Abstract
Weed evolution from crops involves changes in key traits, but it is unclear how genetic and phenotypic variation contribute to weed diversification and productivity. Weedy rice is a conspecific weed of rice (Oryza sativa) worldwide. We used principal component analysis and hierarchical clustering to understand how morphologically and evolutionarily distinct US weedy rice populations persist in rice fields in different locations under contrasting management regimes. Further, we used a representative subset of 15 sequence-tagged site fragments of expressed genes from global Oryza to assess genome-wide sequence variation among populations. Crop hull color and crop-overlapping maturity dates plus awns, seed (panicle) shattering (> 50%), pigmented pericarp and stature variation (30.2% of total phenotypic variance) characterize genetically less diverse California weedy rice. By contrast, wild-like hull color, seed shattering (> 50%) and stature differences (55.8% of total phenotypic variance) typify genetically diverse weedy rice ecotypes in Arkansas. Recent de-domestication of weedy species-such as in California weedy rice-can involve trait combinations indistinguishable from the crop. This underscores the need for strict seed certification with genetic monitoring and proactive field inspection to prevent proliferation of weedy plant types. In established populations, tillage practice may affect weed diversity and persistence over time. © 2017 Society of Chemical Industry.
Highlights
Understanding the evolutionary genetics of adaptation to human-mediated practices like small and large-scale production agriculture is critical to address global challenges including the security of food, fuel, bioproduct, and fiber production [1]
The highest FST estimate was 0.077, between CRR1 and CRR4 at STS085. These low values indicate no population structure and no divergence of weedy rice in the fields sampled, which supports the appropriateness of a genetic diversity assessment for California weedy rice
Measures of genetic diversity for California weedy rice within each field as well as for weedy rice within all fields combined are very low (Table 3), consistent with a recent founder event, or strong population bottleneck. These values are a full order of magnitude lower than what was calculated for strawhull (SH) and blackhull (BHA) weedy rice ecotypes collected from the southern US [21]
Summary
A central challenge in agriculture is to harness the genetic variation controlling key traits in crops to produce stable populations that can be planted, managed, and harvested effectively. Evolutionary models frame and explain the domestication, continued improvement, and management of cultivated plants. Examining these processes sheds light on the roles of selection and demography on genetic interactions of populations and species during adaptation [2]. The additive genetic variance associated with a given domestication trait may control how easy it is to fix a population for a trait value, for traits that are vastly different from wild or weedy close relatives
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