Evolutionary inferences from genomic pattern of polymorphism in Arabidopsis and rice

Understanding the genetic basis of adaptation is a primary goal of evolutionary biology and describing the effects of natural selection on patterns of genomic variability is an important aspect of this effort. We implemented a molecular population genetics approach to investigate the potential role of selection in shaping nucleotide diversity in high-diversity regions of the Arabidopsis genome and across a non-recombining region of a rice centromere.;A genome-wide scan for high-diversity genes in the A. thaliana genome was conducted to identify chromosomal regions with levels and patterns of nucleotide polymorphism that were consistent with the action of balancing selection. Detailed investigations of linked loci across multiple high-diversity regions revealed several candidate genes that might harbor balanced polymorphisms. These genes include SOLUBLE STARCH SYNTHASE I (SSI), PLASTID TRANSCRIPTIONALLY ACTIVE 7 (PTAC7), and BELL LIKE HOMEODOMAIN 10 (BLH10). To investigate possible functional differences that might be maintained by alternate alleles of these loci we tested for allele specific expression differences and examined the distribution of nonsynonymous polymorphism across each gene. We observe multiple replacement polymorphisms within and in the 32 amino acids just upstream of the protein-protein interacting BELL domain at the BLH10 locus and allele-specific expression differences at both SSI and PTAC7.;To investigate the relationship between recombination and diversity and to examine centromere evolutionary dynamics we sequenced fragments from ∼18 expressed single copy genes distributed across a ∼3.3 Mb region encompassing rice centromere 8 in ∼ 20 individuals each of three domesticated O. sativa varieties (indica, temperate japonica, and tropical japonica) as well as from the wild progenitor, O. rufipogon. Theory predicts that diversity might be low in this non-recombining region due to hitchhiking with selected variants. We find that both temperate japonica and tropical japonica centromere 8 regions possess significantly elevated levels of nucleotide variation when compared to an empirical genome-wide distribution while indica and O. rufipogon show decreased diversity. HKA tests do not support the hypothesis that natural selection is acting at loci in this region. Demography and selective interference might best explain patterns of diversity and divergence at rice centromere 8.