A Sequence Variation in GmBADH2 Enhances Soybean Aroma and Is a Functional Marker for Improving Soybean Flavor

Abstract

The vegetable soybean (Glycine max L. Merr.) plant is commonly consumed in Southeast Asian countries because of its nutritional value and desirable taste. A “pandan-like” aroma is an important value-added quality trait that is rarely found in commercial vegetable soybean varieties. In this study, three novel aromatic soybean cultivars with a fragrant volatile compound were isolated. We confirmed that the aroma of these cultivars is due to the potent volatile compound 2-acetyl-1-pyrroline (2AP) that was previously identified in soybean. A sequence comparison of GmBADH1/2 (encoding an aminoaldehyde dehydrogenase) between aromatic and non-aromatic soybean varieties revealed a mutation with 10 SNPs and an 11-nucleotide deletion in exon 1 of GmBADH2 in Quxian No. 1 and Xiangdou. Additionally, a 2-bp deletion was detected in exon 10 of GmBADH2 in ZK1754. The mutations resulted in a frame shift and the introduction of premature stop codons. Moreover, genetic analyses indicated that the aromatic trait in these three varieties was inherited according to a single recessive gene model. These results suggested that a mutated GmBADH2 may be responsible for the aroma of these three aromatic soybean cultivars. The expression and function of GmBADH2 in aromatic soybean seeds were confirmed by qRT-PCR and CRISPR/Cas9. A functional marker developed on the basis of the mutated GmBADH2 sequence in Quxian No. 1 and Xiangdou was validated in an F2 population. A perfect association between the marker genotypes and aroma phenotypes implied that GmBADH2 is a major aroma-conferring gene. The results of this study are potentially useful for an in-depth analysis of the molecular basis of 2-AP formation in soybean and the marker-assisted breeding of aromatic vegetable soybean cultivars.

Global Status of Vegetable Soybean

“…The authors developed PCR-based SNP markers for utilization in breeding programs. This was recently confirmed by Qian et al [ 113 ] in three novel aromatic vegetable soybean varieties (QX1, ZK1754, and XD). The pandan-like fragrant variety Chiang Mai 84-2 has been developed to replace the variety Kaori for export to Japan [ 43 ].…”

Combined Metabolomic and Quantitative RT-PCR Analyses Revealed the Synthetic Differences of 2-Acetyl-1-pyrroline in Aromatic and Non-Aromatic Vegetable Soybeans

“…As shown in previous studies [ 4 , 15 , 17 , 24 , 38 ], the BADH2 gene can be mutated by the loss of two bases in the 10th exon, three SNPs and the deletion of eight bases in the seventh exon, or a seven-base deletion in the second exon. Our analysis of the BADH2 gene sequence revealed that the similar mutation is present in ZK1754, in which there are two TT deletions in the tenth exon.…”

“…In addition, the mutations in OsBADH1 also give rise to aroma in rice [ 14 , 22 ]. Similarly, in aromatic soybeans, a 2-base (TT) deletion in exon ten of GmBADH2 (Glyma05g01770) results in a premature stop codon, leading to non-functional GmBADH2 [ 23 , 24 ]. Suppression of the expression of the GmBADH2 gene by RNAi or CRISPR-Cas9 also confers aroma to non-aromatic soybean [ 4 , 24 ].…”

“…Similarly, in aromatic soybeans, a 2-base (TT) deletion in exon ten of GmBADH2 (Glyma05g01770) results in a premature stop codon, leading to non-functional GmBADH2 [ 23 , 24 ]. Suppression of the expression of the GmBADH2 gene by RNAi or CRISPR-Cas9 also confers aroma to non-aromatic soybean [ 4 , 24 ]. Moreover, the synthesis of 2AP might also be affected by the expression of the GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), TPI (Triosephosphate isomerase), P5CR (Pyrroline-5-carboxylate reductase), PRODH (Proline dehydrogenase), P5CS (Δ 1 -pyrroline-5-carboxylate synthetase), and OAT (Ornithine aminotransferase).…”

Biosynthesis of 2-Acetyl-1-pyrroline in Fragrant Rice: Recent Insights into Agro-management, Environmental Factors, and Functional Genomics

“…Additionally, GmBADH2 was functionally characterized using a CRISPR-Cas9 system with improved aroma in Tianlong No. 1 cultivar . Sorghum, the fifth largest cereal crop in the world, also has one copy of the SbBADH2 gene.…”