QTL qLDC5 regulates primary root branching in an auxin-dependant manner

L-type lateral root (LLR) density is a key determinant of root system architecture that affects nutrient acquisition in rice, particularly under low-phosphorus conditions. While previous studies identified genotypic differences in LLR density together with a QTL enhancing LLR density on crown roots (qLDC5) from donor landrace'DJ123', little is known about the genetic and physiological basis of this trait. We showed that LLR densities on crown and primary roots were closely correlated and confirmed higher LLR density on primary roots in donor DJ123 compared to the African upland rice variety NERICA4 using non-destructive X-ray micro-computed tomography. We further confirmed the effect of qLDC5 in a field experiment conducted in Madagascar for LLR density on primary roots. LLR densities on primary and crown roots therefore, appear under similar genetic control. Developmental analyses revealed that DJ123 and NDJ188 - a derivative line harbouring qLDC5 - initiate significantly more lateral root primordia than NERICA4, with a higher proportion progressing to elongation. Branching phenotypes of these genotypes differed markedly in their responses to exogenous auxin treatment. Within the qLDC5 region, the auxin biosynthesis gene OsYUCCA2 and auxin response factor OsARF15 were strongly upregulated in DJ123. Transcriptome analysis also revealed an indirect auxin-mediated regulatory network underlying LLR variation. Differentially expressed genes common to DJ123 and NDJ188 were enriched for ent-kaurene and gibberellin metabolism, including the robust induction of OsGA2ox5. These findings suggest qLDC5 increases lateral root density by coordinating gibberellin, auxin, and terpene pathways, thereby regulating both lateral root initiation and elongation.