The function of the root system is crucial for plant survival, such as anchoring plants, absorbing nutrients and water from the soil, and adapting to stress. MYB transcription factors constitute one of the largest transcription factor families in plant genomes with structural and functional diversifications. Members of this superfamily in plant development and cell differentiation, specialized metabolism, and biotic and abiotic stress processes are widely recognized, but their roles in plant roots are still not well characterized. Recent advances in functional studies remind us that MYB genes may have potentially key roles in roots. In this review, the current knowledge about the functions of MYB genes in roots was summarized, including promoting cell differentiation, regulating cell division through cell cycle, response to biotic and abiotic stresses (e.g., drought, salt stress, nutrient stress, light, gravity, and fungi), and mediate phytohormone signals. MYB genes from the same subfamily tend to regulate similar biological processes in roots in redundant but precise ways. Given their increasing known functions and wide expression profiles in roots, MYB genes are proposed as key components of the gene regulatory networks associated with distinct biological processes in roots. Further functional studies of MYB genes will provide an important basis for root regulatory mechanisms, enabling a more inclusive green revolution and sustainable agriculture to face the constant changes in climate and environmental conditions.

Alfin-like proteins (ALs) form a plant-specific transcription factor (TF) gene family involved in the regulation of plant growth and development, and abiotic stress response. In this study, 30 ALs were identified in Brassica napus ecotype ‘Zhongshuang 11’ genome (BnaALs), and unevenly distributed on 15 chromosomes. Structural characteristic analysis showed that all of the BnaALs contained two highly conserved domains: the N terminal DUF3594 domain and the C-terminal PHD-finger domain. The BnaALs were classified into four groups (Group I-IV), supported by conserved intron–exon and protein motif structures in each group. The allopolyploid event between B. oleracea and B. rapa ancestors and the small-scale duplication events in B. napus both contributed to the large BnaALs expansion. The promoter regions of BnaALs contained multiple abiotic stress cis-elements. The BnaALs in I-IV groups were mainly expressed in cotyledon, petal, root, silique, and seed tissues, and the duplicated gene pairs shared highly similar expression patterns. RNA-seq and RT-qPCR analysis showed that BnaALs were obviously induced by low nitrogen (LN) and low phosphorus (LP) treatments in roots. Overexpressing BnaAL02 and BnaAL28 in Arabidopsis demonstrated their functions in response to LN and LP stresses. BnaAL28 enhanced primary roots’ (PRs) length and lateral roots’ (LRs) number under LP and LN conditions, where BnaAL02 can inhibit LR numbers under the two conditions. They can promote root hair (RH) elongation under LP conditions; however, they suppressed RH elongation under LN conditions. Our result provides new insight into the functional dissection of this family in response to nutrient stresses in plants.

Brassica napus L. is one of the most important oil crops in the world, and improving its nitrogen efficiency is a key strategy for enhancing low-nitrogen tolerance and increasing yield. Ammonium transporters (AMTs) play critical roles in NH₄⁺ transport in plants and significantly influence nitrogen use efficiency and yield. To identify promising candidate AMT genes for rapeseed improvement, this study systematically analyzed the evolution and expression of AMT genes across the Archaeplastida plants, especially in Brassica species of the U’s triangle. A total of 368 AMT genes were identified from 35 Archaeplastida species, including 180 AMT1 and 188 AMT2 homologs. Gene duplication analysis revealed that small-scale duplication (SSD) was the primary mechanism driving gene expansion from aquatic algae to angiosperms in both AMT1 and AMT2 families, which were under the influence of purifying selection. In the U’s triangle, allopolyploidization, particularly whole-genome duplication (WGD), was the primary mechanism for AMT expansion, accompanied by gene loss. Expression profiling indicated that most BnAMTs respond to hormonal and low-nitrogen signals and exhibit tissue-specific expression patterns. Notably, four candidate genes (BnAMT1;5, BnAMT1;12, BnAMT2;2, BnAMT2;4) exhibited high expression levels and responsiveness to low-nitrogen stress. Haplotype analysis further linked specific polymorphisms in BnAMT1;5 and BnAMT2;2 to variations in plant height and yield. Collectively, these findings elucidate the evolutionary processes and regulatory mechanisms of AMTs, laying a foundation for enhancing nitrogen utilization efficiency in B. napus and other crops.

The root system is vital for Brassica napus water/nutrient uptake and anchorage, highlighting the importance of identifying root development genes (RDGs). In this study, we identified 218 RDGs in B. napus through homology-based retrieval. Phylogenetic analysis of 22 representative species revealed that the RDGs are widely present in plants ranging from aquatic algae to angiosperms. RDGs in B. napus expanded through whole-genome duplication (WGD) events between Brassica rapa and Brassica oleracea ancestors and smaller duplications specific to B. napus. Promoter analysis identified 115 cis-elements, mainly abiotic stress-related and light-responsive. Transcription factor networks showed regulation by BBR-BPC, MIKC_MADS, AP2, and GRAS families. Transcriptome analysis under multiple stresses revealed that low nitrogen (LN) induced the most pronounced changes, with >50% (109/218) of RDGs differentially expressed in roots. Furthermore, we screened the BnaSHR-6 gene, which is co-localized in both primary roots (PR) and lateral roots (LR), and responds strongly to LN. Phenotypic analysis revealed that the BnaSHR-6 gene regulates the growth and development of both PR and LR under LN conditions, and confers a degree of resistance. These findings advance our understanding of RDGs in B. napus and provide valuable gene resources for subsequent molecular breeding.