Transcriptional Analysis Reveals the Differences in Response of Floral Buds to Boron Deficiency Between Two Contrasting <i>Brassica napus</i> Varieties

Boron (B) is an essential micronutrient for the development of crops, and its reproductive stage is particularly sensitive to B deficiency. <i>Brassica napus</i> L., as an important oil-crop species, is extremely vulnerable to B deficiency. The typical B-deficient symptom of “flowering without seed setting” usually results in severe yield loss. However, few studies have focused on the response of the reproductive organs to B deficiency. In this study, the B-efficient variety “Zhongshuang 11” (ZS11) and the B-inefficient variety “Westar 10” (W10) of <i>Brassica napus</i> were selected to be cultivated at the developmental stage (BBCH15) in a pot experiment, both with and without B supply. Clear phenotype differences in B deficiency between the two varieties’ flowers appeared only at the reproductive stage, and only W10 showed symptoms of delayed flower opening, stigma exsertion, and resulted in abortion. Transcriptome analysis for the early buds of both varieties between B supply (+B) and free (−B) treatments revealed that W10 had more differentially expressed genes (DEGs) corresponding to its greater susceptibility to −B. As two potential mechanisms to improve B-efficient utilization, we focused on analyzing the expression profiles of B transporter-related genes and phytohormone metabolism-related genes. <i>BnaC05.NIP7;1</i>, <i>BnaC08.NIP3;1,</i> and <i>BnaBOR2s</i> were identified as the key genes which could enhance the capacity of B translocation to buds of ZS11. Additionally, combined with a phytohormone concentration measurement, we showed that a significant increase in IAA and a drastic decrease in JA could predominantly lead to the abnormal development of W10’s buds. <i>BnaC02.NIT2</i> (<i>Nitrilase 2</i>) and <i>BnaKAT5s</i> (<i>3-Ketoacyl-CoA Thiolase 5</i>), which are IAA and JA biosynthesis genes, respectively, could be the key genes responsible for the changes in IAA and JA concentrations in W10’s buds under −B. These candidate genes may regulate the genotype differences in the response of the rapeseed reproductive stage to −B between different B-efficient varieties. It also has potential to breed rapeseed varieties with B-efficient utilization in the reproductive stage, which would improve the seed yield under −B condition.