Tolerance to drought is a quantitative trait, with a complex phenotype, often confounded by plant phenology. Breeding for drought tolerance is further complicated since several types of abiotic stress, such as high temperatures, high irradiance, and nutrient toxicities or deficiencies can challenge crop plants simultaneously. Although marker-assisted selection is now widely deployed in wheat, it has not contributed significantly to cultivar improvement for adaptation to low-yielding environments and breeding has relied largely on direct phenotypic selection for improved performance in these difficult environments. The limited success of the physiological and molecular breeding approaches now suggests that a careful rethink is needed of our strategies in order to understand better and breed for drought tolerance. A research programme for increasing drought tolerance of wheat should tackle the problem in a multi-disciplinary approach, considering interaction between multiple stresses and plant phenology, and integrating the physiological dissection of drought-tolerance traits and the genetic and genomics tools, such as quantitative trait loci (QTL), microarrays, and transgenic crops. In this paper, recent advances in the genetics and genomics of drought tolerance in wheat and barley are reviewed and used as a base for revisiting approaches to analyse drought tolerance in wheat. A strategy is then described where a specific environment is targeted and appropriate germplasm adapted to the chosen environment is selected, based on extensive definition of the morpho-physiological and molecular mechanisms of tolerance of the parents. This information was used to create structured populations and develop models for QTL analysis and positional cloning.

The grain yield of wheat is influenced by genotype, environment and genotype-by-environment interaction. A mapping population consisting of 182 doubled haploid progeny derived from a cross between the southern Australian varieties ‘Trident’ and ‘Molineux’, was used to characterise the interaction of previously mapped grain yield quantitative trait locus (QTL) with specific environmental covariables. Environments (17) used for grain yield assessment were characterised for latitude, rainfall, various temperature-based variables and stripe rust infection severity. The number of days in the growing season in which the maximum temperature exceeded 30°C was identified as the variable with the largest effect on site mean grain yield. However, the greatest QTL-by-environmental covariable interactions were observed with the severity of stripe rust infection. The rust resistance allele at the Lr37/Sr38/Yr17 locus had the greatest positive effect on grain yield when an environment experienced a combination of high-stripe rust infection and cool days. The grain yield QTL, QGyld.agt-4D, showed a very similar QTL-by-environment covariable interaction pattern to the Lr37/Sr38/Yr17 locus, suggesting a possible role in rust resistance or tolerance. Another putative grain yield per se QTL, QGyld.agt-1B, displayed interactions with the quantity of winter and spring rainfall, the number of days in which the maximum temperature exceeded 30°C, and the number of days with a minimum temperature below 10°C. However, no cross-over interaction effect was observed for this locus, and the ‘Molineux’ allele remained associated with higher grain yield in response to all environmental covariables. The results presented here confirm that QGyld.agt-1B may be a prime candidate for marker-assisted selection for improved grain yield and wide adaptation in wheat. The benefit of analysing the interaction of QTL and environmental covariables, such as employed here, is discussed.

Grain yield forms one of the key economic drivers behind a successful wheat (Triticum aestivum L.) cropping enterprise and is consequently a major target for wheat breeding programmes. However, due to its complex nature, little is known regarding the genetic control of grain yield. A doubled-haploid population, comprising 182 individuals, produced from a cross between two cultivars ‘Trident’ and ‘Molineux’, was used to construct a linkage map based largely on microsatellite molecular makers. ‘Trident’ represents a lineage of wheat varieties from southern Australia that has achieved consistently high relative grain yield across a range of environments. In comparison, ‘Molineux’ would be rated as a variety with low to moderate grain yield. The doubled-haploid population was grown from 2002 to 2005 in replicated field experiments at a range of environments across the southern Australian wheat belt. In total, grain yield data were recorded for the population at 18 site-year combinations. Grain yield components were also measured at three of these environments. Many loci previously found to be involved in the control of plant height, rust resistance and ear-emergence were found to influence grain yield and grain yield components in this population. An additional nine QTL, apparently unrelated to these traits, were also associated with grain yield. A QTL associated with grain yield on chromosome 1B, with no significant relationship with plant height, ear-emergence or rust resistance, was detected (LOD ≥2) at eight of the 18 environments. The mean yield, across 18 environments, of individuals carrying the ‘Molineux’ allele at the 1B locus was 4.8% higher than the mean grain yield of those lines carrying the ‘Trident’ allele at this locus. Another QTL identified on chromosome 4D was also associated with overall gain yield at six of the 18 environments. Of the nine grain yield QTL not shown to be associated with plant height, phenology or rust resistance, two were located near QTL associated with grain yield components. A third QTL, associated with grain yield components at each of the environments used for testing, was located on chromosome 7D. However, this QTL was not associated with grain yield at any of the environments. The implications of these findings on marker-assisted selection for grain yield are discussed.

A doubled haploid population constructed from a cross between the South Australian wheat cultivars ‘Trident’ and ‘Molineux’ was grown under winter field conditions, under field conditions over summer and under artificial light both with and without vernalisation. The duration from planting to ear-emergence was recorded and QTL associated with heading date were detected using a previously constructed genetic linkage map. Associations were shown with chromosomal regions syntenous to previously identified photoperiod ( Ppd-B1 ) and vernalisation ( Vrn-A1 ) sensitive loci. Additional QTL associated with time to heading were also identified on chromosomes 1A, 2A, 2B, 6D, 7A and 7B. Comparisons between the genetic associations observed under the different growing conditions allowed the majority of these loci to be classified as having either photoperiod-sensitive, vernalisation-sensitive or earliness per se actions. The identification of a photoperiod-sensitive QTL on chromosome 1A provides evidence for a wheat gene possibly homoeologous to Ppd-H2 previously identified on chromosome 1H of barley. The occurrence of a putative major gene for photoperiod sensitivity observed on chromosome 7A is presented. The combined additive effects at these loci accounted for more than half the phenotypic variance in the duration from planting to ear-emergence in this population. The possible role of these loci on the adaptation of wheat in Australia is discussed.

Improving the end-use quality of wheat is a key target for many breeding programmes. With the exception of the relationship between glutenin alleles and some dough rheological characters, knowledge concerning the genetic control of wheat quality traits is somewhat limited. A doubled haploid population produced from a cross between two Australian cultivars 'Trident' and 'Molineux' has been used to construct a linkage map based largely on microsatellite molecular makers. 'Molineux' is superior to 'Trident' for a number of milling, dough rheology and baking quality characteristics, although by international standards 'Trident' would still be regarded as possessing moderately good end-use quality. This population was therefore deemed useful for investigation of wheat end-use quality. A number of significant QTL identified for dough rheological traits mapped to HMW and LMW glutenin loci on chromosomes 1A and 1B. However, QTL associated with dough strength and loaf volume were also identified on chromosome 2A and a significant QTL associated with loaf volume and crumb quality was identified on chromosome 3A. A QTL for flour protein content and milling yield was identified on chromosome 6A and a QTL associated with flour colour reported previously on chromosome 7B was confirmed in this population. The detection of loci affecting dough strength, loaf volume and flour protein content may provide fresh opportunities for the application of marker-assisted selection to improve bread-making quality.

A genetic linkage map consisting of 211 molecular markers has been generated using a doubled- haploid population derived from a cross between the Australian barley variety Clipper and the Algerian landrace Sahara 3771. The map was used in subsequent trait mapping studies to locate the genes conferring boron tolerance and cereal cyst nematode resistance from Sahara 3371 and to map several plant type and developmental genes. Closely linked markers to the trait loci have been identified and are now being widely implemented in Australian breeding programs.

The barley mapping population Mundah × Keel was devised to characterise and map chromosome regions associated with improved growth and grain yield on sandy soils of low fertility. A low level of polymorphism between the parents proved problematic for the construction of a detailed linkage map of this population. Despite this, significant quantitative trait loci (QTLs) for specific traits were detected, providing an insight into the probable chromosome regions associated with sand adaptation. In addition, this population is being employed to identify loci associated with the expression of traits for moisture stress and frost tolerance, and resistance to spot form of net blotch and leaf scald.

YLM, a codominant polymerase chain reaction (PCR) marker linked to Yd2 , could substantially improve the precision and efficiency of barley yellow dwarf virus (BYDV) resistance breeding. The aim of this study was to assess the effectiveness of YLM in a marker-assisted introgression programme and to quantify associations between the presence of Yd2 and other agronomic and quality traits. The Yd2 gene was introgressed into a BYDV-susceptible background through two cycles of marker-assisted backcrossing. BC2 F-2 -derived lines, either carrying or not carrying the YLM allele associated with resistance, were compared in the presence and absence of BYDV. The YLM marker was shown to be effective in the introgression of Yd2 . Lines carrying the YLM allele associated with resistance produced significantly fewer leaf symptoms and showed a reduction in yield loss when infected with BYDV. There were no deleterious effects associated with the introgression of Yd2 on grain yield, grain size or malting quality. The implications of marker-assisted selection for Yd2 on barley improvement are discussed.

The usefulness of marker assisted selection (MAS) to improve diastatic power was demonstrated by selecting quantitative trait loci (QTLs) and structural gene alleles involved in enhanced diastatic power and activity of its component hydrolytic enzymes from Alexis, Amagi Nijo, Harrington, Haruna Nijo, and Sloop. Six unmapped breeders' populations involving these donor sources of malting quality were used for MAS. For each population, individual lines were pooled into classes separated on the basis of either the presence or absence of malting quality parent marker alleles at each of 9 identified loci (QTLs or structural genes). Diastatic power, β-amylase, and α-amylase activities were determined for each line, and used to compare alternative marker allele class means. Lines carrying malting parent marker alleles at a chromosome 5H locus abg463 were associated with 21–44% higher α-amylase activity levels, depending on the cross. The malting parent alleles at the chromosome 4H Bmy1 locus were associated with increased diastatic power and β-amylase activity. A simple PCR marker detecting the Bmy1 locus was found to be effective in screening for improved diastatic power, β-amylase activity, and thermostability. Lines carrying malting parent alleles at the chromosome 2H Bmy2 locus produced differences in diastatic power and β-amylase activity that, after adjusting for the correlated effect of malt protein, became non-significant. The Alexis allele of the chromosome 1H EBmac501 locus was associated with significant differences in all traits for a population carrying this source. The implication of these results to the improvement of diastatic power through MAS is discussed.

A map for the barley doubled haploid population Amagi Nijo × WI2585 was constructed to examine manganese efficiency derived from Amagi Nijo. Manganese efficiency conferred by the previously identified locus Mel1 was validated. No other loci contributing to manganese efficiency were identified, possibly because of poor maker coverage in some regions. The map was additionally used to look for loci contributing to some aspects of malting quality. A locus on 2HL was found to be associated with malt extract, and 2 loci on 4HL and 5H, respectively, were found to be associated with diastatic power.

Malt extract represents the soluble material extracted from malt during the mashing process of barley. The measurement of malt extract is used by maltsters and brewers to assess the quality of the barley they are purchasing and is therefore one of the most important parameters used by breeders to assess the quality of new barley varieties before release. This paper identifies and investigates several regions (quantitative trait loci, QTLs) found to be associated with malt extract and discusses the uses of these regions for marker assisted selection (MAS).Eight regions of the barley genome were found to be associated with malt extract in 3 mapping populations. Five regions were found in the Sloop/Alexis and Sloop-sib/Alexis mapping populations on chromosomes 1H, 2H, 3H, 4H, and 5H. Two regions were found in the Chebec/Harrington population on chromosomes 1H and 5H and a single region was found on chromosome 2H in the Galleon/Haruna Nijo mapping population. Markers from 6 of these regions were investigated using several breeding populations with a high malt extract variety as a parent. The 'allele' from the high malt extract parent was found to be associated with a significant increase in malt extract in 4 regions, 2 regions on chromosome 2H and 2 regions on chromosome 5H.

Estimation of genetic diversity in a crop species can assist in the evaluation of germplasm collections as potential gene pools to improve the performance of cultivars. Molecular markers offer the opportunity to assess variation at the DNA sequence level and, as such, have become an important tool in plant genetics (Gebhardt et al.,1991). Restriction fragment length polymorphisms (RFLPs) have led to the integration of DNA markers into molecular genetic studies and plant breeding programmes, and have been used extensively in investigations of genetic diveristy in both wild and cultivated barley (Hordeum spp.) (Graner et al., 1994; Melchinger et al., 1994). RFLPs are co-dominant and locus-specific markers that are unequalled for many applications. In particular, they are well suited for the construction of linkage maps (Graner et al., 1991; Heun et al., 1991) and, because of their locus specificity, allow for synteny studies (Tanksley et al., 1992; Ahn and Tanksley, 1993). However, the procedures involving RFLPs are labour intensive, expensive and few loci are detected per assay. Recently a number of locus-specific PCR-based markers such as sequencetagged sites (Vanichanon et al., 2000) and microsatellites (simple sequence repeats) (Litt and Luty, 1989) have been developed. These marker systems are rapid, technically simple and require only small amounts of DNA. Microsatellites have been used with some success in cereals (Saghai Maroof et al., 1994; Roder et al., 1995) and offer the potential as co-dominant PCR-based markers with uniform genome coverage. Microsatellites show a high level of polymorphism and are particularly suited to identifying a large number of alleles at a specific locus. However, the development of locus-specific markers is time-consuming, expensive and relatively few loci are detected per assay.

Scald (Rhynchosporium secalis) is one of the most damaging leaf and stem diseases of barley grown in southern Australia. The development of resistant cultivars is the most effective means of controlling scald. However, the highly variable nature of the scald pathogen has often resulted in resistance conferred by single major genes being rendered ineffective. Breeding and selection for non-race specific, durable resistance, or the adoption of major gene deployment strategies such as gene pyramiding, could largely overcome this problem. Four cultivars of barley (Guardian, Halcyon, Sultan, Waveney) were evaluated as potential sources of scald resistance, suitable for gene introgression and pyramiding programs in southern Australia. Each of these prospective donor parents was backcrossed to the susceptible recurrent parent Sloop through one cycle of backcrossing. All 4 cultivars were resistant to scald isolates common in southern Australia. No factors, either deleterious or beneficial to grain yield, were associated with scald resistance genes from Guardian, Halcyon, and Waveney. Scald resistance genes carried by Sultan were found to be associated with lower grain yield. Both resistant and susceptible first backcross lines derived from Guardian produced a lower proportion of plump grain than the recurrent parent Sloop. A greater number of backcrosses and large population size may be required to successfully introgress scald resistance genes from Sultan and Guardian into germplasm adapted to southern Australian conditions. The development of molecular markers linked to resistance genes in these parents will allow efficient introgression and pyramiding of scald resistance genes from Waveney, Halcyon, and Sultan.