Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10

Abstract

Maize domestication is one of the greatest feats of artificial selection and evolution, wherein a weedy plant in Central Mexico was converted through human-mediated selection into the most productive crop in the world. In fact, the changes were so astounding that it took much of the last century to identify modern maize's true ancestor. Through modern genetic studies, the molecular basis of this evolution is being unraveled. Maize's new morphology and adaptation to diverse environments required selection at thousands of loci, and we are beginning to understand the magnitude and rates of these genetic changes. Most of the known major genes have experienced strong selection, but only small regions surrounding the selected genes exhibit substantially reduced genetic diversity. Here, we report the discovery of a large region on chromosome 10 involved in adaptation or domestication that has been the target of strong selection during maize domestication. Unlike previously described regions in the maize genome, 1.1 Mb and >15 genes lost genetic diversity during selection at this region. Finally, the prospects of a detailed understanding of maize evolution are discussed with consideration of both top-down and bottom-up approaches.Although man does not cause variability and cannot even prevent it, he can select, preserve, and accumulate the variations given to him by the hand of nature almost in any way that he chooses; and thus he can certainly produce a great result.Charles Darwin (1) W ith its meager ear containing only 2 entwined rows of well-armored kernels, teosinte grows on Mexican hillsides. This grass might easily have been overlooked were it not for its abundant variation, a gift not lost on early agriculturists. Within the last 10,000 years, early Native Americans were able to transform teosinte into a plant whose ears would feed the world. It was a transformation so striking and so complex that some researchers did not believe it was possible, leading to years of competing theories and intense debate. But as Darwin himself recognized, when the desires of humans meet the diversity of nature the result can indeed be astounding.The molecular revolution of the last 2 decades has provided compelling evidence that teosinte is the progenitor of modern maize. Here, we discuss the rich genetic diversity at the source of this morphological conversion and examine how human selection has impacted this diversity. One key question concerning maize domestication remains to be resolved: was maize domestication the result of selection on a small number of loci with large effects, a large number of loci with small effects, or both? Recent genetic evidence has provided clues about the relative contributions of large-effect and small-effect loci. We discuss how future studies will help unravel the mysteries surrounding maize domestication and how this information is key to future improvements of maize.

Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia

“…The present study provides an empirical case showing how plants adapt to specific or local environments by keeping the balance between resource accumulation and stress avoidance. Our results also echo the report that minor-effect QTLs contributed to the adaptation of maize to northern environments (47). Thus, we anticipate that more minor-effect QTLs contributing to crop adaptation and diversification will be uncovered with increased knowledge of plant genomes and more genome-wide association studies.…”

“…This notion is supported by recent molecular genetic studies and sequence analyses (47,48). For example, the rice shattering4 and QTL of seed shattering in chromosome 1 that control shattering in rice are among the major loci of large effect selected early during rice domestication (15,16,49); however, accumulating evidence suggests that there are other shatter-controlling genes differentially fixed within different subpopulations of rice (48).…”

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

“…LD may persist over even longer distances in regions containing targets of selection. For example, reductions in diversity around targets of selection in maize and rice have been shown to persist over large regions (250 kb to 1.1 Mb) containing multiple additional genes (Palaisa et al 2004;Olsen et al 2006;Tian et al 2009). …”

Inbreeding drives maize centromere evolution

“…CML333, the sole maize inbred still using CEN5M, reacquired this CentC-rich centromere from a wild relative via two CEN5-proximal recombinations ∼1.3 ka, recent enough to retain large amounts of its CentC. Previously identified domestication loci (9,27) were used to validate our dating methods (SI Appendix, Text S2).…”