Considerable genetic variation in agronomic nitrogen (N) use efficiency (NUE) has been reported among genotypes of Brassica napus. However, the physiological and molecular mechanisms underpinning these differences remain poorly understood. In this study, physiological and genetic factors impacting NUE were identified in field trials and hydroponic experiments using two B. napus genotypes with contrasting NUE. The results showed that the N‐efficient genotype (D4‐15) had greater N uptake and utilization efficiencies, more root tips, larger root surface and root volume, and higher N assimilation and photosynthesis capacity than the N‐inefficient genotype (D2‐1). Genomic analysis revealed that D4‐15 had a greater genome diversity related to NUE than D2‐1. By combining genomic and transcriptomic analysis, genes involved in photosynthesis and C/N metabolism were implicated in conferring NUE. Co‐expression network analysis of genes that differed between the two genotypes suggested gene clusters impacting NUE. A nitrate transporter gene BnaA06g04560D (NRT2.1) and two vacuole nitrate transporter CLC genes (BnaA02g11800D and BnaA02g28670D) were up‐regulated by N starvation in D4‐15 but not in D2‐1. The study revealed that high N uptake and utilization efficiencies, maintained photosynthesis and coordinated C/N metabolism confer high NUE in B. napus, and identified candidate genes that could facilitate breeding for enhanced NUE in B. napus.

Summary Brassinosteroids (BRs) are pivotal phytohormones involved in the control of root development. Boron (B) is an essential micronutrient for plants, and root growth is rapidly inhibited under B deficiency conditions. However, the mechanisms underlying this inhibition are still unclear. Here, we identified BR‐related processes underlying B deficiency at the physiological, genetic, molecular/cell biological and transcriptomic levels and found strong evidence that B deficiency can affect BR biosynthesis and signalling, thereby altering root growth. RNA sequencing analysis revealed strong co‐regulation between BR‐regulated genes and B deficiency‐responsive genes. We found that the BR receptor mutants bri1‐119 and bri1‐301 were more insensitive to decreased B supply, and the gain‐of‐function mutants bes1‐D and pBZR1‐bzr1‐D exhibited insensitivity to low‐B stress. Under B deficiency conditions, exogenous 24‐epibrassinolide rescued the inhibition of root growth, and application of the BR biosynthesis inhibitor brassinazole exacerbated this inhibitory effect. The nuclear‐localised signal of BES1 was reduced under low‐B conditions compared with B sufficiency conditions. We further found that B deficiency hindered the accumulation of brassinolide to downregulate BR signalling and modulate root elongation, which may occur through a reduction in BR6ox1 and BR6ox2 mRNA levels. Taken together, our results reveal a role of BR signalling in root elongation under B deficiency.

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