Crop plants as models for understanding plant adaptation and diversification

Abstract

Since the time of Darwin, biologists have understood the promise of crop plants and their wild relatives for providing insight into the mechanisms of phenotypic evolution. The intense selection imposed by our ancestors during plant domestication and subsequent crop improvement has generated remarkable transformations of plant phenotypes. Unlike evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and other experimental approaches. Moreover, since domestication has repeatedly generated a suite of “domestication syndrome” traits that are shared among crops, opportunities exist for gaining insight into the genetic and developmental mechanisms that underlie parallel adaptive evolution. Advances in our understanding of the genetic architecture of domestication-related traits have emerged from combining powerful molecular technologies with advanced experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies may be combined with high-throughput evaluations of the various “omics” involved in trait transformation, revealing a diversity of underlying causative mutations affecting phenotypes and their downstream propagation through biological networks. We summarize the state of our knowledge of the mutational spectrum that generates phenotypic novelty in domesticated plant species, and our current understanding of how domestication can reshape gene expression networks and emergent phenotypes. An exploration of traits that have been subject to similar selective pressures across crops (e.g., flowering time) suggests that a diversity of targeted genes and causative mutational changes can underlie parallel adaptation in the context of crop evolution.

Genetic and epigenetic modifications to the BBAA component of common wheat during its evolutionary history at the hexaploid level

“…Especially, allopolyploidy, by doubling merged genomes from different species, is associated with evolution and domestication of several major crops, including wheat, cotton and several crops in the Brassica family alone (Olsen and Wendel 2013;Chalhoub et al 2014). Although the molecular basis underlying the evolutionary success of polyploidy remains poorly understood, in cases of allopolyploidy, rapid genetic, epigenetic and gene expression changes evoked by the combined effects of genome merge (hybridization) and WGD have been increasingly considered as major factors in bestowing evolutionary advantages to allopolyploidy (Wendel 2000;Pires et al 2004;Adams and Wendel 2005;Comai 2005;Chen and Ni 2006;Gaeta et al 2007;Doyle et al 2008;Flagel et al 2012;Madlung and Wendel 2013).…”

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

“…The ability to respond to environmental signals is the hallmark of adaptation and underlies tolerance to biotic and abiotic stresses. For domesticated crop species like Asian rice (Oryza sativa), adaptive gene expression patterns associated with environmental changes can ensure high yields under a range of climatic conditions (Mickelbart et al, 2015;Olsen and Wendel, 2013).…”

Archaeological and genetic insights into the origins of domesticated rice

“…These four loci represented an early view into the future of rice domestication genetics based on functional genes: following the identification of these domestication and improvement genes, new genes were identified at a rapid rate (76,77). In general, when surveys included a broad sampling of rice varieties, the allele associated with a domesticated state showed one of three patterns: (i) the allele was unique to japonica (78,79), (ii) the same allele was found in a subset of both japonica and indica (80, 81), or (iii) the same allele was found in the majority of japonica and indica varieties (82,83).…”