**5. Applications of QTL and molecular markers in breeding for drought tolerance**

#### **5.1 QTL mapping**

*Drought - Detection and Solutions*

consequence, protein activity.

features in common with plant senescence [77].

The further study on stem [16] carried out on cultivar 'Tiber' showed changed abundances under drought of proteins that can be classified in the same categories as leaf proteins. The proteins with increased abundance indicate the importance of maintaining protein homeostasis to mitigate this stress. There was increased abundance of proteins involved in protein synthesis, proteolysis and protein folding. Among them, the protein with the greatest abundance was 70 kDa heat shock

The complexity of the response of plants to drought is further emphasized by reports indicating that posttranslational modifications (PTMs) of proteins also play an important role. These include covalent modifications of a number of cell proteins that follow protein biosynthesis and are usually catalyzed by enzymes. There are different types of PTMs, among them glycosylation, that are recognized as being very important in plants and in their response to stress [73, 74]. This type of PTM affects protein stability, interaction with other proteins, protein trafficking and, as a

Only a small number of the proteomic studies that have been carried out address

specifically protein glycosylation and changes in abundance of glycoproteins in crops under abiotic stress [17]. One of them is our study of glycosylated proteins in leaves of common bean stressed by drought [17]. 'Tiber,' previously identified as relatively tolerant to drought [46, 47], was investigated. Thirty-five glycoproteins with changed abundance were detected. Their structures showed high mannose, complex and hybrid types of N-glycans, most of them being associated with the cell wall (many cell wall-degrading enzymes, such as, β-glucosidase, α-arabinofuranosidase and β-xylosidase, were more abundant under drought), with the stress response (such as, ascorbate oxidase, purple acid phosphatase and reticulin oxidase-like protein that were also more abundant) and with proteolysis and protein folding (such as, the precursor of subtilisin-like serine protease, nicastrin, the precursor of cysteine protease and protein disulfide isomerase that were less abundant) [17]. It follows from the studies reported above that proteome analysis of common bean under drought has revealed the participation of proteins involved in proteolysis [15, 17]. Many proteins, after their synthesis, need to be activated by highly regulated proteolytic cleavage of specific peptide bonds that removes parts of their peptide chains. Activation of regulated proteolysis and simultaneous inhibition of uncontrolled proteolysis are vital for cell survival under dehydration stress. All beneficial changes in metabolism under drought require the active involvement of controlled proteolysis that regulates the turnover rates of specific enzymes and/or proteins involved in cell signaling, and ensures degradation of oxidatively damaged, improperly folded and irreversibly denatured proteins [75, 76]. On the other hand non-specific, uncontrolled proteolysis can be damaging to cells, leading to random breakdown of the majority of cell proteins. Such protein degradation, provoked by drought, results mainly in the disruption of cell membranes and exhibits many

Proteolysis is catalyzed by proteases whose activity is regulated mainly by specific plant protease inhibitors both detected by transcriptomics and/or proteomics [76]. The latter are important, not only for inhibiting proteases activated on drought, but also for osmoprotection, since many of them are highly hydrophilic. The striking diversity of plant proteases and of their inhibitors in each species [76] coupled with the fact that very few of their natural substrates are known [78], complicates research in this field. In addition, it appears that the changes in abundance of many proteases in plants stressed by drought have not been detected by

protein that chaperones the correct folding of proteins [16].

**4.3 Postranslational modifications in the response to drought**

**116**

Quantitative trait locus (QTL) mapping is an established approach for detecting loci associated with complex quantitative traits, such as, plant tolerance to drought. In common bean multiple populations derived from crosses of susceptible and tolerant parental genotypes, belonging to either a single gene pool, or both Andean and Mesoamerican gene-pools, have been genotyped and genetic linkage maps constructed [18, 85]. Their precision and resolution have been greatly improved by novel sequencing technology and genetic markers, such as, SNPs. For instance, two inter-gene pool populations of 'BAT93' × 'JaloEEP558' and 'DOR364' × 'G19833' have been genotyped repeatedly using a variety of marker systems, ranging from SSR and amplified fragment length polymorphism (AFLP) to SNP [18, 85]. The efforts have culminated in consensus linkage map generation joining both major inter-gene pool maps as well as serving as a core for integration with Mesoamerican linkage map [18]. These approaches have enabled identification of numerous QTLs, controlling resistance to various viral, bacterial and fungal pathogens as well as multigenic traits such as tolerance to drought, biomass production, yield partitioning, and micronutrient accumulation [86, 87].

Drought response-associated QTLs in common bean have been reported in association with yield, phenology, canopy biomass and biomass partitioning. A Mesoamerican and Andean inter-gene pool genetic map with high marker coverage was utilized to detect phenological and seed weight QTLs associated with drought tolerance [88], while intra-gene pool Mesoamerican mapping population has been utilized to identify drought-associated QTL for phenological and yield-related traits [89] as well as QTL for photosynthate acquisition, accumulation and remobilization traits in drought stress [90].

The translation of reported QTLs into practical use has, however, been limited, due to highly variable common bean germplasm and strong influence of the environmental conditions on the presence of minor QTLs. It would be ideal to perform the validation of the QTL in crop production areas. Establishing controlled and uniform growth conditions for evaluation of a large recombinant inbred line (RIL) population, exceeding hundred genotypes, can however prove difficult and not very practical, so a compromise approach for validation of major QTL could consist of testing a subsample of the most diverse RILs for a selected segregation trait in multiple trials sites [5]. Much of the work in QTL mapping and development of drought-tolerant cultivars has been performed based on the traits of the drought resistance sources of Mesoamerican origin, such as those belonging to the race Durango [5].

#### **5.2 Marker-assisted selection and breeding for drought tolerance**

For decades DNA markers have been the most widely used molecular markers in crop improvement, due to their abundance and polymorphisms. Markerassisted selection enables precise and effective selection of common bean genotypes with specific traits and can greatly facilitate the selection process in breeding [91, 92]. These markers are potentially very useful in trait selection and breeding applications, and have been utilized in our procedures, to offer additional informative value on the common bean genotypes included in the breeding program (not published). The advantage of such an approach is that a broad range of economically important traits can be covered, including disease resistance, abiotic stress tolerance, high yield, earliness, phosphorus uptake, and root morphology. However, the practical utilization of molecular markers is at the beginning, also due to lacking validation across the genotypes of the diverse common bean germplasm.

The marker-assisted selection is especially effective in selection for simple and single gene traits, and has been applied for selection for resistance genes for various common bean diseases of viral, bacterial and fungal origin [93, 94]. Selection for quantitative traits such as quantitative resistance or drought tolerance presents a great challenge as it can involve multiple major and minor QTLs controlling the trait [91]. Improved understanding of the complex drought response mechanisms on the level of physiology and molecular biology has enabled identification of potential molecular markers, which could help us distinguish between drought resistant and susceptible genotypes. Among the recently reported markers associated with the drought response in common bean are AQPs whose expression is discussed in the present chapter under Section 4.1. On the other hand several potentially useful molecular markers associated with drought response traits, such as high yield under drought, have been identified using QTL mapping in a segregating RIL populations [89, 90, 95].

Common strategy of common bean breeding programs for resistance to drought is selection of best yielding genotypes that are cultivated in drought-exposed conditions [37, 41]. In addition to that application of novel breeding approaches

**119**

*Drought Stress Response in Agricultural Plants: A Case Study of Common Bean...*

not frequently used in common bean breeding has been described [5]. Recurrent selection has been utilized for breeding for drought resistance in genotypes within the same gene-pool, following a process of pre-breeding in which multiple potential parental genotypes with drought resistance traits are created [40]. Another breeding method, advanced backcrossing, could be potentially useful for simultaneous transfer of multiple genes for improving drought resistance traits across genepools [5]. These breeding approaches could greatly benefit with the future developments in the research of plant drought response mechanisms and discovery of associated

Drought tolerance is gaining importance in the breeding of common bean for higher yields under the changing environmental conditions. Studying drought tolerance is thus important in order to understand the underlying mechanisms and to identify markers that could help distinguish the more tolerant common bean genotypes. A highly diverse common bean germplasm, adapted to various growth and climatic conditions, constitutes a valuable pool of traits including potential drought tolerance traits. On the other hand, the great complexity of the common bean response to drought on physiological and molecular levels presents a great problem for more effective breeding. The challenge for the future will be to integrate the data obtained by various approaches that include screening of the transcriptome, proteome and metabolome, using advanced bioinformatics and systems biology, identifying molecular markers and QTLs and elucidating the

The contribution of Dr. Marko Maras and Dr. Mateja Zupin to our studies presented is greatly acknowledged. The authors thank Professor Roger H. Pain for critically reviewing the manuscript. This work was supported by the Slovenian Research Agency (P4-0072, L4-7520) and the Ministry of Agriculture, Forestry and

*DOI: http://dx.doi.org/10.5772/intechopen.86526*

molecular markers.

underlying pathways.

**Acknowledgements**

Food (L4-7520).

**Conflict of interest**

The authors declare no conflict of interest.

**6. Conclusion**

*Drought Stress Response in Agricultural Plants: A Case Study of Common Bean... DOI: http://dx.doi.org/10.5772/intechopen.86526*

not frequently used in common bean breeding has been described [5]. Recurrent selection has been utilized for breeding for drought resistance in genotypes within the same gene-pool, following a process of pre-breeding in which multiple potential parental genotypes with drought resistance traits are created [40]. Another breeding method, advanced backcrossing, could be potentially useful for simultaneous transfer of multiple genes for improving drought resistance traits across genepools [5]. These breeding approaches could greatly benefit with the future developments in the research of plant drought response mechanisms and discovery of associated molecular markers.
