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The Plant Genome
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The first paper, by Ha et al., represents the latter. At first glance it appears to simply be SNP assay development for two QTLs for root-knot nematode resistance in soybean. However, to develop those SNPs the authors took advantage of the extensive genomic resources available for soybean. They identified BACs associated with markers closely linked to their QTL by querying genomic databases and then accessed the BAC sequence from GenBank. The BAC sequences were then used to help identify SNPs.
The paper by Fengler et al., a contribution from DuPont Co. researchers, takes both a local and global view of genetic recombination within the maize genome. Genetic to physical distance relationships had been addressed previously only in small, defined regions. These authors use a high-density genetic map of maize, integrated with a highly resolved BAC contig map to compare the distribution of gene density and recombination frequency along chromosomes. They show that despite overall patterns of recombination along the length of chromosomes, local variations can be extreme.
Hudson and collaborators advanced the application of microarrays in their paper on the analysis of Brassica seed germination. These authors developed an approach for using microarrays across species boundaries; Arabidopsis to Brassica. Their research involved virtual development of oligonucleotide arrays of probe sets homologous to Arabidopsis genes (designating as non-useable those probes not yielding a strong signal in Brassica), and specifically designed analysis software. Once developed, they demonstrated the application of the system by investigating the expression profiles during germination of Brassica seed, with some surprising results.
Flower color has long been a phenotypic trait used as a marker in genetic studies. Although biochemical pathways for flower pigmentation have been mostly described, many of the genes involved in those pathways have not been identified. The paper by Zabala and Vodkin is an extension of The Plant Genome from the realm of genomics into molecular genetics; something we will see more of in coming issues. In this paper the authors present molecular evidence that they have likely identified the gene encoded by the W1 locus in soybean; a locus defined genetically in 1923. This result integrates an important marker with the genetic map and forthcoming whole-genome sequence. Interestingly the gene is expressed at such low levels that only sensitive RT-PCR techniques could detect transcripts.
Population-based mapping of complex traits was first conducted in humans. These ‘association’ approaches are now being applied to crops. The Hamblin et al. paper reports the results of their assessment of the potential for linkage disequilibrium (association) mapping of variation in endosperm quality in sorghum. They identified SNPs in candidate genes for endosperm quality, measured the abundance of those SNPs and evaluated the location of those SNPs in the genes. They were able to capture the haplotypic diversity of the genic regions using a small number of SNPs. This suggested to them that association mapping in sorghum can probably be done with few markers, relative to a more diverse species such as maize.
Speaking of maize and its complex genome, Gore and collaborators test the feasibility of using maize oligonucleotide expression arrays to identify single feature polymorphisms (SFPs) in maize genes (equivalent to SNPs). The rationale is that if individual oligos on an array show ‘significant and reproducible’ differences in hybridization intensity between genotypes, it may serve as a marker (SFP). Because accurate scoring of SFPs requires a high level of gene enrichment the authors tested several enrichment methods. Although the results of this study were modest compared to those conducted in simpler genomes, this paper marks the first such report in a plant with a genome size 20 X that of Arabidopsis and comprised of mostly LTR-retrotransposons. When this approach is perfected for large complex genomes it promises to provide a fast and relatively cheap method to genotype large numbers of individuals.
The physiological effects of a low phytic acid mutant(lpa) in barley are better understood as a result of global gene expression studies reported here by Bowen et al. Crops with reduced phytate may have improved nutritional value and may reduce environmental phosphorous pollution. But, altered plant and seed performance of some lpa mutants suggests that the results of the mutation(s) may impact multiple pathways. These authors studied changes in global gene expression in a barley lpa mutant. They concluded that in barley, the effects of the barley M955 lpa mutation on seed development seemed to occur through changes in gene expression affecting starch synthesis and carbon transport. They didn't observe any changes in expression of genes directly involved in phytate synthesis.
I hope you enjoy these papers. Together they represent our commitment to publishing reports on development, translation and application of genomic resources for crop improvement.
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