Mapping Quantitative Trait Loci in MAGIC Lines Uncovers Hormone-Responsive Genes Controlling Adventitious Root Development.

The Multi-Parent Advanced Generation Inter-Cross (MAGIC) population is a powerful tool for dissecting the genetic architecture controlling natural variation in complex traits. In this work, the natural variation available in MAGIC lines was evaluated by mapping quantitative trait loci (QTLs) for primary root length (PRL), lateral root number (LRN), lateral root length (LRL), adventitious root number (ARN), and adventitious root length (ARL). We analyzed the differences in the root structure of 139 MAGIC lines by measuring PRL, LRN, LRL, ARN, and ARL. Through QTL mapping, we identified new potential genes that may be responsible for these traits. Furthermore, we detected single-nucleotide polymorphisms (SNPs) in the coding regions of candidate genes in the founder accessions and the recombinant inbred lines (RILs). We identified a significant region on chromosome 1 associated with AR formation. This region encompasses 316 genes, many of which are involved in auxin and gibberellin signaling and homeostasis. We discovered SNPs in the coding regions of these candidate genes in the founder accessions that may contribute to natural variation in AR characteristics. Additionally, we found a novel gene that encodes a protein from the hydroxyproline-rich glycoprotein family, which exhibits differential SNPs in accessions with contrasting AR formation. This study provides genetic insights into the natural variation in AR numbers using MAGIC lines linked to hormone-related genes.