Nitrogen (N), phosphorus (P), and potassium (K) are the three most important mineral nutrients for crop growth and development. We previously constructed a genetic map of unigenes (UG-Map) based on their physical positions using a RIL population derived from the cross of “TN18 × LM6” (TL-RILs). In this study, a total of 18 traits related to mineral use efficiency (MUE) of N/P/K were investigated under three growing seasons using TL-RILs. A total of 54 stable QTLs were detected, distributed across 19 chromosomes except for 3A and 5B. There were 50 QTLs associated with only one trait, and the other four QTLs were associated with two traits. A total of 73 candidate genes for stable QTLs were identified. Of these, 50 candidate genes were annotated in Chinese Spring (CS) RefSeq v1.1. The average number of candidate genes per QTL was 1.35, with 45 QTLs containing only one candidate gene and nine QTLs containing two or more candidate genes. The candidate gene TraesCS6D02G132100 (TaPTR gene) for QGnc-6D-3306 belongs to the NPF (NRT1/PTR) gene family. We speculate that the TaPTR gene should regulate the GNC trait.

The basic Helix-Loop-Helix (bHLH) transcription factor family is crucial for plant growth, development, and stress response regulation. Despite previous studies on the bHLH gene family in Lagerstroemia indica, many bHLH genes remain unidentified, hindering further research on LibHLHs. Here, we identified 150 LibHLHs from the genome of L. indica and categorized them into 12 subfamilies (comprising 25 subgroups) showing conservation within subgroups. Cis-acting element analysis suggests roles in plant development, and responses to light, hormones, and stress. Examination of gene expression patterns highlighted the potential involvement of specific genes, such as LibHLH25 in subgroup IIIf, LibHLH68, LibHLH106, and LibHLH142 in subgroup IIIb, and LibHLH112 in subgroup VIIa, in anthocyanin biosynthesis in leaves of L. indica. This investigation enhances our comprehension of the complexity of the bHLH gene family and highlights the potential roles of LibHLHs in anthocyanin biosynthesis in L. indica, offering valuable insights for future genetic breeding endeavors.