Tissue-specific expression of maize domestication and crop improvement loci

Authors: HUFFORD, KRISITINA - UNIV. OF CA - IRVING; CANARAN, PAYAN - COLD SPRING HARBOR LAB; Ware, Doreen; McMullen, Michael; GAUT, BRANDON - UNIV. OF CA - IRVING

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/5/2007
Publication Date: 5/15/2007
Citation: Hufford, K., Canaran, P., Ware, D., Mcmullen, M.D., Gaut, B. 2007. Tissue-specific expression of maize domestication and crop improvement loci. Plant Physiology. 144:1642-1653.

Interpretive Summary: Domestication, the taming of wild species for the purpose of producing cultivated crops, results in the artificial selection of genes. In maize comparison between modern corn and its wild ancestors provides a unique opportunity to understand the nucleotide sequence diversity associated with morphological differences, such as the number, size, and protein content of seeds that occurred during domestication and modern crop improvement. In this research we ask three questions; what portion of genes were selected early in domestication or later in modern crop improvement, are genes involved in regulation more likely to be targets of artificial selection than other classes of genes and are selected genes more likely to be expressed in one tissue than another. Using 30 candidates we found equal numbers of genes were selected in early domestication and modern crop breeding. We found that genes involved in gene regulation are no more likely to be selected than genes of other function. We demonstrated that candidate genes were more likely to be expressed in the maize ear relative to vegetative tissues such as maize shoot, leaf and root tissue. This is an important observation as the maize ear underwent dramatic morphological alteration upon domestication and has been a continuing target of selection for maize yield. Therefore, we conclude that selected genes are more likely to be expressed in tissues that experienced high levels of morphological divergence during domestication and crop improvement.

Technical Abstract: The domestication of maize 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 over expressed 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 conclude that selected genes are more likely to be expressed in tissues that experienced high levels of morphological divergence during domestication and crop improvement.