An Analysis of Genetic Diversity Across the Maize Genome Using Microsatellites

Abstract

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genomewide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection. B ETWEEN 5000 and 10,000 years ago, humans dotion, and artificially high diversity at genes under diversifying selection. mesticated virtually all major crop species used by modern agricultural societies (Smith 2001). This feat These two processes-selection targeted on agronomic genes and drift due to the domestication bottleneck was accomplished through artificial selection for traits that improved agronomic qualities. As a result of this affecting the entire genome-are the principal factors that influence the amount and distribution of genetic process, favorable alleles at loci controlling agronomic traits were brought to fixation in the population during variation in crop genomes as compared to their wild the domestication period. After the initial domesticaprogenitors. Studies on isozymes and gene sequences tion, the continued practice of selective breeding alrevealed a general reduction of genetic variation in lowed additional favorable alleles to sweep through the crops as a result of the domestication bottleneck (Doecrop species, while diversifying selection in response bley et al. 1984; Eyre-Walker et al. 1998; Hilton and to the different environments encountered during the Gaut 1998); however, these exploratory studies ingeographic expansion of the crop caused regional fixavolved relatively few loci and thus the generality of their tion of distinct favorable alleles. As a consequence of results needs confirmation. Our knowledge of the imthis complex history of selection, only a limited portion pact of selection on diversity in crops is more restricted of the population contributed to each subsequent gensince very few agronomic genes have been identified and eration. Some anticip...

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