Molecular Marker Assisted Approaches (MMAA) for enhancing Low Water Stress Tolerance in Common Bean: An Update  

Sajad Majeed Zargar1 , Muslima Nazir2 , Nancy Gupta1 , Sufia Farhat1 , Reetika Mahajan1 , R K Salgotra1 , Randeep Rakwal3,4,5 , Ganesh Kumar Agrawal4,5 , Rakeeb Ahmad Mir6
1. School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu-180009, India
2. Department of Botany, Jamia Hamdard University, Hamdard Nagar, New Delhi-110062, India
3. Organization for Educational Initiatives, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
4. Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
5. GRADE Academy Private Limited, Adarsh Nagar-13, Main Road, Birgunj, Nepal
6. Center for Biodiversity Studies, BGSB University, Rajouri, J&K-185234, India
Author    Correspondence author
Molecular Plant Breeding, 2014, Vol. 5, No. 14   doi: 10.5376/mpb.2014.05.0014
Received: 28 Sep., 2014    Accepted: 12 Oct., 2014    Published: 26 Nov., 2014
© 2014 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Zargar et al., Molecular Marker Assisted Approaches (MMAA) for enhancing low water stress tolerance in Common bean: An update, Molecular Plant Breeding, 2014, Vol.5, No. 14 1-12 (doi: 10.5376/mpb.2014.05.0014)

Abstract

Common bean (Phaseolus vulgaris L.) is an important leguminous crop from the nutritional point of view, as it is rich in micronutrients as well as protein content. Drought stress is a major abiotic stress which reduces yield of crops to a major extent. Common bean is mostly cultivated under rain-fed conditions and due to very frequent droughts at the critical growth stages, there is a reduction in its average yield to a larger extent. Therefore, there is an urgent need of developing drought resistant common bean cultivars. Advances in omics approaches have opened a path to tackle many unresolved problems pertaining to crop sustainability. In this review we have discussed various options of using genomics-based approaches, mainly molecular marker assisted approaches (MMAA) to address drought tolerance in common bean. Moreover, we have also emphasized the limitations of conventional breeding approaches in tackling complex traits in crop plants.

Keywords
Drought; Common bean; Molecular markers; Candidate genes; Association mapping

1 Importance of common bean as food crop
Common bean(Phaseolus vulgaris L.) is a truly diploid species (2n=22) belonging to family Fabaceae and having genome size of 650 Mb. It is an annual herbaceous plant that displays a wide range of growth habits, from bush types, to climbers (Van Schoonhoven and Pastor- Corrales, 1987). It originated in Central and South America and is being cultivated as a major food crop in many tropical, subtropical and temperate areas of the Americas, Europe, Africa and Asia (Wortmann et al., 2006). Common bean represents about 50% of grain legumes consumed by the world (McClean et al., 2004). The bean seed is rich in proteins, fiber, carbohydrates, minerals (iron and zinc), and essential vitamins (such as biotin, vitamin A) (Beebe et al., 2000). 20-25% seed protein is present in common bean, which majorly contains phaseolin (Ma and Bliss, 1978). Being an excellent source of polyunsaturated fatty acids, beans have no cholesterol. Common bean contain a group of phenolic compounds, flavonoids or bioflavonoids that have oestrogenic properties, act as anti-oxidants, inhibit inflammation, and have a defensive mechanism against various microbial infections. Beans have been reported to play a pivotal role as anti-cancer, anti-depressant, anti-leukemia, cardio-protective, estrogenic, hepato-protective, chemo-preventive, anti-diabetic, diuretic, and diaphoretic agents (Rafi and Vastano, 2002). Thus, common beans are likely to improve health and nutritional status of the human body due to various pharmaceutical properties and the potential to alleviate micronutrient malnutrition, which is otherwise a major threat.

2 Impact of drought on crop agriculture
Drought stress is a global phenomenon and also a major concern. It is predicted that yields from rain-fed farming in some south Asian countries including India could fall by up to 30% by 2050 (IPCC, 2007). The tropical arid and desert regions of developing countries are highly threatened by the drought (Khor, 2008). It is estimated to affect 38% of the world area (Dilley et al., 2005). Due to climate change it is expected that there will be increased frequency of drought and floods (Lillemo et al., 2005; Jarvis et al., 2010). Many tropical and sub-tropical drought prone regions such as southern Africa, much of Mexico, parts of south-west USA, southern Europe, Australia and India, are expected to receive less rainfall, leading to increased water stress (Lobell and Burke, 2010). For future global food security, climate change is the major challenge (Lobell and Burke, 2010), and hence there is an urgent need to plan for development of drought tolerant crop varieties having high water use efficiency (WUE), so that these are adapted to water stress at various stages of growth and development, and hence mitigate the negative impact of drought stress.
2.1 Drought and common bean: Implications
Drought stress is a global issue affecting the production and productivity of every crop species. Since the population of the world is expected to exceed 9 billion by 2050 (Zargar et al., 2011), feeding so many mouths in changing climatic conditions would be a big challenge. The food production must increase by 70% to provide sustenance to the increasing global population. The science based crop improvement strategy is an option to address this challenge and attain sustainability in food production and global food security, and an immediate need is to work for development of drought resilient crop varieties with high WUE.
In common bean terminal drought stress is one of the major causes of yield reduction. The “terminal drought stress”,which refers to drought stress at the time of seed growth (grain filling) has major impact on yield reduction. Since 60% of common bean production in the developing world including India occurs under rain-fed conditions (Graham and Ranalli, 1997), it leads to a low average global production of beans (<900 kg per ha) (Singh, 2001). Therefore, it appears that drought stress is a worldwide production constraint for common bean (Boutraa and Sanders, 2001; Szilagyi, 2003; Ramos et al., 1999; Singer et al., 1997).
Keeping in view the changing climate and the losses in bean production that occur due to drought stress, there is an urgent need to breed common bean drought tolerant varieties that can sustain under low water conditions. At present we are in process of evaluation of diverse common bean germplasm under rain-fed conditions, in order to identify some desirable genotypes that can withstand drought stress. Such genotypes will act as a valuable genetic resource for the development of drought tolerant common bean varieties. Further genetics/genomics studies are being conducted and we hope that these studies will help us in tracking novel genes/ QTLs for improving drought tolerance of common bean through molecular breeding involving marker-assisted selection (MAS).
2.2 Drought tolerance a complex trait
Drought tolerance is the ability of a plant to survive, reproduce and sustain reasonable yields under moderate water stress (Mariot, 1989). Drought tolerance is a quantitative complex trait with low heritability for which appropriate selection criteria is largely absent (Schneider et al., 1997; Blair et al., 2012). Further, drought tolerance is highly influenced by the environment because of which improvement of a crop is difficult through conventional breeding by reducing the gap between the genotype-phenotype (Asfaw et al., 2012). Furthermore, drought stress is accompanied by other abiotic stresses like high temperature and nutrient deficiencies, which further complicate the breeding efforts (Fleury et al., 2010). To overcome this, breeders need to screen a very large number of genotypes and then select the desired ones.
Due to advances in crop genomic approaches, it is now easy to locate genes/QTLs on chromosomes and also their individual effect (techniques of QTL mapping and association mapping), which was a difficult process few decades back. Identification of major genes/ QTLs contributing for drought tolerance in common bean and their introgression in the backgrounds of our choice through marker assisted selection can be proved as a useful strategy for developing drought tolerant genotypes.
3 Identification of QTLs/genes for drought tolerance in common bean: Molecular marker assisted approaches (MMAA)
3.1 Linkage mapping for identification of QTLs
QTL mapping studies conducted to study the genetic control of drought tolerance in common bean confirms that drought tolerance is a complex quantitative trait controlled by large number of genes (Schneider et al., 1997; Blair et al., 2012). In common bean, QTL/genes for drought tolerance have been reported on different chromosomes using diverse parameters like seed yield, yield per plant, 100 seed weight, canopy biomass, pod harvest index (%), pod partitioning index, stem biomass reduction, harvest index, soil plant analysis development (SPAD), leaf chlorophyll reading, canopy temperature depression, number of pods per plant, seeds per pod, days to flowering, days to maturity, and grain filling duration in few earlier studies (Blair et al., 2012; Asfaw et al., 2012).
Mukeshimana and coworkers used the recombinant inbred lines (RILs) population derived from a cross of drought tolerant line SEA5 and drought susceptible line CAL96 cultivar for identification of drought related QTLs/genes in common bean (Mukeshimana et al., 2014). They evaluated this population under drought stress and non-stress conditions for various parameters and finally identified a total of 14 QTLs (drought-related traits) under drought that were consistently mapped in different environments. Asfaw and co-workers used a recombinant inbred lines (RILs) population developed from the Mesoamerican intragene pool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress (Asfaw et al., 2012). They used two approaches for identification of QTLs related to drought tolerant traits, one is the multi-environment mixed model and another is composite interval mapping and identified 9 and 69 QTLs respectively. Phenotypic variation explained by QTLs mapped through composite interval mapping ranged up to 37%, and the most consistent QTL were for SPAD leaf chlorophyll reading and pod partitioning traits. Composite interval mapping for identification of QTLs in recombinant inbred lines (RILs) population derived from a cross between the drought tolerant BAT477 and drought susceptible DOR364 lines of common bean has been used for identification of QTLs for different drought tolerance related traits (Blair et al., 2012). Figure 1, depicts the QTL mapping approach for improvement of low water stress tolerance in crop plants like common bean.


Figure 1 QTL mapping, association mapping and candidate gene (CG) approaches for identification of QTLs/genes for drought tolerance in common bean

3.2 Genome-wide association studies
Linkage disequilibrium (LD) based association mapping (AM), initially used in human genetics, has been suggested as an alternative approach for QTL mapping in crop species. The QTL detection is based on correlating genotype with phenotype in germplasm collections or natural populations. AM offers several advantages over bi-parental linkage mapping which includes: (i) exploitation of all recombination events that have taken place during the evolutionary history of a crop species, resulting in much higher mapping resolution, (ii) less time required in mapping QTL as there is no need to develop a specialized mapping population, rather a natural germplasm collection of a crop species is sufficient, and (iii) a higher number of alleles can be sampled compared to linkage mapping where only two alleles are usually surveyed (Neale and Savolainen, 2004; Breseghello and Sorrells, 2006; Remington et al., 2001). Further QTL mapping does not provide precise information on QTLs; hence LD based AM has been suggested as an alternative approach for QTL mapping in crop species.
Till date there is no available literature that supports the association mapping studies for drought tolerance in common bean. Although, the LD based association mapping has been carried out in common bean for the identification of QTLs/genes for other traits such as common bacterial blight, pod fiber (PF), seeds per pod (SPP), plant type (PT), growth habit (GH), and days to flowering (DF) (Shi et al., 2011; Neml et al., 2014). Keeping this in view, we have started a program on association mapping for discovering/validating genes for drought tolerance. In this connection, we are already evaluating a collection of ~150 common bean genotypes collected from different regions of Jammu & Kashmir, India for different drought tolerance related parameters. Further genetics/genomics studies will be carried out for identifying some novel genes/ QTLs that may address the problem of drought stress in common bean through molecular breeding involving marker-assisted selection (MAS). Figure 1, depicts the association mapping approach for improvement of low water stress tolerance in crop plants like common bean.
4 Marker assisted selection (MAS)
In a well-designed marker assisted breeding program for drought tolerance in common bean, the mapped genes/ QTLs contributing for various drought tolerance traits can be introgressed in desirable background to attain drought tolerance in common bean. In contrast to conventional breeding which takes six backcross generations to yield 99.2 % recurrent parent genome (Allard, 1999), marker assisted selection takes only 2-3 generations to recover most of the genome of recurrent parent along with the gene of interest from donor parent (Tanksley et al., 1989). Figure 2, represents the strategy used in conventional breeding as well as marker assisted selection for transferring the desirable trait in a particular background. MAS also reduces the amount of linkage drag which is an important hindrance affecting the breeding program (Frisch and Melchinger, 1999). As such we could not find any literature, pertaining to MAS for enhancing drought tolerance in common bean. MAS has been used for enhancing other traits in common bean such as common bacterial blight resistance (Boyle and Kelly, 2007; Yu et al., 2000), common mosaic virus resistance (Hegay et al., 2013), common mosaic potyvirus resistance (Miklas et al., 2000). Although MAS is precise and takes lesser time but it is essential to validate and fine map the identified QTLs for drought tolerance and to identify tightly linked markers. Detection of QTL and its validation has to be carried out using large population (>200 individual) across several locations. Also their expression needs to be confirmed in the target/new genetic background. The epigenetic effects are confirmed by using more than one population in parallel to different genetic backgrounds. To identify desirable QTL combinations for use in diverse situations, it is important to know the kind and extent of epistatic interactions. All this can be achieved by the combination of a number of factors like high-throughput precise phenotyping, high throughput genotyping, proper experimental strategy, accurate analysis and liberal funding for smooth conduct of overall research.


Figure 2 Conventional breeding (left side) and marker-assisted selection (MAS) (right side) approaches for introgression of drought tolerant genes in common bean. Conventional breeding needs eight to nine generation and MAS needs four to five generation for introgression of drought tolerant genes in common bean

4.1 Candidate genes for improving drought tolerance in common bean
Candidate genes (CG) are DNA sequences of known biological functions involved in the development or physiology of a trait. They may be structural genes or genes involved in a regulatory or biochemical pathway which affect trait expression (Vinod et al., 2006). A candidate gene hypothesis states that “a significant proportion of the quantitative trait loci (QTL) affecting trait variation are in fact CGs associated with that trait” (Rothschild and Soller, 1997). The CG approach involves choosing the CG, finding primer sequences to amplify the gene, uncovering polymorphism, developing a convenient procedure for large scale genotyping, identifying a population for association studies, carrying out an association study of the CG with trait phenotype and verifying the uncovered associations (Vinod et al., 2006). Till date there is no document supporting the CG approach in common bean, but in other crops like cereals CG approaches have been successfully utilized to determine the genetic nature of some biotic and abiotic stresses (Vinod et al., 2006; Faris et al., 1999; Ramalingam et al., 2003; Zheng et al., 2003). Here we present a list of candidate genes, after an exhaustive search in the public database and an elaborate literature survey for candidate gene products and/or regulatory sequences associated with enhanced drought tolerance (Table 1). These candidate genes can be used to find their association with different traits related to drought tolerance. Figure 1, represents, the CG approach for improvement of low water stress tolerance in crop plants like common bean.


Table 1 List of candidate genes providing drought tolerance in plants

5 Vision and future prospects
In order to mitigate the negative impacts of drought stress in common bean it is very important to develop drought tolerant high yielding varieties. Advances in genomics pave the way to provide resistance for this complex trait. Through these techniques the QTLs/genes associated with drought tolerance can be identified which after validating into different genetic background can be subsequently used for breeding drought tolerant varieties through marker-assisted selection (MAS). Table 2 represents the work done to increase drought tolerance in different crops till date. This information can be useful for developing similar strategies for enhancing low water
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