A unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers is developed and provides a powerful complement to currently available methods for association mapping.
It is reported that palm sequences evolve at a rate of 2.61 x 10(-9) substitution per synonymous site per year, a rate which is slower than most plant nuclear genes, and synonymous rates in nuclear Adh genes show a marked decrease in palms relative to grasses, paralleling the pattern found at the plastid rbcL locus.
The structure of the adh1 region appears to be standard relative to the other gene-containing regions of the maize genome, thus suggesting that retrotransposon insertions have increased the size of the corn genome from approximately 1200 Mb to 2400 Mb in the last three million years.
A comparison of genetic diversity between the landrace and inbred samples showed that inbreds retained 77% of the level of diversity of landraces, on average, suggesting that genome-wide surveys for association analyses require SNPs every 100–200 bp.
The analyses indicate that coalescent times for duplicated sequences fall into two distinct groups, corresponding to roughly 20.5 and 11.4 million years, which strongly discounts the possibility that the maize genome is the product of a genomic allotetraploid event, and also suggests that one of the two ancestral diploids shares a more recent common ancestor with sorghum than it does with the other ancestraldiploid.
Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4% of these genes experienced artificial selection, and candidate selected genes with putative function in plant growth are clustered near quantitative trait loci that contribute to phenotypic differences between maize and teosinte.
It is argued that the current colinearity paradigm requires reassessment, because it is clear that grass genomes are evolutionarily labile for many characteristics, including genome size and chromosome number.
Simulations help confirm previous suggestions that silent sites are saturated, leaving no evidence of heterogeneity in synonymous substitution rates, and confirm previous findings that substitution rates in the chloroplast genome are subject to both lineage-specific and locus-specific effects.
The 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47, based on 8.3× dideoxy sequence coverage, is reported, indicating pervasive selection for a smaller genome in this outcrossing species.