**5. Perspectives on the functional genomics of common bean**

lines presented significant reduction on PHI while no differences were observed for the most

Despite the availability of traits that might be evaluated in field conditions, the environment turns out to be a critical component interfering with results from one site to another. Drought field trials performed with the RIL population of the crossing BAT 477 × DOR 364, previously referred to the greenhouse experiment, showed significant variability across four locations evaluated [104]. A QTL analysis associating the field traits to a previous set of molecular markers disposed in a linkage map [106] showed significant QTL–environment interactions. Therefore, determining if one cultivar is tolerant to drought does not necessarily mean it will respond well to all environments, in a sense that it must be tested in multiple environments

**Figure 5.** Strategies for phenotyping common beans for drought tolerance. Greenhouse experiments and field trials are complimentary strategies for evaluating several parameters and defining drought-tolerance levels. Recurring to wild beans based on environmental data might also be useful to select for beans adapted to drought episodes. Those evalua‐ tions altogether may be used toward the development of new varieties and the identification of genomic regions asso‐ ciated with the phenotypes evaluated as well as the functional role of candidate genes that are under characterization.

Although greenhouse and field methods have been developed to identify drought-tolerant genotypes and gene markers associated to such parameters, recent efforts have also been focused on the identification of sources of drought tolerance in wild beans spanning the natural area of distribution of *P. vulgaris* [107]. However, reliable estimations of drought tolerance in wild beans are not easy to establish, and attempts toward the development of new methods have been in course. Potential evapotranspiration models coupled with precipitation regimes were used to define a drought index for a series of wild bean accessions. Considering this factor along with the population structure might be a useful tool to analyze the levels of drought

All these methods might be useful to carefully understand the phenotypic basis of drought tolerance variation in common bean genotypes. With standardized methods for the traits one might be interested, the accuracy between the association of molecular data and phenotypes might be much higher. It may be applied to QTL and association mapping studies, which link genome-wide molecular markers such as microsatellites, SNP, and gene-specific markers to

tolerance and use these materials for introgression of alleles of interest [107].

resistant lines [105].

138 Abiotic and Biotic Stress in Plants - Recent Advances and Future Perspectives

to check for its performance.

As mentioned before, common bean is not a species amenable for genetic transformation with the aim to test genes and to do functional studies. Thus, genomic mapping, transcriptomic and proteomic studies in contrasting genotypes, phases of development, different treatment/ growth conditions, etc. are currently the most used approaches to identify genes linked to determined loci, verify changes in plant metabolism, and ultimately identify candidate genes suitable for molecular breeding or functional analyses.

The "omics" technologies and bioinformatics tools for large-scale data analysis have become essential to understanding the molecular systems that underlie various plant functions [109]. Despite common bean has been receiving increasing edible and economic importance, an investigation at a comprehensive omics level has been lacking in comparison to other model legume crops. As the genome sequences of *P. vulgaris* has become recently available, a new chapter has been opened for research with this crop. The genome release has provided a great miscellany of candidate genes that should be useful to improve common bean toward several different goals and approaches.

When considering abiotic stresses, some interesting NGS-related transcriptome data associat‐ ed to drought [99] and salt-stress tolerance [100] as well as proteomic data related to drought [110], chilling [111], and osmotic stresses [112] have already been accessed. The consequential integration of a wide spectrum of omics data sets is then essential to promote translational research to engineer plant systems in response to the emerging demands of humanity.

Nevertheless, there is a big lack of information regarding interaction among stress sources. A recent trend for other crops has been the study of the effects of combined stress treatments such as drought versus salt, drought versus heating, drought × salt × nutrition, among others. These new studies try to represent most appropriately what really happens in the field, since plants are often subjected to multiple stresses. This should also be extended to the level of abiotic versus biotic stresses since many diseases are coupled with abiotic stresses at a certain stage of development of common bean. The available research on genomic, transcriptomic, and proteomic level on isolate stress-inductive factors should now be reunited in an attempt to elucidate the most complex phenomena involved in stress interactions. And, that should be extended to another level of complexity, which is establishing the interaction of both abiotic and biotic stress sources on common bean.

Regarding plant/pathogen interaction, until the moment the pathosystem *Phaseolus vulgaris*/ *Colletotrichum lindemuthianum* was only investigated in an incompatible interaction. However, there are other combinations of genotype and pathogen races that lead to a compatible interaction and remain to be studied in order to compare these systems and understand which mechanisms are really responsible for the resistance.

Still, considering plant/pathogen interaction, in the past years, the LMD (laser micro-dissec‐ tion) technology has been applied to study individual cells of plant-infected tissue and/or pathogen structures. This is because the way plant tissues were collected to do quantitative analyzes, as transcriptomic and proteomic, could generate a dilution of those cells in direct contact with the fungus into the whole tissue. This type of analysis allows a specific and localized evaluation. The LMD technique is based on the coordinated use of microscopy, laser and robotic, to localize, dissect, and capture cellular material [113]. This method has been important in selection and sampling of cells or cellular content in enough quantity and quality for DNA, RNA, protein, and metabolite analyzes, even in high throughput. Our group is employing this technology to study *P. vulgaris*/*C. lindemuthianum* interaction and *P. vulgaris*/ mycorrhiza interaction under drought stress.

Looking for stress-resistance sources in other species and introgressing genes to common bean is another alternative for genomic improvement. A good example relies on the research that has been done for drought tolerance in common bean, based on interspecific crosses with other species of *Phaseolus*, such as tepary beans (*P. acutifolius*). They naturally span from the desert highlands of northwest Mexico to the southwest of the USA and thus they are good sources of drought, heat, and cold tolerance [114]. An interesting feature of tepary beans is their root system, which reveals extremely fine roots with rapid penetration in the soil with profuse branching, which enables quick access to limited soil water [115].
