Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci

Abstract

The domestication of maize (Zea mays sp. mays) from its wild progenitors represents an opportunity to investigate the timing and genetic basis of morphological divergence resulting from artificial selection on target genes. We compared sequence diversity of 30 candidate selected and 15 reference loci between the three populations of wild teosintes, maize landraces, and maize inbred lines. We inferred an approximately equal ratio of genes selected during early domestication and genes selected during modern crop breeding. Using an expanded dataset of 48 candidate selected and 658 neutral reference loci, we tested the hypothesis that candidate selected genes in maize are more likely to have transcriptional functions than neutral reference genes, but there was no overrepresentation of regulatory genes in the selected gene dataset. Electronic northern analysis revealed that candidate genes are significantly overexpressed in the maize ear relative to vegetative tissues such as maize shoot, leaf, and root tissue. The maize ear underwent dramatic morphological alteration upon domestication and has been a continuing target of selection for maize yield. Therefore, we hypothesize that genes targeted by selection are more likely to be expressed in tissues that experienced high levels of morphological divergence during domestication and crop improvement.

Figure 1.

Graph of pairwise nucleotide diversity (π) for the 30 candidate selected loci and 15 pooled neutral reference loci in populations of maize inbreds, landraces, and teosintes. Loci are sorted into domestication and crop improvement categories based on MLHKA results. Nucleotide diversity for the 15 neutral reference genes are pooled within populations.

Figure 2.

Tissue expression patterns for results of e-northern screens of all cDNA libraries, including both normalized and nonnormalized libraries, for neutral reference loci (RG) and candidate selected loci (SG). Expression patterns for ear and shoot tissues are illustrated separately. Error bars represent ±1 se.

Figure 3.

Tissue expression patterns for results of e-northern screens of nonnormalized cDNA libraries for neutral reference loci (RG) and candidate selected loci (SG). Expression patterns for ear and shoot tissues are illustrated separately. Error bars represent ±1 se.

Figure 4.

Tissue expression patterns for results of e-northern screens of nonnormalized libraries for 48 candidate crop improvement (CI) and domestication (D) genes. Error bars represent ±1 se.