A molecular marker map in 'Kanota' × 'Ogle' hexaploid oat (Avenaspp.) enhanced by additional markers and a robust framework

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota × Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed individually within the most likely framework interval using χ2 tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.Key words: molecular marker, RFLP, linkage map, oat, Avena

Gene and repetitive sequence annotation in the Triticeae

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes

Quantitative trait locus analysis of wheat quality traits

Milling and baking quality traits in wheat (Triticum aestivum L.) were studied by QTL analysis in the ITMI population, a set of 114 recombinant inbred lines (RILs) generated from a synthetic-hexaploid (W7985) x bread-wheat (Opata 85) cross. Grain from RILs grown in U.S., French, and Mexican wheat-growing regions was assayed for kernel-texture traits, protein concentration and quality, and dough strength and mixing traits. Only kernel-texture traits showed similar genetic control in all environments, with Opata ha alleles at the hardness locus Ha on chromosome arm 5DS increasing grain hardness, alkaline water retention capacity, and flour yield. Dough strength was most strongly influenced by Opata alleles at 5DS loci near or identical to Ha. Grain protein concentration was associated not with high-molecular-weight glutenin loci but most consistently with the Gli-D2 gliadin locus on chromosome arm 6DS. In Mexican-grown material, a 2DS locus near photoperiod-sensitivity gene Ppd1 accounted for 25% of variation in protein, with the ppd1-coupled allele associated with higher (1.1%) protein concentration. Mixogram traits showed most influence from chromosomal regions containing gliadin or low-molecular-weight glutenin loci on chromosome arms 1AS, 1BS, and 6DS, with the synthetic hexaploid contributing favorable alleles. Some RI lines showed quality values consistently superior to those of the parental material, suggesting the potential of further evaluating new combinations of alleles from diploid and tetraploid relatives, especially alleles of known storage proteins, for improvement of quality traits in wheat cultivars