A genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.

Rapeseed (Brassica napus L.) is a major oil crop worldwide that is vigorously promoted for cultivation in China. Boron (B) is an essential micronutrient for plant growth and development. However, the agricultural soils in rapeseed planting areas often show either B deficiency or severe B deficiency. Increasing the resistance to B deficiency is a pivotal goal in the breeding of rapeseed, yet the genetic basis for variations in B efficiency-related traits remains unclear. In this study, a natural population with 391 rapeseed accessions and a nutrient solution system were used to investigate B efficiency-related traits, including relative root length (RRL), shoot dry weight (SDW), root dry weight (RDW), and B efficiency coefficient (BEC), all of which exhibited extensive phenotypic variations under B deficiency. Through a genome-wide association study (GWAS) of B efficiency-related traits using high-density SNP markers obtained from whole-genome resequencing, 106 significantly associated SNPs were identified by employing both the general linear model and the mixed linear model. Among these SNP loci, two prominent SNP clusters were detected on chrA03: 14,087,835–14,764,672 and chrC03: 20,110,319–22,135,492 at low B levels across three repeated experiments of multiple traits. Integrating those results with a transcriptome analysis, four genes exhibiting higher differentially expressed fold-change along with favorable haplotypes within the promoter or coding region, BnaA03g29020D, BnaA03g29440D, BnaC03g33010D, and BnaC03g34490D, were identified as candidate genes that could potentially be involved in efficient B utilization, and their favorable haplotypes were found to improve seedling growth and productivity under B deficiency. Considering the lack of B mineral resources in China, the rapid and accurate identification of more B-efficient alleles and studying the genetic mechanism underlying crop responses to B deficiency have important theoretical and practical significance for cultivating B-efficient varieties and maintaining green, sustainable agriculture.