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QTLs and genes for tolerance to abiotic stress in cereals

Cereal Genomics, Page: 253-315
2005
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  • Citations
    33
    • Citation Indexes
      33
  • Captures
    67

Book Chapter Description

The improvements in crops yield achieved during the past decades are now limited by water availability (Passioura, 2002), which is considered to be the most challenging environmental stress. The release of cultivars characterized by increased tolerance to drought and other abiotic stresses will largely depend on our ability to tailor crops genomes accordingly. Even though some of its aspects may remain unfamiliar, the genomic approach, when appropriately intersected with other relevant disciplines, will positively impact our understanding of plant metabolism and, eventually, our breeding activities (Miflin, 2000; Tuberosa et al., 2002a; Morandini and Salamini, 2003). Genomics interfaced with crop modelling approaches provides a means to help dissecting G × E interactions and to resolve the hierarchical complexity underlying yield into traits that might be under simpler genetic control (Asseng et al., 2002; Asseng et al., 2003; Reymond et al., 2003; Tardieu, 2003). Essentially, models are constructed as decision-making tools for management but may be of use in detecting prospective traits for selection within a breeding programme. Using sound information on crop physiology and empirical relationships, these models can simulate crops performance, including G × E interactions (Slafer, 2003). Specific models integrating different level of complexity to predict biomass and yield as a function of environmental variables are available (Asseng et al., 2002; Asseng et al., 2003). Such models can integrate information on the genetic basis of yield, which is included in the form of genetic coefficients. In future, it may be possible to incorporate in these models information concerning the action of single QTLs (Reymond et al., 2003; Tardieu, 2003) in order to optimize MAS programmes. Further opportunities for collaboration between modellers and geneticists in ideotype breeding for high crop yield have recently been illustrated (Yin et al., 2003). As to the traits to be dissected through QTL analysis and other molecular approaches in programmes aimed at improving drought tolerance, photosynthetic efficiency (for an example in maize, see Jeanneau et al., 2003) and root architecture are likely to receive greater attention. These traits cannot be easily manipulated through conventional approaches. Other traits may also provide meaningful contributions, should it be possible to devise appropriate screening techniques and if sources of genetic variability suitable for QTL discovery and cloning are available. One example is offered by mycorrhizal colonization, a complex trait whose manipulation may influence water use and nutrient uptake of crops. Although QTLs for mycorrhizal responsiveness have been reported in maize (Kaeppler et al., 2000), limited information is available on the genetic control of the interaction between mycorrhiza and crops roots (Barker et al., 2002). On the molecular side, extensive EST databases and unigene sets derived from cDNA libraries of different tissues and organs, involved in stress tolerance, are excellent sources for building functional maps that in some cases could help in the identification of plausible candidates for QTLs (Bohnert and Cushman, 2000; Ishimaru et al., 2001c). The release of the entire genome sequences of Arabidopsis (Bevan et al., 2001) and rice (Goff et al., 2002) has greatly increased the level of resolution of comparative mapping studies exploiting syntenic relationships. The application of this approach to rice and related cereals has revealed a more complex picture (Goff et al., 2002) than that previously reported through the coarser comparative analysis based on the map position of common RFLP markers (Gale and Devos, 1998). However, accumulating evidence for the abundance of chromosomal rearrangements and the recent demonstration on the lack of microcollinearity among cereals (Sorrells et al., 2003) may discourage the map-based cloning approach for isolation of loci controlling important quantitative traits. From a strictly organizational standpoint, the degree of genome rearrangements that have occurred in different species after diverging from a common ancestor proportionally reduce the possibility for the successful exploitation of synteny among genomes of distantly related species, as is the case with Arabidopsis and cereals (Paterson et al., 1996; Gale and Devos, 1998; Van Buuren et al., 2002; Bowers et al., 2003). Thus, in practical terms, relying extensively on a phylogenetically distant species as a model (e.g., Arabidopsis as a model for cereals) may have, on a case-bycase basis, its own shortcomings both from a genomic and physiological standpoint. The future availability of sequence information for whole genomes will greatly enhance the accuracy of gene/QTL discovery based on LD approaches. When sequencing information is unavailable, haplotype analysis of a set of populations can also provide useful information for QTL discovery (Jansen et al., 2003). Physical maps of contiged genomic clones (e.g., BACs) will allow for the mapping of any sequence, even if no polymorphism is available, thus streamlining the process of building highly saturated maps, an essential prerequisite to positional cloning of QTLs. More importantly, polymorphisms at ORFs will allow us to identify sequence variation with functional relevance at the phenotypic level and to validate candidate genes for tolerance to abiotic stress. Assigning a function to genes and validating their roles will be facilitated by a number of experimental approaches, such as RNA-mediated interference (Cogoni and Macino, 2000), forward and reverse mutagenesis (Maggio et al., 2001), including homologous recombination (Hanin and Paszkowski, 2003) and TILLING (Targeting Induced Local Lesions IN Genomes; Till et al., 2003). Model species other than rice may also play an increasingly important role for the discovery of genes/QTLs that may help in improving tolerance of cereals to abiotic stresses. This may be particularly true with model species like Arabidopsis, which, as compared to cereals, is comparatively easy to phenotype in large numbers. The small size and very short life cycle, the small genome, the availability of the annotated genome sequence, and a vast number of mutants coupled with a very efficient transformation system, all contribute to make Arabidopsis a particularly attractive species for the identification of QTLs and genes regulating the response to abiotic stress. The work carried out in Arabidopsis will be of particular value in elucidating the molecular mechanisms involved in the perception of abiotic stress as well as in the signal transduction pathway leading to the activation of the suite of genes involved in the adaptive response to stress. Surprisingly, so far only limited work has been carried out in Arabidopsis to identify QTLs for tolerance to abiotic stresses. Recently, the discovery of a number of genes (e.g., DREB, Jaglo-Ottosen et al., 1998; Kasuga et al., 1999) quickly triggered by abiotic stresses and encoding for transcription factors controlling the expression of drought-responsive genes has sparked great interest for investigating their role in crops. DREB homologues have been identified in maize (van Buuren et al., 2002) and wheat (Vagujfalvi et al., 2003), where a DREB gene has been shown to be a strong candidate for a QTL conferring freezing tolerance. Future efforts to improve tolerance to abiotic stress should emphasize allele mining in a germplasm context broader than that presently explored, which has been mainly limited to elite materials. The exploitation of a wider genetic basis will provide additional opportunities to identify rare alleles capable of improving crop adaptation to harsh environments and increasing their sustainability. In this connection, the utilization of the advanced-backcross QTL analysis (ABQA) approach will be instrumental for identifying valuable QTL alleles in wild accessions and for introgressing such alleles in a reasonably short time into elite germplam Additionally, progenies obtained from subsequent intercrossings of multiparental mating schemes including highly contrasted genotypes will improve our capacity to identify and resolve QTLs. As compared to the biparental crosses that are traditionally deployed for QTL discovery, multiparental mating schemes explore a wider allelic diversity and a larger number of unique recombination events (Li et al., 2001; Korstanje and Paigen; Mott and Flint, 2002), thus providing increased opportunities to unveil at a much finer genetic resolution the presence of a QTL. Although setting up and implementing such multiparental crossing schemes is a costly undertaking, the benefits expected from this approach certainly make this a worthy investment, particularly in a long-term perspective.

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