Bud shapes dictate tiller-rhizome transition in African perennial rice (Oryza longistaminata).

Rhizome formation of Oryza longistaminata was dependent on the bud shape. The loci qBS3.1, qBS3.2 and qBS3.3 for controlling rhizome formation were functional redundant under Oryza longistaminata background. The rhizome, a root-like underground stem, is the key organ for grasses to achieve perennial growth. Oryza longistaminata, the only rhizomatous wild Oryza species with the same AA genome as cultivated rice, is an important germplasm for developing perennial rice. Our study found that the rhizome formation of O. longistaminata was dependent on the bud shape: the dome-like axillary bud (dome bud) usually penetrated through the leaf sheaths, developing into rhizome (extravaginal branching), but the flat axillary bud (flat bud) wrapped by the leaf sheaths only developed into tiller (intravaginal branching). The genetic loci (QTL) controlling the bud shape (BS) were mapped by entire population genotyping method (F population from crossing O. longistaminata with Balilla (Oryza sativa) and selective genotyping mapping method (BCF population from backcrossing F with Balilla). A total of twelve loci were identified, including four major-effect QTL: qBS2, qBS3.1, qBS3.2 and qBS3.3, and the genetic network of these twelve loci was established. The dome bud lost the potential to develop into rhizome with the increase in backcross generations under Balilla background. Considering the rapid loss of rhizome under Balilla background, the near-isogenic lines under O. longistaminata background were used to identify the effect of major-effect loci. According to the BCF, BCF and BCF under O. longistaminata background, there was some functional redundancy among qBS3.1, qBS3.2 and qBS3.3. Our results provided a new perspective for analyzing the genetic basis of perenniality and laid the foundation for fine mapping and verification of related genes.