacterial spot of pepper.

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregating populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6. We identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. This research enhances marker-assisted selection of bs5 and bs6 in breeding programs and is a crucial step towards elucidating the molecular mechanisms underlying the resistances.

Dynamic QTL-based ecophysiological models to predict phenotype from genotype and environment data.

BACKGROUND: Predicting the phenotype from the genotype is one of the major contemporary challenges in biology. This challenge is greater in plants because their development occurs mostly post-embryonically under diurnal and seasonal environmental fluctuations. Most current crop simulation models are physiology-based models capable of capturing environmental fluctuations but cannot adequately capture genotypic effects because they were not constructed within a genetics framework. RESULTS: We describe the construction of a mixed-effects dynamic model to predict time-to-flowering in the common bean (Phaseolus vulgaris L.). This prediction model applies the developmental approach used by traditional crop simulation models, uses direct observational data, and captures the Genotype, Environment, and Genotype-by-Environment effects to predict progress towards time-to-flowering in real time. Comparisons to a traditional crop simulation model and to a previously developed static model shows the advantages of the new dynamic model. CONCLUSIONS: The dynamic model can be applied to other species and to different plant processes. These types of models can, in modular form, gradually replace plant processes in existing crop models as has been implemented in BeanGro, a crop simulation model within the DSSAT Cropping Systems Model. Gene-based dynamic models can accelerate precision breeding of diverse crop species, particularly with the prospects of climate change. Finally, a gene-based simulation model can assist policy decision makers in matters pertaining to prediction of food supplies.

Towards a multiscale crop modelling framework for climate change adaptation assessment.

Predicting the consequences of manipulating genotype (G) and agronomic management (M) on agricultural ecosystem performances under future environmental (E) conditions remains a challenge. Crop modelling has the potential to enable society to assess the efficacy of G × M technologies to mitigate and adapt crop production systems to climate change. Despite recent achievements, dedicated research to develop and improve modelling capabilities from gene to global scales is needed to provide guidance on designing G × M adaptation strategies with full consideration of their impacts on both crop productivity and ecosystem sustainability under varying climatic conditions. Opportunities to advance the multiscale crop modelling framework include representing crop genetic traits, interfacing crop models with large-scale models, improving the representation of physiological responses to climate change and management practices, closing data gaps and harnessing multisource data to improve model predictability and enable identification of emergent relationships. A fundamental challenge in multiscale prediction is the balance between process details required to assess the intervention and predictability of the system at the scales feasible to measure the impact. An advanced multiscale crop modelling framework will enable a gene-to-farm design of resilient and sustainable crop production systems under a changing climate at regional-to-global scales.

The genetic control of leaf allometry in the common bean, Phaseolus vulgaris.

BACKGROUND: To maximize photosynthetic efficiency, plants have evolved a capacity by which leaf area scales allometrically with leaf mass through interactions with the environment. However, our understanding of genetic control of this allometric relationship remains limited. RESULTS: We integrated allometric scaling laws expressed at static and ontogenetic levels into genetic mapping to identify the quantitative trait loci (QTLs) that mediate how leaf area scales with leaf mass and how such leaf allometry, under the control of these QTLs, varies as a response to environment change. A major QTL detected by the static model constantly affects the allometric growth of leaf area vs. leaf mass for the common bean (Phaseolus vulgaris) in two different environments. The ontogenetic model identified this QTL plus a few other QTLs that determine developmental trajectories of leaf allometry, whose expression is contingent heavily upon the environment. CONCLUSIONS: Our results gain new insight into the genetic mechanisms of how plants program their leaf morphogenesis to adapt to environmental perturbations.

Developmental Pleiotropy Shaped the Roots of the Domesticated Common Bean (Phaseolus vulgaris).

Roots have been omitted from previous domestication analyses owing mostly to their subterranean nature. We hypothesized that domestication-associated changes in common bean (Phaseolus vulgaris) roots were due to direct selection for some aboveground traits that also affect roots, and to indirect selection of root traits that improved aboveground plant performance. To test this hypothesis, we compared the root traits of wild and domesticated accessions and performed a multistep quantitative trait locus (QTL) analysis of an intra-Andean recombinant inbred family derived from a landrace and a wild accession. Multivariate analysis of root traits distinguished wild from domesticated accessions and showed that seed weight affects many root traits of young seedlings. Sequential and methodical scanning of the genome confirmed the significant effect of seed weight on root traits and identified QTLs that control seed weight, root architecture, shoot and root traits, and shoot traits alone. The root domestication syndrome in the common bean was associated with genes that were directly selected to increase seed weight but had a significant effect on early root growth through a developmental pleiotropic effect. The syndrome was also associated with genes that control root system architecture and that were apparently the product of indirect selection.

Differential transcriptome patterns associated with early seedling development in a wild and a domesticated common bean (Phaseolus vulgaris L.) accession.

Genes that control "Domestication Syndrome" traits were direct targets of selection, like those controlling increased seed size in the common bean. However, selection for this trait brought about unintentional selection on genes controlling seedling growth. We hypothesized that wild and domesticated plants have different early seedling growth patterns as an indirect consequence of selection for a larger seed size during domestication, and those differences resulted from changes in gene expression patterns of the wild ancestor. Large seeds pose a challenge to reserve remobilization during early heterotrophic growth, particularly during a transition towards more fertile alluvial soils. To address our hypothesis, we characterized the patterns of gene expression of cotyledon, root, and leaf tissues of 7-day old seedlings of a wild and a landrace accession of the common bean. Differential expression analyses detected genes with contrasting patterns of expression between the two genotypes in all three tissues. Some of the differentially expressed genes with contrasting genotypic patterns are known to have domestication-related signatures of selection. Among these genes were some transcription factors associated with key roles in development. These genes may represent targets of indirect selection and ultimately explain the growth phenotypic differences between wild and domesticated seedlings.

An ecophysiologically based mapping model identifies a major pleiotropic QTL for leaf growth trajectories of Phaseolus vulgaris.

Crop modeling, a widely used tool to predict plant growth and development in heterogeneous environments, has been increasingly integrated with genetic information to improve its predictability. This integration can also shed light on the mechanistic path that connects the genotype to a particular phenotype under specific environments. We implemented a bivariate statistical procedure to map and identify quantitative trait loci (QTLs) that can predict the form of plant growth by estimating cultivar-specific growth parameters and incorporating these parameters into a mapping framework. The procedure enables the characterization of how QTLs act differently in response to developmental and environmental cues. We used this procedure to map growth parameters of leaf area and mass in a mapping population of the common bean (Phaseolus vulgaris L.). Different sets of QTLs are responsible for various aspects of growth, including the initiation time of growth, growth rate, inflection point and asymptotic growth. A major QTL of a large effect was identified to pleiotropically affect trait expression in distinct environments and different traits expressed on the same organism. The integration of crop models and QTL mapping through our statistical procedure provides a powerful means of building a more precise predictive model of genotype-phenotype relationships for crops.

Physiological, molecular and ultrastructural analyses during ripening and over-ripening of banana (Musa spp., AAA group, Cavendish sub-group) fruit suggest characteristics of programmed cell death.

BACKGROUND: Programmed cell death (PCD) is a part of plant development that has been studied for petal senescence and vegetative tissue but has not been thoroughly investigated for fleshy fruits. The purpose of this research was to examine ripening and over-ripening in banana fruit to determine if there were processes in common to previously described PCD. RESULTS: Loss of cellular integrity (over 40%) and development of senescence related dark spot (SRDS) occurred after day 8 in banana peel. Nuclease and protease activity in the peel increased during ripening starting from day 2, and decreased during over-ripening. The highest activity was for proteases and nucleases with apparent molecular weights of 86 kDa and 27 kDa, respectively. Images of SRDS showed shrinkage of the upper layers of cells, visually suggesting cell death. Decrease of electron dense areas was evident in TEM micrographs of nuclei. CONCLUSION: This study shows for the first time that ripening and over-ripening of banana peel share physiological and molecular processes previously described in plant PCD. SRDS could represent a morphotype of PCD that characterizes a structural and biochemical failure in the upper layers of the peel, thereafter spreading to lower and adjacent layers of cells. © 2017 Society of Chemical Industry.

A Predictive Model for Time-to-Flowering in the Common Bean Based on QTL and Environmental Variables.

The common bean is a tropical facultative short-day legume that is now grown in tropical and temperate zones. This observation underscores how domestication and modern breeding can change the adaptive phenology of a species. A key adaptive trait is the optimal timing of the transition from the vegetative to the reproductive stage. This trait is responsive to genetically controlled signal transduction pathways and local climatic cues. A comprehensive characterization of this trait can be started by assessing the quantitative contribution of the genetic and environmental factors, and their interactions. This study aimed to locate significant QTL (G) and environmental (E) factors controlling time-to-flower in the common bean, and to identify and measure G × E interactions. Phenotypic data were collected from a biparental [Andean × Mesoamerican] recombinant inbred population (F11:14, 188 genotypes) grown at five environmentally distinct sites. QTL analysis using a dense linkage map revealed 12 QTL, five of which showed significant interactions with the environment. Dissection of G × E interactions using a linear mixed-effect model revealed that temperature, solar radiation, and photoperiod play major roles in controlling common bean flowering time directly, and indirectly by modifying the effect of certain QTL. The model predicts flowering time across five sites with an adjusted r-square of 0.89 and root-mean square error of 2.52 d. The model provides the means to disentangle the environmental dependencies of complex traits, and presents an opportunity to identify in silico QTL allele combinations that could yield desired phenotypes under different climatic conditions.

Maternal Effects on Seed and Seedling Phenotypes in Reciprocal F 1 Hybrids of the Common Bean (Phaseolus vulgaris L.).

Maternal control of seed size in the common bean provides an opportunity to study genotype-independent seed weight effects on early seedling growth and development. We set out to test the hypothesis that the early heterotrophic growth of bean seedlings is determined by both the relative amount of cotyledon storage reserves and the genotype of the seedling, provided the hybrid genotype could be fully expressed in the seedlings. The hypothesis was tested via comparison of seed weight and seedling growth phenotypes of small-seeded (wild, ~0.10 g) and large-seeded (landrace, ~0.55 g) parents and their reciprocal F1 hybrids. Akaike's Information Criteria were used to estimate growth parameters and identify the phenotypic model that best represented the data. The analysis presented here indicates that the hybrid embryo genotype is not fully expressed during both seed and seedling growth and development. The analysis presented here shows that seed growth and development are controlled by the sporophyte. The strong similarity in seed size and shape of the reciprocal hybrid seed with seeds of the maternal parents is evidence of this control. The analysis also indicates that since the maternal sporophyte controls seed size and therefore the amount of cotyledon reserves, the maternal sporophyte indirectly controls early seedling growth because the cotyledons are the primary nutrient source during heterotrophic growth. The most interesting and surprising results indicated that the maternal effects extended to the root architecture of the reciprocal hybrid seedlings. This phenomenon could not be explained by seed size, but by alterations in the control of the pattern of gene expression of the seedling, which apparently was set by a maternally controlled mechanism. Although seed weight increase was the main target of bean domestication, it also had positive repercussions on early-growth traits and stand establishment.

Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives.

Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2-4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.

Plastic expression of heterochrony quantitative trait loci (hQTLs) for leaf growth in the common bean (Phaseolus vulgaris).

Heterochrony, that is, evolutionary changes in the relative timing of developmental events and processes, has emerged as a key concept that links evolution and development. Genes associated with heterochrony encode molecular components of developmental timing mechanisms. However, our understanding of how heterochrony genes alter the expression of heterochrony in response to environmental changes remains very limited. We applied functional mapping to find quantitative trait loci (QTLs) responsible for growth trajectories of leaf area and leaf mass in the common bean (Phaseolus vulgaris) grown in two contrasting environments. We identified three major QTLs pleiotropically expressed under the two environments. Further characterization of the temporal pattern of these QTLs indicates that they are heterochrony QTLs (hQTLs) in terms of their role in influencing four heterochronic parameters: the timing of the inflection point, the timing of maximum acceleration and deceleration, and the duration of linear growth. The pattern of gene action by the hQTLs on each parameter was unique, being environmentally dependent and varying between two allometrically related leaf growth traits. These results provide new insights into the complexity of genetic mechanisms that control trait formation in plants and provide novel findings that will be of use in studying the evolutionary trends.

Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L.

High density genetic maps are a reliable tool for genetic dissection of complex plant traits. Mapping resolution is often hampered by the variable crossover and non-crossover events occurring across the genome, with pericentromeric regions (pCENR) showing highly suppressed recombination rates. The efficiency of linkage mapping can further be improved by characterizing and understanding the distribution of recombinational activity along individual chromosomes. In order to evaluate the genome wide recombination rate in common beans (Phaseolus vulgaris L.) we developed a SNP-based linkage map using the genotype-by-sequencing approach with a 188 recombinant inbred line family generated from an inter gene pool cross (Andean x Mesoamerican). We identified 1,112 SNPs that were subsequently used to construct a robust linkage map with 11 groups, comprising 513 recombinationally unique marker loci spanning 943 cM (LOD 3.0). Comparative analysis showed that the linkage map spanned >95% of the physical map, indicating that the map is almost saturated. Evaluation of genome-wide recombination rate indicated that at least 45% of the genome is highly recombinationally suppressed, and allowed us to estimate locations of pCENRs. We observed an average recombination rate of 0.25 cM/Mb in pCENRs as compared to the rest of genome that showed 3.72 cM/Mb. However, several hot spots of recombination were also detected with recombination rates reaching as high as 34 cM/Mb. Hotspots were mostly found towards the end of chromosomes, which also happened to be gene-rich regions. Analyzing relationships between linkage and physical map indicated a punctuated distribution of recombinational hot spots across the genome.

Towards a comprehensive picture of the genetic landscape of complex traits.

The formation of phenotypic traits, such as biomass production, tumor volume and viral abundance, undergoes a complex process in which interactions between genes and developmental stimuli take place at each level of biological organization from cells to organisms. Traditional studies emphasize the impact of genes by directly linking DNA-based markers with static phenotypic values. Functional mapping, derived to detect genes that control developmental processes using growth equations, has proven powerful for addressing questions about the roles of genes in development. By treating phenotypic formation as a cohesive system using differential equations, a different approach-systems mapping-dissects the system into interconnected elements and then map genes that determine a web of interactions among these elements, facilitating our understanding of the genetic machineries for phenotypic development. Here, we argue that genetic mapping can play a more important role in studying the genotype-phenotype relationship by filling the gaps in the biochemical and regulatory process from DNA to end-point phenotype. We describe a new framework, named network mapping, to study the genetic architecture of complex traits by integrating the regulatory networks that cause a high-order phenotype. Network mapping makes use of a system of differential equations to quantify the rule by which transcriptional, proteomic and metabolomic components interact with each other to organize into a functional whole. The synthesis of functional mapping, systems mapping and network mapping provides a novel avenue to decipher a comprehensive picture of the genetic landscape of complex phenotypes that underlie economically and biomedically important traits.

Systems mapping: how to map genes for biomass allocation toward an ideotype.

The recent availability of high-throughput genetic and genomic data allows the genetic architecture of complex traits to be systematically mapped. The application of these genetic results to design and breed new crop types can be made possible through systems mapping. Systems mapping is a computational model that dissects a complex phenotype into its underlying components, coordinates different components in terms of biological laws through mathematical equations and maps specific genes that mediate each component and its connection with other components. Here, we present a new direction of systems mapping by integrating this tool with carbon economy. With an optimal spatial distribution of carbon fluxes between sources and sinks, plants tend to maximize whole-plant growth and competitive ability under limited availability of resources. We argue that such an economical strategy for plant growth and development, once integrated with systems mapping, will not only provide mechanistic insights into plant biology, but also help to spark a renaissance of interest in ideotype breeding in crops and trees.

From flower to seed: identifying phenological markers and reliable growth functions to model reproductive development in the common bean (Phaseolus vulgaris L.).

The lack of dependable morphological indicators for the onset and end of seed growth has hindered modeling work in the common bean (Phaseolus vulgaris L.). We have addressed this problem through the use of mathematical growth functions to analyse and identify critical developmental stages, which can be linked to existing developmental indices. We performed this study under greenhouse conditions with an Andean and a Mesoamerican genotype of contrasting pod and seed phenotypes, and three selected recombinant inbred lines. Pods from tagged flowers were harvested at regular time intervals for various measurements. Differences in flower production and seed and pod growth trajectories among genotypes were detected via comparisons of parameters of fitted growth functions. Regardless of the genotype, the end of pod elongation marked the beginning of seed growth, which lasted until pods displayed a sharp decline in color, or pod hue angle. These results suggest that the end of pod elongation and the onset of color change are reliable indicators of important developmental transitions in the seed, even for widely differing pod phenotypes. We also provide a set of equations that can be used to model different aspects of reproductive growth and development in the common bean.

Ethylene-induced overproduction of reactive oxygen species is responsible for the development of watersoaking in immature cucumber fruit.

Watersoaking is an ethylene-induced disorder observed in some members of the Cucurbitaceae including cucumber (Cucumis sativus L.), watermelon (Citrullus lanatus Thunb. Matsum and Nakai), and tropical pumpkin (Cucurbita moschata Duch.). Previous studies have found that immature beit-alpha cucumber (cv. Manar) exhibit watersoaking after 6d of continuous exposure to 10 µLL(-1) ethylene in air (21 kPa O(2)). The present study was designed to investigate the early dynamics of ethylene responses in immature cucumber fruit in order to provide insight into the watersoaking triggering mechanism. Changes in respiration, epidermal color, firmness, reactive oxygen species (ROS) production and electrolyte leakage were evaluated as a function of time under different ethylene concentrations and exposure duration. Ethylene concentrations exceeding 10 µLL(-1) did not accelerate changes in any of the evaluated responses. The first detectable change was a significant rise in respiration on day 2, followed by a significant rise in ROS on day 4, and significant degreening, mesocap softening, and increased electrolyte leakage on day 6; the latter responses coincident with incipient watersoaking. Varying the duration of exposure to ethylene indicated that the critical exposure time is between 2 and 4d. Notably, all deleterious responses to ethylene were suppressed under a hypoxic atmosphere. A model is proposed in which ethylene induces a sharp increase in respiration with a concomitant sharp rise in ROS, which the immature fruit is incapable of quenching. The resulting production of excess ROS leads to discoloration and membrane deterioration, leading to the release of cytoplasmic content, rapid softening, and the visual symptom of watersoaking.

Characterization of two recessive genes controlling resistance to all races of bacterial spot in peppers.

Bacterial spot, one of the most damaging diseases of pepper, is caused by Xanthomonas euvesicatoria. This pathogen has worldwide distribution and it is particularly devastating in tropical and sub-tropical regions where high temperatures and frequent precipitation provide ideal conditions for disease development. Three dominant resistance genes have been deployed singly and in combination in commercial cultivars, but have been rendered ineffectual by the high mutation rate or deletion of the corresponding cognate effector genes. These genes are missing in race P6, and their absence makes this race virulent on all commercial pepper cultivars. The breeding line ECW12346 is the only source of resistance to race P6 in Capsicum annuum, and displays a non-hypersensitive type of resistance. Characterization of this resistance has identified two recessive genes: bs5 and bs6. Individual analysis of these genes revealed that bs5 confers a greater level of resistance than bs6 at 25 degrees C, but in combination they confer full resistance to P6 indicating at least additive gene action. Tests carried out at 30 degrees C showed that both resistances are compromised to a significant extent, but in combination they provide almost full resistance to race P6 indicating a positive epistatic interaction at high temperatures. A scan of the pepper genome with restriction fragment length polymorphism and AFLP markers led to the identification of a set of AFLP markers for bs5. Allele-specific primers for a PCR-based bs5-marker have been developed to facilitate the genetic manipulation of this gene.

Mapping genes for plant structure, development and evolution: functional mapping meets ontology.

One of the fundamental tasks in biology is the identification of genes that control the structure and developmental pattern of complex traits and their responses to the environment during trait development. Functional mapping provides a statistical means for detecting quantitative trait loci (QTLs) that underlie developmental traits, such as growth trajectories, and for testing the interplay between gene action and development. Here we describe how functional mapping and studies of plant ontology can be integrated so as to elucidate the expression mechanisms of QTLs that control plant growth, morphology, development, and adaptation to changing environments. This approach can also be used to construct an evo-devo framework for inferring the evolution of developmental traits.

Hybrid weakness controlled by the dosage-dependent lethal (DL) gene system in common bean (Phaseolus vulgaris) is caused by a shoot-derived inhibitory signal leading to salicylic acid-associated root death.

Certain crosses of common bean (Phaseolus vulgaris) result in temperature-dependent hybrid weakness associated with a severe root phenotype. This is controlled by the interaction of the root- and shoot-expressed semidominant alleles dosage-dependent lethal 1 (DL(1)) and DL(2), which communicate via long-distance signaling. Previously, apparent reciprocal effects on root growth and the restoration of normal root growth by exogenous sucrose led to the hypothesis that the dosage-dependent lethal (DL) system may control root-shoot carbon partitioning. Here, recombinant inbred lines were used to map the DL loci and physiological and biochemical analysis, including metabolite profiling, was used to gain new insights into the signaling interaction and the root phenotype. It is shown that the DL system does not control root-shoot carbon partitioning and that roots are unlikely to die from carbon starvation. Instead, root death likely occurs by defense-related programmed cell death, as indicated by salicylic acid accumulation. DL(2)-expressing cotyledons supply a potent inhibitory signal that is sufficient to cause such death in DL(1)-expressing roots. These data implicate the DL system in defense-related signaling and provide support for the recent hypothesis of defense-related autoimmunity as a potential isolating mechanism in plant speciation, in particular, setting a precedence for the potential roles of long-distance signaling and temperature dependence.