Identification of maize lateral root density genes resources through integrated RNA-seq and BSA-seq analyses

As the primary organ responsible for water and nutrient uptake, the root system plays a vital role in maize growth and yield formation. Understanding the genetic basis of root architectural traits—particularly lateral root density (LRD)—is crucial for advancing high-yield breeding strategies. In this study, an F₂ population was developed from a cross between Danhuang 02 (high LRD) and HRB16041 (low LRD). Bulked segregant analysis coupled with high-throughput sequencing (BSA-seq) was conducted to identify genomic loci significantly associated with LRD. In parallel, transcriptome sequencing of lateral root tissues from eight diverse maize inbred lines was performed to explore candidate genes regulating LRD at the seedling stage. BSA-seq identified 240 significantly associated SNPs and 2420 InDels, involving 235 candidate genes located in regulatory regions, alternative splicing sites, or coding sequences. RNA-seq analysis revealed 1979 differentially expressed genes (DEGs) associated with LRD, including 954 up-regulated and 1025 down-regulated genes. Integrated analysis of BSA-seq and RNA-seq data identified 12 overlapping genes as strong candidates for regulating LRD. qRT-PCR validation suggested that <italic>Zm00001d033708</italic> and <italic>Zm00001d045720</italic> may act as positive regulators of lateral root density, while <italic>Zm00001d040375</italic> may function as a negative regulator. This study provides valuable genetic resources and candidate genes for understanding and improving lateral root development in maize.