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Abstract. The quality of barley for the range of end uses from animal feed to brewing is determined by many genes, making the breeding of new barley varieties difficult. Understanding of the molecular basis of barley quality has been advanced by biochemical studies. More recently, molecular genetic tools are allowing the analysis of the biochemical factors contributing to grain quality. Many genetic loci influencing key quality attributes have been identified by gene mapping. Limited success has been reported in using this information to select for quantitative trait loci for these quality traits in plant breeding. Genomic techniques allowing more detailed analysis of variations in the barley genome in relation to quality promise to extend significantly the value of molecular genetic approaches to barley quality improvement. Definition of the genetic basis of malting quality requires the identification of the genes involved in germination and endosperm modification. Feed quality remains difficult to define. Recent advances are likely to accelerate the rate of discovery, providing new options for analysis of barley quality.

This chapter compares the components and structures of dicotyledon cell walls, monocotyledon cell walls, Peridophyte cell walls and gymnosperm cell walls. The evolution of cell walls is described.

In this chapter some of the salient features of polyploidy in plants, including a brief description of its prevalence and modes of formation are discussed. Several model systems are presented for the study of polyploids and provide example case studies, hoping to illuminate how the 'internal' and 'external' processes associated with polyploidy contribute to evolutionary success and to the generation of biodiversity.

Empirical studies have shown that an inverse relationship exists between primer site conservation and evolutionary relationship between test taxa, with the threshold distance after which no amplification can be expected being lower in plants than in animals. However, there is still an insufficient number of studies investigating the use of heterologous SSR primers in plants. The current understanding of interspecific amplification of microsatellites in plants is the main focus of this chapter.

Genetic associations of morphological, biochemical, and DNA markers with economically important traits can be used for indirect selection of the traits. Chromosomal linkage between pseudo-black chaff and the stemrust resistance gene Sr2, and between the red glume gene (Rg1) and the stripe rust resistance gene Yr10, have been used in this way for many years. Similarly, linkages between disease resistance genes, such as Sr38,Lr37, and Yr17, have been used to achieve resistance to multiple diseases while selection is performed for resistance to one disease. Alleles at the Glu loci, assessed as protein differences, have been used as predictors of dough strength. More recently, DNA markers have been developed and used, especially to select for resistance to cereal cyst nematode, a trait which is difficult and expensive to assess with conventional bioassays. We found that the major use of DNA markers was for selection for traits of substantial economic importance, which were primarily determined by a single gene, and where the non-marker assay was expensive and unreliable. The other uses of markers were for pyramiding several genes influencing one trait, or for rapid backcrossing.

SSR markers closely linked to 18 loci that control 16 important barley traits were assessed for their applicability in Australian barley breeding programs. A panel of 40 genotypes routinely used by the South Australian Barley Improvement Program (SABIP) was used to examine the usefulness of these SSR markers for marker assisted selection (MAS). The success of monitoring a trait locus from donor to recipient lines ranged from 10 to 98%, depending on the marker. SSRs with a high polymorphic information content (PIC) value were found to be the most useful for application in MAS. The assessment also indicated that SSRs derived from genomic sequences were more successful for MAS than those designed from expressed sequence tags. A total of 130 SSR markers were screened among 2 panels of Australian barley genotypes to determine which markers would be the most useful for discriminating Australian germplasm. PIC values generated by this screening were also compared with those generated using a panel of European barley genotypes. Using ordinary correlations (parametric), rank correlations (non-parametric), and partial correlations (multi-variate), a strong association was found between the 2 Australian panels, but no or weak correlation was observed between the 2 Australian panels and the European dataset. It can therefore be concluded that PIC values generated by SSR markers screened with European genotypes cannot be used to predict the usefulness of an SSR marker for discriminating Australian genotypes. From PIC values generated in this study, 36 SSR markers have been selected for the discrimination of Australian genotypes. These markers all show high and/or consistent PIC values among Australian and European barley genotypes.A R 0 2 1 7 8 S S R m a r k e r s f o r p l a n t b r e e d i n g i n b a r l e y A . K a r a k o u s i s e t a l .

The Isa gene from barley--an intronless gene expressed in maternal tissues of the seed--has a likely role in defence against pathogens. The protein product--bi-functional alpha-amylase/subtilisin inhibitor--inhibits the seed's own amylase in addition to the bacterial protease subtilisin and fungal xylanase. Sixteen barley genotypes were targeted to amplify and sequence the Isa gene region to detect sequence polymorphisms, since little is known about genetic diversity at this locus. A total of 80 single nucleotide polymorphisms (SNPs) and 23 indels were detected in 2,164 bp of sequence containing the Isa transcript, promoter and 3' non-transcribed region (overall one SNP per 27 bp and one indel per 94 bp), with eight sequence-based haplotypes distinguishable amongst the 16 varieties. Sequencing a polymorphic region in the promoter in an additional 27 barley genotypes increased the number of sequence-based haplotypes discovered to 11. However there is low haplotype diversity amongst the cultivated barley varieties sampled, with most varieties represented by a single haplotype. There was minor amino acid diversity in the protein, with five out of ten SNP sites in the coding region predicted to produce amino acid substitutions. SNP analysis indicated a history of recombination events--a minimum of seven based on the initial eight haplotypes from the whole sequenced region. Most of the recombination events occurred in the highly polymorphic regions, the 3' non-transcribed region and sequences flanking a microsatellite in the Isa promoter.