Data from: More than one way to evolve a weed: Parallel evolution of U.S. weedy rice through independent genetic mechanisms

Many different crop species were selected for a common suite of
‘domestication traits’, which facilitates their use for studies of
parallel evolution. Within domesticated rice (Oryza sativa), there has
also been independent evolution of weedy strains from different cultivated
varieties. This makes it possible to examine the genetic basis of parallel
weed evolution and the extent to which this process occurs through shared
genetic mechanisms. We performed comparative QTL mapping of weediness
traits using two recombinant inbred line populations derived from crosses
between an indica crop variety and representatives of each of the two
independently evolved weed strains found in US rice fields, strawhull (S)
and blackhull awned (B). Genotyping-by-sequencing provided dense marker
coverage for linkage map construction (average marker interval
<0.25 cM), with 6016 and 13 730 SNPs mapped in F5 lines of the S
and B populations, respectively. For some weediness traits (awn length,
hull pigmentation and pericarp pigmentation), QTL mapping and sequencing
of underlying candidate genes confirmed that trait variation was largely
attributable to individual loci. However, for more complex quantitative
traits (including heading date, panicle length and seed shattering), we
found multiple QTL, with little evidence of shared genetic bases between
the S and B populations or across previous studies of weedy rice.
Candidate gene sequencing revealed causal genetic bases for 8 of 27 total
mapped QTL. Together these findings suggest that despite the genetic
bottleneck that occurred during rice domestication, there is ample genetic
variation in this crop to allow agricultural weed evolution through
multiple genetic mechanisms.