Mutations in the promoter, intron and CDS of two FAD2 generate multiple alleles modulating linoleic acid level in yellow mustard

Linoleic acid (C18:2) is an important polyunsaturated fatty acid in the seed oil of many crops. Here, we report that mutations in the promoter, intron and CDS of the FAD2 genes SalFAD2.LIA1 and SalFAD2.LIA2 generate three alleles LIA (1a), LIA (1b) and lia (1) and two alleles LIA (2) and lia (2), respectively, controlling the C18:2 variation (4.4–32.7%) in yellow mustard. The allelic effect on increasing C18:2 content is LIA (1a) > LIA (1b) > lia (1), LIA (2) > lia (2), and LIA (1a) > LIA (2). The five FAD 2 alleles each contain two exons, one intron and a promoter adjacent to exon 1. LIA (1a) has a 1152 bp CDS, a 1221 bp intron with promoter function and a 607 bp promoter. Compared with LIA (1a), the intron of LIA (1b) has reduced promoter activity and that of LIA (2) and lia (2) has no promoter function due to extensive SNP and indel mutations. lia (1) differed from LIA (1b) by having an insertion of 1223 bp retrotransposon in its intron. lia (2) with mutations in the promoter has reduced promoter activity compared with LIA (2). This study revealed that complex quantitative variation of trait phenotype in plants could be modulated by multiple alleles of oligogenic loci resulting from mutations in the regulatory region and CDS.