Convergent evolution of root system architecture in two independently evolved lineages of weedy rice

Abstract

Summary Root system architecture (RSA) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de‐domesticated form of rice, to study the evolution of weed‐associated RSA traits and the extent to which they evolve through shared or different genetic mechanisms. We characterised 98 two‐dimensional and three‐dimensional RSA traits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL) mapping to compare genetic architecture between the weed strains. The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a ‘weedy’ RSA phenotype. Notably, comparative QTL mapping revealed little evidence for shared underlying genetic mechanisms. Our findings suggest that despite the double bottlenecks of domestication and de‐domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedy RSA traits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below‐ground contact as a competitive strategy.

Diverse genetic mechanisms underlie worldwide convergent rice feralization

“…In particular, genome scans can reveal whether adaptations in weedy rice that superficially resemble phenotypic reversions to wild rice (e.g., seed shattering and dormancy) have arisen through changes at the same loci that were targets of selection during domestication (e.g., through second-site suppression of domestication alleles), or through changes at loci that were not involved in the domestication process. Genome sequence analysis can further reveal whether adaptations for weediness in independently evolved strains have occurred through shared or independent genetic mechanisms, thereby shedding light on the extent to which the feralization process is genetically constrained [7,8].…”

Re‐acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de‐domestication

“…Recent genetic and genomic studies (He et al, 2017;Li et al, 2017;Qiu et al, 2017;Vigueira et al, 2019) have provided in-depth genome-level insights into the evolution of weedy rice. The diverse weedy rice lines have convergently evolved phenotypes through independent genetic mechanisms (Li et al, 2017;Wedger & Olsen, 2018;Wedger et al, 2019). The key evolutionary process requires only a few genetic changes for the emergence of wild-like traits (Li et al, 2017), and generally involves novel genes rather than the mutational reversion of domestication genes Thurber et al, 2010;Xia et al, 2011;Qi et al, 2015).…”

A Comparative Analysis of Quantitative Metrics of Root Architecture

“…Correlations also exist among phene aggregates; maximum depth and major ellipse axis were highly correlated; convex hull area , convex hull volume , maximum width , and minor ellipse axis were also highly correlated as seen in several other studies. Major ellipse axis and maximum depth are measures of rooting depth [ 54 ] and were correlated with primary root length. Maximum width , minor ellipse axis , and convex hull are phene aggregates which characterize expansion in sense of the outer shape of the root system [ 55 ].…”