Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations

Abstract

Key message fap1 mutation is caused by a G174A change in GmKASIIIA that disrupts a donor splice site recognition and creates a GATCTG motif that enhanced its expression. Abstract Soybean oil with reduced palmitic acid content is desirable to reduce the health risks associated with consumption of this fatty acid. The objectives of this study were: to identify the genomic location of the reduced palmitate fap1 mutation, determine its molecular basis, estimate the amount of phenotypic variation in fatty acid composition explained by this locus, determine if there are epistatic interactions between the fap1 and fap nc loci and, determine if the fap1 mutation has pleiotropic effects on seed yield, oil and protein content in three soybean populations. This study detected two major QTL for 16:0 content located in chromosome 5 (GmFATB1a, fap nc ) and chromosome 9 near BARCSOYSSR_09_1707 that explained, with their interaction, 66-94 % of the variation in 16:0 content in the three populations. Sequencing results of a putative candidate gene, GmKASIIIA, revealed a single unique polymorphism in the germplasm line C1726, which was predicted to disrupt the donor splice site recognition between exon one and intron one and produce a truncated KASIIIA protein. This G to A change also created the GATCTG motif that enhanced gene expression of the mutated GmKASIIIA gene. Lines homozygous for the GmKASIIIA mutation (fap1) had a significant reduction in 16:0, 18:0, and oil content; and an increase in unsaturated fatty acids content. There were significant epistatic interactions between GmKASIIIA (fap1) and fap nc for 16:0 and oil contents, and seed yield in two populations. In conclusion, the fap1 phenotype is caused by a single unique SNP in the GmKASIIIA gene.

A genome-wide association study of seed composition traits in wild soybean (Glycine soja)

“…Because this predominant saturated fatty acid in cultivated soybeans is associated with cardiovascular problems [38], efforts have been made to reduce its level [5, 39, 40]. Considerable success has been achieved with the discovery of alleles at two independent loci , fap1 on chromosome nine and fap3 on chromosome five, either of which can reduce palmitic acid levels to as low as 6% or even lower [41, 42]. Unfortunately, these alleles also tend to decrease overall yield [42] and thus compromise their usefulness in soybean breeding regimes.…”

“…Considerable success has been achieved with the discovery of alleles at two independent loci , fap1 on chromosome nine and fap3 on chromosome five, either of which can reduce palmitic acid levels to as low as 6% or even lower [41, 42]. Unfortunately, these alleles also tend to decrease overall yield [42] and thus compromise their usefulness in soybean breeding regimes. This suggests that a useful alternate might be to screen wild soybeans for accessions with reduced palmitic acid levels to identify novel genes for eventual transfer to domesticated varieties.…”

The Interaction of the Soybean Seed High Oleic Acid Oil Trait With Other Fatty Acid Modifications

“…While null alleles of the KAS III gene in Arabidopsis may be lethal, the soybean genome contains KAS III orthologues on chromosome 09 and 18 that may allow more nuanced phenotypic changes to be revealed by mutation in one or the other gene. The fap1 mutation from C1726 was mapped to Glyma.09g277400, a KAS III variant with a splice‐site mutation (Cardinal et al, ). Selection for this allele in soybean results in lower palmitic acid but no other obvious plant phenotypes, perhaps because of a functionally redundant homologue on chromosome 18.…”

“…Reductions in palmitic acid in soybean seed oil have also been achieved (Cardinal et al, ; De Vries, Fehr, Welke, & Dewey, ; Wilcox & Cavins, ). Several independent mutations in a soybean acyl‐ACP thioesterase B enzyme encoded by the FATB‐1A gene on chromosome 5 (Glyma.05g012300) have been identified and characterized (Cardinal et al, ; De Vries et al, ; Gillman et al, ; Thapa, Carrero‐Colón, & Hudson, ).…”

“…Several independent mutations in a soybean acyl‐ACP thioesterase B enzyme encoded by the FATB‐1A gene on chromosome 5 (Glyma.05g012300) have been identified and characterized (Cardinal et al, ; De Vries et al, ; Gillman et al, ; Thapa, Carrero‐Colón, & Hudson, ). The reduction in soybean seed saturated fatty acids from a splice‐site mutation in a β‐ketoacyl‐[acyl‐carrier‐protein] synthase III gene (KAS III; Glyma.09g277400) was an unexpected result (Cardinal et al, ). The role of the KAS III enzyme was thought to be fundamental to the initiation of fatty acid biosynthesis.…”