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.

Is nitrogen accumulation in grain legumes responsive to growth or ontogeny?

Nitrogen (N) accumulation in legumes is one of the main determinants of crop yield. Although N accumulation from symbiotic nitrogen fixation or N absorption from the soil has been widely investigated, there is no clear consensus on timing of the beginning of N accumulation and the termination of N accumulation and the physiological events that may be associated with these two events. The analyses conducted in this study aimed at identifying the determinant of N accumulation in two grain legume species. Nitrogen accumulation dynamics and mass accumulation and development stages were recorded in the field for several genotypes of common bean (Phaseolus vulgaris) and faba bean (Vicia faba) under different growing conditions. This study showed that during the vegetative stages, N accumulation rate was correlated with mass accumulation rate. However, the maximum accumulation of N did not correspond to the time of the maximum mass accumulation. In fact, for both species, N accumulation was found to persist in seed growth. This challenges a common hypothesis that seed growth causes a decrease in N accumulation because of a shift of the photosynthate supply to support the seed growth. Even more surprising was the shift of the active accumulation of N in faba bean to late in the growing season as compared with common bean. N accumulation by faba bean only was initiated at high rates very late in vegetative growth and persisted at high rates well into seed fill.

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.

Development of a QTL-environment-based predictive model for node addition rate in common bean.

KEY MESSAGE: This work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate. To select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day- 1) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50-90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.

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.

Determination of coefficient defining leaf area development in different genotypes, plant types and planting densities in peanut (Arachis hypogeae L.).

Rapid leaf area development may be attractive under a number of cropping conditions to enhance the vigor of crop establishment and allow rapid canopy closure for maximizing light interception and shading of weed competitors. This study was undertaken to determine (1) if parameters describing leaf area development varied among ten peanut (Arachis hypogeae L.) genotypes grown in field and pot experiments, (2) if these parameters were affected by the planting density, and (3) if these parameters varied between Spanish and Virginia genotypes. Leaf area development was described by two steps: prediction of main stem number of nodes based on phyllochron development and plant leaf area dependent based on main stem node number. There was no genetic variation in the phyllochron measured in the field. However, the phyllochron was much longer for plants grown in pots as compared to the field-grown plants. These results indicated a negative aspect of growing peanut plants in the pots used in this experiment. In contrast to phyllochron, there was no difference in the relationship between plant leaf area and main stem node number between the pot and field experiments. However, there was genetic variation in both the pot and field experiments in the exponential coefficient (PLAPOW) of the power function used to describe leaf area development from node number. This genetic variation was confirmed in another experiment with a larger number of genotypes, although possible G × E interaction for the PLAPOW was found. Sowing density did not affect the power function relating leaf area to main stem node number. There was also no difference in the power function coefficient between Spanish and Virginia genotypes. SSM (Simple Simulation model) reliably predicted leaf canopy development in groundnut. Indeed the leaf area showed a close agreement between predicted and observed values up to 60000 cm2 m-2. The slightly higher prediction in India and slightly lower prediction in Niger reflected GxE interactions. Until more understanding is obtained on the possible GxE interaction effects on the canopy development, a generic PLAPOW value of 2.71, no correction for sowing density, and a phyllochron on 53 °C could be used to model canopy development in peanut.

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.