Wheat ESTs mapped to deletion bins in the distal 42% of the long arm of chromosome 4B (4BL) were ordered in silico based on blastn homology against rice pseudochromosome 3. The ESTs spanned 29 cM on the short arm of rice chromosome 3, which is known to be syntenic to long arms of group-4 chromosomes of wheat. Fine-scale deletion-bin and genetic mapping revealed that 83% of ESTs were syntenic between wheat and rice, a far higher level of synteny than previously reported, and 6% were nonsyntenic (not located on rice chromosome 3). One inversion spanning a 5-cM region in rice and three deletion bins in wheat was identified. The remaining 11% of wheat ESTs showed no sequence homology in rice and mapped to the terminal 5% of the wheat chromosome 4BL. In this region, 27% of ESTs were duplicated, and it accounted for 70% of the recombination in the 4BL arm. Globally in wheat, no sequence homology ESTs mapped to the terminal bins, and ESTs rarely mapped to interstitial chromosomal regions known to be recombination hot spots. The wheat–rice comparative genomics analysis indicated that gene evolution occurs preferentially at the ends of chromosomes, driven by duplication and divergence associated with high rates of recombination.

The Rc locus regulates pigmentation of the rice bran layer, and selection for the rc allele (white pericarp) occurred during domestication of the crop. White bran is now ubiquitous among cultivated varieties throughout rice growing regions of the world. We identified a new allele that arose by natural mutation within the rc pseudogene of the cultivar 'Wells'. The mutation restored the reading frame of the gene, and reverted the bran layer pigmentation to red (wild-type). By sequencing the Rc locus in plants derived from red seeds, and linkage analysis in a segregating population, we were able to demonstrate that mutation within rc resulted in the new, dominant, wild-type allele Rc-g.

False smut (Ustilaginoidea virens) and kernel smut (Neovossia horrida) are diseases of rice (Oryza sativa) that reduce both grain yield and quality. False smut is an emerging disease worldwide that is rapidly gaining in importance, whereas kernel smut has historically been a chronic minor disease with sporadic outbreaks that cause considerable losses. Highly effective disease control was obtained for susceptible cultivars by employing conservation tillage (69% reduction in false smut), continuous rice cropping (88% reduction in false smut), and moderate nitrogen fertility rates (34 and 60% reductions in false smut and kernel smut, respectively). Combining these treatments nearly eliminated smuts from cultivars that were fully susceptible under conventional cultivation practices. Furthermore, using a nursery designed to promote smut diseases, two rice hybrids were identified that possessed kernel smut resistance under the most favorable disease conditions. The genetic basis of the resistance is unknown. However, the utility for disease control is great because hybrids occupy significant portions of production rice acreage.