Identification of genetic loci for salt tolerance in Brassica napus at the germination stage using a genome-wide association study

Abstract

Brassica napus is a leading crop used to repair and utilize saline-alkali land. Cultivating salt-tolerant varieties of B. napus is therefore an effective means of increasing the productivity of saline-alkali land. However, the molecular regulation of salt tolerance during germination in B. napus is still unclear. In this study, seeds from an association panel containing 202 diverse accessions were treated with different concentrations of NaCl solution (200, 250, and 300 mM), and their relative germination rates (RGRs) were calculated on Days 3 and 7 after treatment. Based on phenotypic data obtained over six experiments, a total of 2749 single nucleotide polymorphisms (SNPs) significantly related to RGR were identified using a genome-wide association study (GWAS) analysis, and eight candidate genes were identified in candidate intervals. The RGR of seeds treated with 250 mM NaCl for 7 days was identified as a useful index of salt tolerance in B. napus, and 10 accessions with RGRs of 90–98 % were screened as excellent salt-tolerant germplasm resources. Finally, two of the identified SNPs were designed as SNP markers to screen salt-tolerant germplasm resources. These results provide a theoretical basis on which to determine the molecular mechanism of salt tolerance in B. napus at the germination stage.