Genetic Variability

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9.2.1.1 The Breeding Program Gene Pool

The genetic constitution of wheat is both tetraploid (i.e., containing four sets of chromosomes, as in the case of Triticum turgidum or durum wheat) and hexaploid (i.e., containing six sets of chromosomes, as in the case of Triticum aestivum L. or bread wheat), and this presents both opportunities and difficulties for its improvement. Durum wheat is a fusion of two diploid species and its genetic constitution is denoted as AABB, whereas bread wheat originated from a cross between tetra-ploid AABB species and a third diploid species to produce a hexaploid AABBDD constitution.

Diploid species (with two sets of chromosomes) such as rice and barley carry less diversity both within the cultivated gene pool and among the ancestral species, but they are more easily manipulated genetically. Once the TPE has been defined the breeder must then identify genetic variability conferring improved adaptation to this dominant stress pattern. In some instances there may be more than a single dominant stress in the target region. The first exercise is to identify those materials within the breeding program gene pool with superior performance within the TPE; these are the backbone of the crossing strategy. There are a number of excellent options available for the analysis of MET data, including but not restricted to cumulative cluster analysis that estimates the association among sites and genotypes using unbalanced MET data (DeLacy et al. 1996) and the Shifted Multiplicative Model and Sites Regression model for the analysis of balanced data (Crossa et al. 1993).

9.2.1.2 Landrace Cultivars

The Green Revolution resulted in massive increases in wheat and rice production globally which to some extent narrowed genetic variability as farmers adopted high yielding, short-statured cultivars in most production environments (Warburton et al. 2006). However, farmers in marginal areas did not adopt these modern cultivars at the same rate (Byerlee and Moya 1993). This reduced adoption reflects the risk-averse nature of the farmers in these marginal cropping lands. The higher moisture and temperature stresses that are characteristic of these environments have also lessened the impact of the high yielding, resource responsive germplasm. Landrace collections existing either in situ or in gene banks around the world present a potential source of genetic variability for the improvement of stress tolerance. The first step in their utilization is to screen available collections for response to both drought and heat stress typical of the TPE. However, GIS (geographic information system) tools have improved the efficiency with which this can be done. Instead of screening thousands of lines, information on the geographic location and associated environmental conditions under which the germplasm was collected can be used to identify materials likely to adapt to the TPE (Greene et al. 1999).

Landraces have been found to be more water-use-efficient, extracting water from deeper in the soil profile than modern cultivars and possessing higher soluble stem carbohydrates (Reynolds et al. 2007a, Reynolds and Trethowan 2007). They are also more heat tolerant, characterized by higher leaf chlorophyll and higher stomatal conductance (Hede et al. 1999; Skovmand et al. 2001). One might argue that the stress tolerance that is present in the landraces is the same as that found in modern cultivars as the modern materials were derived from lan-draces. However, genotyping studies show that stress tolerant landraces are generally genetically distant from the more tolerant modern wheats (Moghaddam et al. 2005; Reynolds et al. 2007b). Similarly, in a study of landrace diversity in the backgrounds of 143 commercial rice cultivars in Brazil, it was found that only 14 ancient cultivars contributed 70 percent of the important genes (Guimaraes 2002). Clearly, there is significant scope to broaden the genetic base of important crops using landraces.

9.2.1.3 Synthetic Hexaploid Wheat

As bread wheat is hexaploid, the opportunity exists to exploit variability among its progenitor species. Bread wheat likely arose from a cross between Triticum dicoc-com and Aegilops tauschii following spontaneous chromosome doubling some 8,000-9,000 years ago. It is likely that very few accessions of both species were involved in this initial hybridization and subsequent evolution of wheat (Feldman 2001). Primary synthetic wheat can be generated in the laboratory from crosses between tetraploid wheat, either modern durum wheat (T durum L.) or T. dicoccum, and Aegilops tauschii. These new hexaploids are agronomically poor, difficult to thresh and have poor end-use quality but carry unique genetic diversity. The resultant primaries have been screened for performance in the field under moisture deficit and high temperature stress and useful genetic variability found (Villareal and Mujeeb-Kazi 1999; Yang et al. 2002).

9.2.1.4 Alien Introgression

While the materials discussed so far have at least one genome in common with hexaploid wheat, significant genetic variation exists in the more distantly related tertiary gene pool (Trethowan and Mujeeb-Kazi 2008). The genomes of these materials do not recombine easily with wheat and are therefore difficult to exploit. However, alien chromosome segments have been introduced into wheat using the ph mutant which promotes their pairing (Sears 1976; Gupta et al. 2005). While most of the alien gene introductions todate target disease resistance, there has been useful variability reported for drought and heat tolerance. The replacement of the long arm of chromosome 1B with the short arm of rye chromosome 1R in wheat is probably the best example of alien introgression for both disease resistance and stress tolerance (Rajaram et al. 1983; Villareal et al. 1995). This translocation was found in the winter wheat cultivar Kavkaz and has been shown to increase root vigour and water up-take (Ehdaie et al. 2003). These distant relatives of wheat are a rich source of genetic variability.

9.2.1.5 Characters Important in Conservation Agriculture

As adoption of improved management practices around the world increases, crop cultivars better adapted to water and resource conserving farming practices will be important in improving the overall productivity of the farming system. Of importance to the breeder is the existence of a genotype x tillage practice interaction, as this will indicate whether or not breeding for specific adaptation to conservation agriculture is possible. There is evidence of genotype x tillage practice interactions in wheat for yield and product quality (Gutierrez 2006). However, evidence is conflicting across different crops with non-significant interactions reported for barley (Ullrich and Muir 1986), sorghum (Francis et al. 1986), rice (Melo et al. 2005) and soybean (Elmore 1990) and both significant and non-significant interactions reported for maize (Brakke et al. 1983; Newhouse 1985). The lack of significant interactions likely reflects the small number of genotypes examined in these studies and the fact that all the materials tested were developed under conventional or complete tillage.

It is useful to the breeder if genotype response to conservation agriculture can be broken down into individual traits for selection. Traits considered important in conferring adaptation to conservation agriculture include the length of the emerging shoot or coleoptile (Rebetzke et al. 2007; Trethowan et al. 2001a), coleoptile thickness (Rebetzke et al. 2004), emergence from depth (Trethowan et al. 2005), seedling vigor (Liang and Richards 1999), rate of stubble decomposition (Joshi et al. 2007), root depth (Reynolds and Trethowan 2007), allelopathy (Bertholdsson 2005), N-use-efficiency (Ginkel et al. 2001), disease resistance (Trethowan et al. 2005) and seedling temperature tolerance (Boubaker and Yamada 1991).

9.2.1.6 Root Disease Resistance

No discussion of available genetic variability to improve stress tolerance in wheat is complete without considering resistance to root diseases. In farming systems prone to root rots and nematodes, disease resistance can improve water-use-efficiency by maintaining a healthy root system (Govaerts et al. 2007). The inheritance of these traits is relatively simple, compared to drought and heat response per se, and resistance is therefore more easily manipulated.

Screening plants for resistance to these diseases in the field or green house is difficult and there are many misclassifications of resistance. These escapes or mis-classifications result in a relatively low heritability or low repeatability of the screening procedures. However, molecular markers linked to the genes that confer resistance are available for a number of important traits and can be used to improve the efficiency of gene introduction (Okogbenin et al. 2007).

9.2.1.7 Nutritional Quality

Wheat is one of the world's most important sources of food. It is made into products as diverse as leavened bread, flat bread, steamed bread, noodles, biscuits and cakes and wheat starch is used as an additive in many processed foods. While both processing and nutritional quality is under genetic control, the expression of quality is greatly influenced by the environment in which the crop is grown. The environment includes soil type and fertility, crop management practices and the prevailing weather conditions during crop development.

Micronutrient deficiency in humans, which is caused by inadequate intake of elements such as zinc and iron, impairs normal development and increases the incidence of disease, particularly in children of developing countries (Ezzati et al. 2002; Kennedy et al. 2002; Welch and Graham 2004). Micronutrients are concentrated mainly in the seed coat and embryo of the wheat grain and only small amounts are present in the starchy endosperm (Ozturk et al. 2006), so yield increases alone will not substantially increase micronutrient intake. Refined flours, generated by removing the bran and germ fractions, contain substantially lower concentrations of micro-nutrients than wholemeal flours or grain. There is a trend towards increased consumption of manufactured products developed from refined flour in some developing countries (Pingali 2007). However, these changes are often associated with increasing affluence and the impact of this trend on human nutrition will to some extent be mitigated by improved access to other more nutritional foods.

The elevated temperatures and CO2 and drier conditions predicted in some regions are unlikely to impact upon the nutritional status of the major crops (see also Chapter 7). In some instances the lower crop yields from these more hostile growing conditions may increase micronutrient concentrations as the ratio of endosperm to seed coat will reduce. However, the negative impact of significantly lower productivity will dwarf any perceived benefit. Variation in micronutrient concentration is present in various crop species (Reddy et al. 2005; Menkir 2008;

Murphy et al. 2008). The Fe and Zn concentration in wheat seed appears to be quantitatively controlled (Trethowan et al. 2005; Trethowan 2007) and molecular markers linked to a gene of major effect for Zn and Fe concentration have been reported (Uauy et al. 2006). Nevertheless, as micronutrient concentrations are higher in the seed coat compared to endosperm, improving the micronutrient concentration of the endosperm will be a key objective. Unfortunately, no substantial variation for endosperm Fe and Zn concentration is reported. In these instances it is likely that transgenic approaches will provide the only viable avenue for improving both yield and nutritional status.

Fungal mycotoxins can reduce the nutritional status of foods and in significant concentrations food can become dangerous to ingest. The production of toxins on cereal grain by fungi such as Aspergillus and Fusarium may increase in some regions as these organisms thrive at elevated temperatures and in conditions of plant stress (FAO 2001). There is genetic variation for resistance to these diseases in the wheat gene pool and Fusarium resistant wheat cultivars have been developed and deployed (Mergoum et al. 2006). However, the expression of resistance is generally incomplete and the quantitative nature of inheritance and low heritability makes breeding difficult (Jiang et al. 2007).

9.2.1.8 Product and Processing Quality

Most grain crops are consumed following processing of some sort. Small and shriveled wheat grains called screenings have reduced endosperm development, contain a higher proportion of bran and are more expensive to mill compared to normal grain. In developed countries grain with high levels of screenings is normally not used for food production but fed to animals instead. Screenings tend to increase when crops are subjected to water and/or temperature stress. An association between seed size and the incidence of screenings has been reported and there is scope to increase the seed size of wheat (Sharma and Anderson 2004).

Water and temperature stress can change the chemical composition of grain and its subsequent processing and product quality. In the context of food security, these changes are relatively minor as they largely affect the aesthetic appeal and cost of processing. However, in more advanced economies these affects take on greater significance and breeding for improved end-use quality under stress is important.

Water and temperature stress will alter the protein content and composition of wheat grain and subsequent end-use quality. High temperature is known to negatively impact gluten quality (Blumenthal et al. 1994) with subsequent effects on dough water absorption and the product quality of breads, biscuits, noodles and pasta. Proteins that have upregulated expression upon exposure to heat shock, and are thought to be associated with stability of quality when elevated temperatures occur during grain development, have been identified and partially characterized (Skylas et al. 2002). It appears that there is scope to breed for enhanced heat tolerance by selection for alleles of these proteins that are upregulated after heat stress.

Increased drought stress also enhances the yellow color of yellow alkaline noodles (commonly consumed in eastern Asia) but decreases their initial brightness, and can increase the grain hardness of soft-grained biscuit wheat (Guttieri et al. 2001; Weightman et al. 2008). There is considerable variation in the wheat gene pool for grain protein content and quality, grain hardness, strength and extensibility of dough and starch quality. However, the optimal balance of these properties and the genes that control their expression, in an increasingly variable and hostile growing environment must be determined for the breeder's TPE if realistic selection targets are to be set.

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