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Yellow spot (syn. tan spot), caused by , is an important foliar disease of wheat in Australia that causes losses exceeding 50 % when conditions are favourable for disease development. Although good progress has been made internationally to understand yellow spot resistance, relatively few resistance genes have been identified and mapped in Australian germplasm and only one ( on chromosome 5BL) is in general and known use in Australian breeding programs. Although is an important yellow spot resistance gene, it doesn’t explain the full spectrum of resistance and there is a significant opportunity to enhance expression of yellow spot resistance through identification of resistance factors other than . Six doubled haploid (DH) mapping populations (five of which were fixed for ) were screened for yellow spot resistance at the seedling/tillering and adult plant stages at the Department of Agriculture and Food, Western Australia (DAFWA) and the Department of Environment and Primary Industries Victoria (DEPIVic) from 2009 to 2012. Four of the above populations were screened at the Department of Agriculture, Fisheries and Forestry Queensland (DAFFQ). Frequency distribution of individuals within each population for various levels of yellow spot resistance was continuous indicating that resistance is conditioned by several genes with partial effects. A few lines within each population consistently showed high levels of resistance probably resulting from a combination of several genes with additive effects. Nine new loci for yellow spot resistance were mapped by the Australian Wheat and Barley Molecular Marker Program (AWBMMP) at the University of Adelaide on chromosomes 1AS, 2AS, 5AS, 5AL, 4B, 6BS, 7BL, 2D and 7D in five of the six populations phenotyped so far. High LOD scores of 9–11 have been obtained for some of the QTL with a percentage disease reduction of 24–42 %. Efforts are now focused on identifying additional yellow spot resistance genes using newly developed populations and rapid phenotyping methods and developing a series of fixed lines, each carrying yellow spot resistance genes from various sources, in elite Australian backgrounds. These materials will provide proof-of-concept for achieving better resistance by pyramiding resistance genes, and they should be directly useful as parents for wheat breeding.

Next Generation Sequencing (NGS) is providing new methodologies to improve and complement traditional genetic approaches. These strategies, collectively termed NGS-enabled genetics, consist of identifying variation in bulks of plants that have been assembled based on a specific phenotype of interest. We examined NGS-enabled genetics in hexaploid wheat by using near isogenic lines (NIL) differing across a specific disease resistance locus. RNA-Seq of NILs allowed the identification of SNPs across this locus and helped distinguish allelic SNPs from homoeologous variants. F bulks were assembled based on opposing disease resistance phenotypes and the frequency of the informative allelic SNPs was examined across bulks using RNA-Seq. Variants enriched in the corresponding bulks are expected to be most closely linked to the phenotype of interest and were prioritized for validation. Recent advances in cereal genomics in the form of wheat gene models, sequenced diploid progenitors, and the advances in the Chromosome-based Survey Sequencing Project enabled us to develop a pipeline to automatically design SNP-based markers. These high-throughput assays were used to genotype the original individuals used to assemble the bulks and to generate a genetic map across the target locus. Linked markers are now being incorporated into marker assisted selection programs by breeders.

A better knowledge of the genetic basis of the mechanisms underlying the adaptive response to drought will be instrumental to more effectively deploy marker-assisted selection (MAS) to improve yield potential while optimizing water-use efficiency. Genomics approaches allow us to identify and clone the genes and QTLs that underlie the adaptive response of durum wheat to drought. Linkage and association mapping have allowed us to identify QTLs for traits that influence drought resistance and yield in durum and bread wheat. Once major genes and QTLs that affect yield under drought conditions are identified, their cloning provides a more direct path for mining and manipulating beneficial alleles. While QTL analysis and cloning addressing natural variation will increasingly shed light on mechanisms of adaptation to drought and other adverse conditions, more emphasis on approaches relying on resequencing, candidate gene identification, ‘omics’ platforms and reverse genetics will accelerate the pace of gene/QTL discovery. Genomic selection provides a valuable option to improve wheat performance under drought conditions without prior knowledge of the relevant QTLs. Modeling crop growth and yield based on the effects of major QTLs offers an additional opportunity to leverage genomics information. Although it is expected that genomics-assisted breeding will enhance the pace of durum wheat improvement, major limiting factors are how to (i) phenotype genetic materials in an accurate, relevant and high-throughput fashion and (ii) more effectively translate the deluge of molecular and phenotypic data into improved cultivars. A multidisciplinary effort will be instrumental to meet these challenges.

Despite promising superior performance, hybrid wheat currently occupies only a niche sector in commercial wheat production. However, with the recent development of practicable hybrid seed production systems, a switch from line to hybrid breeding in wheat seems realistic. Here, we discuss what consequence this may have for wheat breeding programs and provide suggestions on how quantitative genetic analysis can contribute to design optimal selection strategies.

An increase in cereal production is required if we are to support a world population of more than nine billion people expected in 2060. For this purpose, plant breeding will serve as a key technology as it did during the Green Revolution of the 1960s. However, the changing climate and decrease in agricultural resources are new challenges that will require consideration. We developed common and durum wheat populations expressing the intraspecific diversity of wild species. We collectively named these populations ‘multiple derivative lines’, and specifically ‘multiple synthetic derivatives’ (MSD) in the case of common wheat. The germplasm in the MSD population shows diverse morphology in regular genetic background enabling accurate selection of desired genotypes/phenotypes associated with abiotic stress tolerance. Accordingly, such plant materials can subsequently be used for various breeding purposes. Abiotic tolerance, especially drought tolerance, is largely determined by the interaction between genotype and environment, making drought-tolerance breeding difficult. Wild species, even the self-pollinating ones, possess high diversity which allows them to adapt to the diverse and fluctuating environments. Accordingly, during wheat breeding for abiotic tolerance, it may be better to consider using diverse populations such as the MSD.

High temperatures pose a serious threat to productivity maintenance and enhancement in wheat. A strategy that has come forward in the CIMMYT breeding program is the development of high yielding early maturing lines that are adapted to high temperature stress especially for South Asia. The high temperature stress in South Asia is classified into terminal high temperature stress where the high temperatures stress occurs during grain filling stages, and continual high temperature stress, where high temperature persists across the wheat growing season. The new high yielding, early maturing and heat tolerant CIMMYT wheat lines were evaluated for grain yield and adaptation across diverse locations in South Asia and Mexico. Trials were conducted for three consecutive years 2009–2010, 2010–2011, and 2011–2012. The results suggest that CIMMYT lines with high yields and early maturity, selected under normal and late sown condition in Cd. Obregon, Mexico, have the potential to adapt and outperform normal maturing check varieties under terminal and continual high temperature stress in South Asia. Earliness favored the plants to escape terminal high temperature stress and also promoted an efficient utilization of available resources under continual high temperature stress to achieve higher grain yield. The simultaneous enhancement of grain yield potential and heat stress tolerance of early maturing wheat lines is likely to be beneficial in enhancing productivity under high temperature stress across South Asia.

Exposure of plants to low, nonfreezing temperatures leads to an increase in freezing tolerance, and this adaptive process, called cold acclimation, involves drastic physiological, biochemical and metabolic changes. Most of these alterations are regulated through changes in gene expression. One of the mechanisms behind development of freezing tolerance is induction of the (cold-responsive)/ (late-embryogenesis-abundant) gene family (Thomashow 1999). In common wheat, major loci controlling freezing tolerance ( and ) have been assigned to the long arm of group five chromosomes (Galiba et al. 1995; Snape et al. 1997). is coincident with a cluster of genes encoding C-repeat binding factors (CBFs) in wheat and barley (Miller et al. 2006; Francia et al. 2007), which directly induce the downstream / gene expression during cold acclimation (Takumi et al. 2008). In expression quantitative trait locus (eQTL) analysis of / and genes, four eQTLs controlling cold-responsive genes were found, and the major eQTL with the greatest effect was located on the long arm of chromosome 5A (Motomura et al. 2013). The 5AL eQTL region, which plays important roles in development of freezing tolerance in common wheat (Motomura et al. 2013), coincides with a region homoeologous to a frost-tolerance locus () reported as a cluster region in einkorn wheat (Vágújfalvi et al. 2003; Miller et al. 2006). Allelic differences at might be a major cause of cultivar differences in extent of freezing tolerance in common wheat (Motomura et al. 2013). It was recently reported that large deletions in the cluster at significantly reduced frost tolerance in tetraploid and hexaploid wheat (Pearce et al. 2013). In barley, two QTLs for low-temperature (LT) tolerance, and , are found on the long arm of chromosome 5H (Francia et al. 2004), and the / genotype affects both the expression of genes at and LT tolerance (Stockinger et al. 2007; Chen et al. 2009). Thus, the barley / and regions function to develop freezing tolerance through / gene expression during cold acclimation. In contrast to barley, the functions of / and / in regulation of cold-responsive gene expression in common wheat remain unclear.

High temperatures (HTs) during grain filling adversely impact grain yield and its end-use quality for wheat. HTs strongly reduce the expression of major enzymes associated with starch synthesis, whereas enzymes associated with defence against stress and protein folding are dramatically increased. Using proteomics tools, the effect of different temperature regimes on storage protein (SP) accumulation was investigated. HT significantly decreased the quantity per grain of individual gliadin and glutenin spots, but at maturity the ratio of gliadin to glutenin was not modified. HT during grain filling strongly reduced starch accumulation, modified the size distribution of starch granules, and to a much lesser extent, reduced the quantity of total proteins per grain. The aggregation and polymerisation of SP was investigated using asymmetric flow field flow fractionation. Previous analyses of near-isogenic hard/soft lines showed that characteristics of glutenin polymers were significantly influenced by puroindoline alleles ( and -), and proteomics analysis showed that a typical mechanism of unfolded protein response occurs in ER, resulting from stress during protein accumulation. Effects of alleles encoding puroindolines, HMW-GS and LMW-GS, and temperature during grain development on glutenin polymer characteristics, dough rheological properties, and bread loaf volume were investigated for 40 cultivars grown in six environments in France. A difference of only 2 °C in average daily air temperature between locations during the grain-filling period resulted in increased molecular mass of the glutenin polymers and dough tenacity, but decreased dough extensibility and bread loaf volume. To compensate these adverse effects, some solutions are suggested.

In the past two decades, three types of starch mutants, (), () and () have been developed in Japan. Each of these lines was obtained by identifying “partial“ mutants with mutations in one or two homeoelogous genes derived from the A, B or D-genomes, followed by crossing to produce fully null mutants. The line lacks the three granule-bound starch synthase I (GBSSI) proteins responsible for amylose synthesis, and HA lacks the three starch synthase IIa (SSIIa) enzymes that are involved in amylopectin synthesis. SW lacks all active GBSSI and SSIIa enzymes. “Partial“ null mutants have also been used to obtain more subtle modifications in starch quality. For example, the single null lines produce starch which is slightly reduced in amylose. This suggested that the identification of other desirable lines using MAS would allow us to further fine-tune starch characteristics. Sixty-four homozygous lines differing in and composition can be selected from progeny of crosses between and . Co-dominant markers for all and genes enabled us to select all 64 lines quickly and effectively. The modulation of starch characteristics serves as a model that demonstrates the utility of mutation identification in combination with MAS in hexaploid wheat. The availability of genome sequence information, combined with new methods of mutation detection, reduces the amount of work involved in finding single mutations in wheat, and one can easily see the potential for expanding this methodology to other traits.

Production of crops is in part limited by consumer demand and utilization. In this regard, world production of durum wheat ( subsp. ) is limited by its culinary uses. The leading constraint is its very hard kernels. Puroindolines, which act to soften the endosperm, are completely lacking in durum. Currently, durum grain is milled on highly specialized mills which produce as their primary objective coarse semolina. Morris and co-workers (2011) described the development of soft kernel durum wheat. The soft kernel trait ( locus) was introgressed into Langdon via , and crossed to the Italian durum cv. Svevo (producing ‘Soft Svevo’). Soft Svevo behaves much like a soft hexaploid wheat with somewhat lower break flour yield, higher water absorption, and smaller cookie diameter. Pilot scale spaghetti manufacture indicated that hydration levels could be reduced to 26–27 % for soft durum, as opposed to about 32 % for commercial semolina. Cooking trials indicated equal-or-better texture, cooking loss and tolerance. Soft Svevo flour performed well in a range of baked goods. These studies demonstrate the stable transfer of the genes from to subsp. . As such, the processing and utilization of durum was dramatically altered. The creation of soft durum therefore increases the potential for wheat production under marginal cropping conditions, while establishing a new wheat class with expanded and novel uses.