Identification of quantitative trait loci for increased α-tocopherol biosynthesis in wild soybean using a high-density genetic map

Abstract

BackgroundSoybean is one of the most important crop sources of tocopherols (Toc). However, the content of α-Toc, an isoform with the highest vitamin E activity in humans, is low in most cultivars. With the aim of broadening genetic variability, we performed quantitative trait locus (QTL) analysis for a high seed α-Toc trait detected in a wild soybean and characterized the sequence polymorphisms and expression profiles of γ-tocopherol methyltransferase (γ-TMT) genes as potential candidates.ResultsA recombinant inbred line population was developed from a cross between the low α-Toc breeding line TK780 and the high α-Toc wild accession B04009. The α-Toc content in seeds correlated strongly with the ratio of α-Toc to γ-Toc contents. QTL analysis using a high-density map constructed with 7710 single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA sequencing detected six QTLs involved in α-Toc biosynthesis. Of these, three in chromosomes (Chr) 9, 11, and 12 produced consistent effects during a 2-year trial. B04009 allele at QTLs in Chr9 and Chr12 and TK780 allele at the QTL in Chr11 each promoted the conversion of γ-Toc to α-Toc, which elevated the seed α-Toc content. SNPs and indels were detected between the parents in three γ-TMT genes (γ-TMT1, γ-TMT2, and γ-TMT3) co-located in the QTLs in Chr9 and Chr12, of which some existed in the cis-regulatory elements associated with seed development and functions. In immature cotyledons, γ-TMT3 was expressed at higher levels in B04009 than TK780, irrespective of two thermal conditions tested, whereas the expression of γ-TMT2 was markedly upregulated under higher temperatures, particularly in B04009.ConclusionsWe identified QTLs consistently controlling α-Toc biosynthesis in wild soybean seeds in 2-year trials. The QTL on Chr9 had been previously identified in soybean, whereas the QTLs on Chr11 and Chr12 were novel. Further molecular dissections and characterization of the QTLs may facilitate the use of high α-Toc alleles from wild soybean in soybean breeding and an understanding of the molecular mechanisms underlying α-Toc biosynthesis in soybean seeds.

Identification of Loci and Candidate Genes Analyses for Tocopherol Concentration of Soybean Seed

“…Glyma.18G115500 (located near QTN rs14143396 on Chr.18) was derived from the superfamily of NAD(P)-linked oxidoreductase. Two genes belonging to the zinc finger superfamily, including Glyma.01G021100 and Glyma.20G113200 located near QTN rs2162876 on Chr.01 and rs35562231 on Chr.20, respectively, might aid in the soybean Toc concentration with higher expressions in soybean seeds and pods ( ) ( Park et al., 2019 ). Glyma.02G102900 is a protein containing plant U-box domain (PUB26), which triggers the accumulation of Toc content by regulating the transient burst of reactive oxygen species (ROS) ( Kadota et al., 2014 ; Li et al., 2014 ; Stahl et al., 2019 ).…”

“…Toc is a member of the family of structurally-related compounds, including α -, β -, γ - and δ -Toc, and four corresponding unsaturated derivatives, α -, β -, γ - and δ -tocotrienols ( Wan et al., 2008 ). All Tocs are amphipathic molecules and contain a polar chromanol head group, which is derived from homogentisic acid and a lipophilic tail from phytyl-diphosphate ( Maheswari et al., 2015 ; Park et al., 2019 ). In soybean oil, the biological activities of four individual Tocs vary with the number and position of methyl groups on the chromanol ring ( Bramley et al., 2000 ).…”

“…The biological activities of α -, β -, γ -, and δ -Toc are 100, 50, 10 and 3% equivalent to that of α -Toc activity ( Kamal-Eldin and Appelqvist, 1996 ; Wan et al., 2008 ). The proportion of α -Toc is usually less than 10% of the total Toc in soybean seeds ( Park et al., 2019 ). The demand for Toc has increased due to the increasing interest in functional foods and meat products.…”

Soybean and wild soybean genetic diversity for new functional food resources, focusing on tocopherol, lutein, and saponin

“…Difference in temperature response may be resulted from genetic variations in genes involved in tocopherol biosynthesis pathway. Park et al (2019) investigated the expression level of three soybean genes (γ-TMT1, γ-TMT2, and γ-TMT3) encoding γtocopherol methyltransferase of developing seeds of TK780 (soybean, low α-tocopherol ratio) and B04009 (wild soybean, high α-tocopherol ratio) grown in 20℃ and 30℃ during seed filling. Previous studies showed that genetic variations in γ-TMT3 are associated with high α-tocopherol ratio in KAS (Dwiyanti et al 2011) and B04009 (Park et al 2019).…”

“…Park et al (2019) investigated the expression level of three soybean genes (γ-TMT1, γ-TMT2, and γ-TMT3) encoding γtocopherol methyltransferase of developing seeds of TK780 (soybean, low α-tocopherol ratio) and B04009 (wild soybean, high α-tocopherol ratio) grown in 20℃ and 30℃ during seed filling. Previous studies showed that genetic variations in γ-TMT3 are associated with high α-tocopherol ratio in KAS (Dwiyanti et al 2011) and B04009 (Park et al 2019). Interestingly, the gene expression analysis showed that only γ-TMT2 expression level increased in both genotypes when temperature increased to 30℃.…”