Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game

Crop weediness,especially that of weedy rice(Oryza sativa f.spontanea),remains mysterious.Weedy rice possesses robust ecological adaptability;however,how this strain originated and gradually formed proprietary genetic features remains unclear?Here,we demonstrate that weedy rice at Asian high latitudes(WRAH)is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice.We also identified novel quantitative trait loci underlying weedy-specific traits,and revealed that a genome block on the end of chromosome 1 is associated with rice weediness.To identify the genomic modifications underlying weedy rice evolution,we generated the first de novo assembly of a high-quality weedy rice genome(WR04-6),and conducted a comparative genomics study between WR04-6 with other rice reference genomes.Multiple lines of evidence,including the results of demographic scenario comparisons,suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication.A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.

Isolation of a Novel Lodging Resistance QTL Gene Involved in Strigolactone Signaling and Its Pyramiding with a QTL Gene Involved in Another Mechanism

Lodging has been a major roadblock to attaining increased crop productivity. In an attempt to understand the mechanism for culm strength in rice, we isolated an effective quantitative trait locus （QTL）, STRONG CULM3 （SCM3）, the causal gene of which is identical to rice TEOSINTE BRANCHED1 （OsTB1）, a gene previously reported to positively control strigolactone （SL） signaling. A near-isogenic line （NIL） carrying SCM3 showed enhanced culm strength and increased spikelet number despite the expected decrease in tiller number, indicating that SL also has a positive role in enhancing culm strength and spikelet number. We produced a pyramiding line carrying SCM3 and SCM2, another QTL encoding AP01 involved in panicle development. The NIL-SCM2＋SCM3 showed a much stronger culm than NIL-SCM2 and NIL-SCM3 and an increased spikelet number caused by the additive effect of these QTLs. We discuss the importance of utilizing suitable alleles of these STRONG CULM QTLs without inducing detrimental traits for breeding.