Molecular sequence variations of the lipoxygenase-2 gene in soybean

Abstract

Soybean lipoxygenase genes comprise a multi-gene family, with the seed lipoxygenase isozymes LOX1, LOX2, and LOX3 present in soybean seeds. Among these, the LOX2 isozyme is primarily responsible for the "beany" flavor of most soybean seeds. The variety, Jinpumkong 2, having null alleles (lx1, lx2, and lx3) lacks the three seed lipoxygenases; so, sequence variations between the lipoxygenase-2 genes of Pureunkong (Lx2) and Jinpumkong 2 (lx2) cultivars were examined. One indel, four single nucleotide polymorphisms (SNPs), a 175-bp fragment in the 5'-flanking sequence, and a missense mutation within the coding region were found in Jinpumkong 2. The distribution of the sequence variations was investigated among 90 recombinant inbred lines (RILs) derived from a cross of Pureunkong × Jinpumkong 2 and in 480 germplasm accessions with various origins and maturity groups. Evidence for a genetic bottleneck was observed: the 175-bp fragment was rare in Glycine max, but present in the majority of the G. soja accessions. Furthermore, the 175-bp fragment was not detected in the 5' upstream region of the Lx2 gene on chromosome (Chr) 13 in Williams 82; instead, a similar 175-bp fragment was positioned in the homeologous region on Chr 15. The findings indicated that the novel fragment identified was originally present in the Lx2 region prior to the recent genome duplication in soybean, but became rare in the G. max gene pool. The missense mutation of the conserved histidine residue of the lx2 allele was developed into a single nucleotide-amplified polymorphism (SNAP) marker. The missense mutation showed a perfect correlation with the LOX2-lacking phenotype, so the SNAP marker is expected to facilitate breeding of soybean cultivars which lack the LOX2 isozyme.

Development of SNP Genotyping Assays for Seed Composition Traits in Soybean

“…SP6A-209 was F5 line carrying sts mutant allele with low stachyose and PI 542044 was germplasm with null trypsin inhibitor (KTI). Due to the unavailability of a segregating population for lipoxygenase assays (MU-Lox-1, MU-Lox-2, and MU-Lox-3), the mutant sources PI 408251 [7], Jinpumkong-2 [8] and PI 205085, and PI 417458 [7] were grown in a greenhouse and tested, respectively, along with a nonmutant genotype, cultivar Williams 82 (Table 1). …”

“…Raffinose and stachyose accumulation is indigestible and causes flatulence in poultry, swine, and pets, thereby reducing the economic and dietary value of soybean seeds [6]. Similarly, lipoxygenase (Lpx) [7, 8] and Kunitz trypsin inhibitor (KTI) [9] are important components of soybean seed composition. Reduced content is preferred for reducing undesirable flavor and antinutritional properties.…”

“…Mature soybean seed consists of three distinct lipoxygenase isozymes, lipoxygenase 1 (Glyma13g42320) , lipoxygenase 2 (Glyma13g42310) , and lipoxygenase 3 (Glyma13g42330) . Mutation in these genes leads to reduced lipoxygenase enzyme activity and results in better quality soybean meal [7, 8, 20]. …”

Impacts of genomic research on soybean improvement in East Asia

“…Using the RILs of a cross between Pureunkong 9 and Jinpumkong 2, a 175-bp fragment was identified within the Lx2 gene on chromosome 13 that is retained in G. soja but has become rare in the G. max. A single-nucleotide-amplified polymorphism (SNAP) marker was subsequently made available for soybean breeders to facilitate the identification of cultivars/lines lacking LOX2 (Shin et al 2008(Shin et al , 2012.…”

Characterization of the lipoxygenase (LOX) gene family in the Chinese white pear (Pyrus bretschneideri) and comparison with other members of the Rosaceae

“…There are three different types of LOX in soybean LOX1, LOX2, and LOX3, while the LOX2 isozyme is primarily responsible for the “beany” flavor of most soybean seeds. A single nucleotide-amplified polymorphism (SNP) marker was found to identify the lack of the LOX2 isozyme, and can be used to assist the breeding and selection in this species [19]. A total of 25 LOX genes were identified in apple by mining the whole assembled apple genome [20].…”