Comparative population genomics of maize domestication and improvement

By M. Hufford, Xun Xu, J. van Heerwaarden, Tanja Pyhäjärvi, Jer-Ming Chia, R. Cartwright, Robert Elshire, Jeffrey Glaubitz, Katherine E. Guill, Shawn M. Kaeppler and 15 more. Nature Genetics, 2012

852 citations recorded by the source corpus.

Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/9f344be440be46d44adb7ebf32061cf119ef6566

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Citations in the corpus

• Population genomic and genome-wide association studies of agroclimatic traits in sorghum (2012, methodology): “Genome-wide single nucleotide polymorphism (SNP) scans of population genetic parameters in crops have been used to identify loci under selection (10, 11) and dissect quantitative traits (11).”
• Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars (2013, background): “This is in contrast to domestication bottlenecks that result in significant changes in population size due to selection for alleles contributing to the domesticated phenotype (17) and the demographic effect linked with sampling from limited geographic areas (39, 40).”
• Plant Defense against Insect Herbivores (2013, background): “What is the reason for this? Is it related to their geographical origins and corresponding selecting agents? Could it be a consequence of the long-running domestication of maize [386]? The emergence of next generation sequencing techniques together with more powerful”
• Natural variations and genome-wide association studies in crop plants. (2014, methodology): “In maize, a comprehensive assessment of selective sweeps was implemented based on the genome-wide resequencing of 75 wild, landrace, and improved maize lines (43).”