Selection of GmSWEET39 for oil and protein improvement in soybean

Abstract

Soybean [Glycine max (L.) Merr.] was domesticated from wild soybean (G. soja Sieb. and Zucc.) and has been further improved as a dual-use seed crop to provide highly valuable oil and protein for food, feed, and industrial applications. However, the underlying genetic and molecular basis remains less understood. Having combined high-confidence bi-parental linkage mapping with high-resolution association analysis based on 631 whole sequenced genomes, we mapped major soybean protein and oil QTLs on chromosome15 to a sugar transporter gene (GmSWEET39). A two-nucleotide CC deletion truncating C-terminus of GmSWEET39 was strongly associated with high seed oil and low seed protein, suggesting its pleiotropic effect on protein and oil content. GmSWEET39 was predominantly expressed in parenchyma and integument of the seed coat, and likely regulates oil and protein accumulation by affecting sugar delivery from maternal seed coat to the filial embryo. We demonstrated that GmSWEET39 has a dual function for both oil and protein improvement and undergoes two different paths of artificial selection. A CC deletion (CC-) haplotype H1 has been intensively selected during domestication and extensively used in soybean improvement worldwide. H1 is fixed in North American soybean cultivars. The protein-favored (CC+) haplotype H3 still undergoes ongoing selection, reflecting its sustainable role for soybean protein improvement. The comprehensive knowledge on the molecular basis underlying the major QTL and GmSWEET39 haplotypes associated with soybean improvement would be valuable to design new strategies for soybean seed quality improvement using molecular breeding and biotechnological approaches.

POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean

“…The phenotypic value of each seed trait analyzed in the study is the accumulative effect of their QTLs across the soybean genome. Multiple causal genes for each seed trait including SWEET10a (also named as SWEET39 ) underlying a major protein and oil QTL have been identified 42 – 44 . The interaction of POWR1 with other QTLs that determine the phenotypic value of the seed traits, however, are still largely unknown.…”

Ensuring Global Food Security by Improving Protein Content in Major Grain Legumes Using Breeding and ‘Omics’ Tools

“…The location of this QTL was subsequently narrowed to 8.4 Mb [162], <1 MB [163], 77.4 kb [137], and even with only three candidate genes [131] on LG20. Likewise, another major SPC QTL, qSeedPro_15, was narrowed to 4 Mb (Zhang et al [164]; see Table 3), overlapping the previously identified genomic region on chromosome 15 [24,131,155,165,166]. Zhang et al [164] elucidated a possible candidate gene Glyma.15G049200 underlying the QTL.…”

“…The authors also elucidated eight novel genomic regions controlling methionine, cysteine, lysine, and threonine contents. A GWAS using whole genome sequencing data of 631 soybean accessions combined with a biparental QTL analysis uncovered a pleotropic gene GmSWEET39 (encoding sugar transporter) controlling SPC and seed oil content in soybean [ 164 ]. The authors also reported that a 2 bp (CC) deletion in Glyma.15G049200 underlying the GmSWEET39 allele rendered high seed oil content and low SPC.…”

“…Current breakthroughs in genome sequencing technologies have facilitated the sequencing of the global germplasm of various crops, including legumes, to underpin novel structural variants (SVs) such as presence/absence and copy number variations prevailing at the genome level [ 232 , 233 ]. An analysis combining association and biparental mapping using WGRS data of 631 soybean genotypes discovered a pleiotropic sugar transporter QTL gene GmSWEET39 on chromosome 15 controlling SPC and seed oil content [ 164 ]. The authors suggested that deletion of 2 bp CC in the underlying causative Glyma.15G049200 gene reduced SPC and enhanced seed oil content.…”

Progress in soybean functional genomics over the past decade

“…GmSWEET15 mediated sucrose export from endosperm to early embryo (Wang et al ., 2019d). GmSWEET10a and GmSWEET10b determined oil and protein contents and seed size simultaneously in soybean through affecting sugar allocation from seed coat to embryo (Miao et al ., 2020; Wang et al ., 2020e; Zhang et al ., 2020c).…”