Identification of a Major QTL Controlling Maize Lateral Root Branching Number Through Integrated BSA-Seq and Transcriptome Analysis

Maize lateral roots play essential roles in plant anchorage, mechanical support, and water and nutrient acquisition. However, the genetic mechanisms underlying lateral root development remain unclear. In this study, an F2 population was generated by crossing the inbred lines B111, which exhibits abundant lateral roots on brace roots, and T4691, which lacks lateral roots on brace roots, to map loci controlling lateral root development. Phenotypic analysis of the F2 population revealed that lateral root branching number (LRN) exhibited quantitative variation. Bulked segregant analysis sequencing (BSA-seq) identified two major QTLs for LRN on chromosomes 7 and 9. Of them, the QTL on chromosome 9, qLRN9, showed stronger significance. Through molecular marker analysis, qLRN9 was further narrowed down to an approximately 1.63 Mb marker interval. To identify the candidate genes, transcriptome analysis was performed using brace root samples with lateral root branches collected from the B111 inbred line at three lateral root developmental stages. In the ~1.63-marker interval, Zm00001eb379100, Zm00001eb378700, Zm00001eb379070 and GRFTF13 were screened for possible candidate genes by integrated analysis of QTL mapping and transcriptome data. These findings provide valuable genetic resources and molecular markers for improving maize root architecture, lodging resistance, and drought tolerance.