Simultaneous changes in seed size, oil content and protein content driven by selection of SWEET homologues during soybean domestication

1Studies have suggested that global agricultural production needs to be doubled by 2050 to meet the rapidly growing population and diet shifts, translating into a need for increasing crop production by 2.4% per year. Soybean is a major, multiuse crop that globally makes up 56% of the oilseed production and >25% of the protein used in human food and animal feed. At the current average rate of annual-yield increase, only 55% of the necessary increase in soybean production can be reached by 2050. Thus, breeding soybeans with higher yields is urgently needed.

2Cultivated soybean (Glycine max [L.] Merr.) was domesticated from wild soybean (G. soja Sieb. & Zucc.) in China over a period of 5000 years. Seeds of wild soybeans are generally smaller and contain higher levels of protein. Cultivated soybeans produce larger seeds with higher oil content (Supplementary Fig. 1). Thus far, it has not been reported that a single gene can simultaneously alter seed size, oil content and protein content, although a number of quantitative trait loci (QTLs) that govern seed size, oil content and protein content in soybean were identified through previous genetic analyses (SoyBase, https://soybase.org/). Therefore, it remains unclear whether the improvement in these traits was achieved by selection of a gene with pleiotropic effects on these traits or by selection of individual genes that only affect each trait.

3Sucrose is the main source of carbon energy delivered via the phloem to developing seeds and sugars derived from sucrose metabolism play pivotal roles in seed development for many species. Previous studies have demonstrated that SWEET proteins play important roles in sugar translocation to seeds and consequently affect seed setting, filling and composition. For example, in Arabidopsis thaliana, mutation of AtSWEET11/12/15 impairs sucrose delivery from seed coat and endosperm to embryo and results in severe seed defects. Similarly, knockout of OsSWEET11 and OsSWEET 15 in rice results in a complete loss of endosperm development. Our previous study also illustrated that knockout of both GmSWEET15a and GmSWEET15b in soybean causes an extremely high rate of seed abortion.

4In this study, we found that a pair of SWEET homologues, GmSWEET10a and GmSWEET10b, underwent stepwise selection that simultaneously altered seed size, oil content and protein content during soybean domestication. Our findings provide practical insights into how to improve soybean-seed traits, in particular seed size and oil content, by optimizing the combination of GmSWEET10a and/or GmSWEET10b alleles.

5Using whole-genome re-sequencing data from >800 accessions with an average coverage depth of >13X for each accession, we identified a selective sweep on chromosome 15 from 3.87 to 4.0 Mb. The fixation of this enlargement was observed by different methods, including calculating the nucleotide diversity (π), the fixation index (FST) and the cross-population extended haplotype homozygosity (XP-EHH) (Fig. 1a). This selective sweep overlapped with several reported QTLs that related to seed size, oil content and protein content (Fig. 1a and Supplementary Table 1). The results indicated that selected gene(s) in this region may be responsible for the simultaneous alternation of seed size, oil content and protein content in soybean domestication.

6This selective sweep included 18 gene orders, among which Glyma.15G049200 (previously named GmSWEET10a) encoded a member of the SWEET family of sugar transporters (Fig. 1a). SWEET proteins play important roles in seed development. Transcriptional profiling data from Phytozome 12 (https://phytozome.jgi.doe.gov/pz/portal.html#) showed that GmSWEET10a was specifically expressed in seed and pod (Fig. 1b). Transcriptome data from Gene Networks in Seed Development (http://seedgenenetwork.net/soybean) indicated that GmSWEET10a was mainly expressed in the seed coat (Supplementary Table 2). Quantitative RT-PCR (qRT-PCR) showed that the expression of GmSWEET10a in the seed coats progressively increased during seed development and reached their peaks at the full-seed stage (S5 stage in Supplementary Fig. 2 and Fig. 1c). In situ RNA hybridization confirmed that GmSWEET10a was preferentially expressed in the thick-walled parenchyma of the seed coat (Fig. 1d and e), which are important for sucrose translocation to the embryo. The known functions of SWEET proteins and the expression pattern of GmSWEET10a indicated that it might be the gene responsible for the simultaneous alternation of seed size, oil content and protein content during soybean domestication.

7To verify our hypothesis, we first investigated the genetic variation of GmSWEET10a in wild and cultivated soybeans using our previously reported re-sequenced population. After removing the polymorphisms with minor allele frequency <0.01 (MAF <0.01), 10 SNPs and In/Dels were found in GmSWEET10a in the re-sequenced population. These 10 genetic variants sorted the population into 12 haplotypes, which were represented by one to a few hundred accessions (Fig. 2a). Median-joining network analysis grouped the 12 haplotypes into three major groups, named H_I (including H_I-1 to H_I-8), H_II and H_III (including H_III-1 to H_III-3). H_I was mainly present in wild soybeans, H_II in landraces and H_III in cultivars (Fig. 2b). Allele-frequency investigation demonstrated that the proportion of H_I was significantly decreased in cultivated soybeans compared to that in wild soybeans, whereas the proportion of H_III was significantly increased in cultivated soybeans, indicating strong artificial selection of GmSWEET10a during soybean domestication (Fig. 2c).

8Second, we looked for associations between the genetic variation of GmSWEET10a and seed-related traits, including seed size (indexed by 100-seed weight), protein content and oil content (indexed by total fatty acid) in the re-sequenced soybean accessions. The results showed that the seed size and the oil content of H_III were significantly higher than those of H_II and that these traits of H_II were significantly higher than those of H_I. In contrast, the protein content of H_III was significantly lower than that of H_II and that of H_II was significantly lower than that of H_I (Fig. 2d). The results indicated that selection at GmSWEET10a during soybean domestication pleiotropically affected the seed size, oil content and protein content. The decrease in protein content could also be a consequence of a rise in the seed size and oil content because the precursor supply may become limiting for protein synthesis when the GmSWEET10a-mediated sugar unloading from seed coats increases the carbohydrate state in developing embryos. Since wild soybeans usually exhibit drastically smaller seeds, higher protein content and lower oil content than cultivated soybean (Supplementary Fig. 1), these three traits were further compared among different haplotypes only in the cultivated soybeans to eliminate the effect of genetic differences between wild and cultivated soybeans. Further, because only a few cultivated accessions had H_I haplotypes, only the differences between H_II and H_III cultivated soybeans were compared. In H_III haplotypes, the seed size and oil content were significantly higher but the protein content was lower than in H_II haplotypes (Supplementary Fig. 3).

9To verify whether GmSWEET10a simultaneously affected the seed size, oil content and protein content, two pairs of near-isogenic lines (NILs) were developed: (i) NILsA carrying either H_I (NILA-H_I) or H_III (NILA-H_III) through a cross of HJ117 (carrying H_I) and JY101 (carrying H_III) (Fig. 2e); and (ii) NILsB carrying either H_II (NILB-H_II) or H_III (NILB-H_III) through a cross of Enrei (carrying H_II) and Suinong 14 (carrying H_III) (Fig. 2f). Phenotypic analysis showed that NILA-H_III or NILB-H_III lines had significantly higher 100-seed weight and oil content and lower protein content than did NILA-H_I or NILB-H_II, respectively (Fig. 2e and f).

10The functions of GmSWEET10a were further confirmed by genetic manipulation. A knockout line, named sw10a, was generated by an Agrobacterium-delivered CRISPR/Cas9 system in the soybean cultivar Williams 82 (Fig. 3a). Compared with Williams 82, sw10a seeds exhibited significantly decreased seed size, lower oil content and increased protein content (Fig. 3c–f). Two independent GmSWEET10a-overexpression lines, OE-10a-1 and OE-10a-2, were generated by introducing an additional copy of the GmSWEET10a genomic sequence into the Williams 82 genome, with a significantly increased transcript level of GmSWEET10a (Fig. 3b). Compared with Williams 82, the seed size and oil content were significantly increased and the protein content was significantly decreased in OE-10a-1 and OE-10a-2 (Fig. 3c–f). A recent study showed that a 9-base pair deletion in the promoter of GmSWEET10a upregulates the expression of GmSWEET10a, which potentially leads to increased oil content in cultivated soybeans. Here, our results in transgenic soybean clarified that the larger seed size, higher oil content and lower protein content in H_III cultivars are indeed caused by the upregulation of GmSWEET10a.

11GmSWEET10b is a close homologue of GmSWEET10a. GmSWEET10b showed an expression pattern similar to, but at higher levels than, GmSWEET10a (Fig. 4a and b, and Supplementary Table 2). In situ RNA hybridization showed that GmSWEET10b also exhibited specific localization in the thick-walled parenchymatous layer of the seed coat, but not in the embryo (Fig. 4c and d). We investigated whether GmSWEET10b also played a role in controlling these three seed traits. GmSWEET10b-knockout and -overexpression lines were generated. The results demonstrated that GmSWEET10b had a similar function to that of GmSWEET10a (Fig. 4e–j). Moreover, a double knockout of both GmSWEET10a and GmSWEET10b in Williams 82 and Huachun 6 genetic backgrounds resulted in significantly smaller seed size, lower oil content and higher protein content than either of the single knockout lines or the WT (Williams 82) (Supplementary Fig. 4), indicating that GmSWEET10b and GmSWEET10a have functional redundancy in controlling seed development.

12Similarly, the genetic variation of GmSWEET10b was investigated in the re-sequenced population. The nucleotide polymorphisms of this gene classified the accessions into 26 haplotypes, which were then sorted into three major groups by further phylogenetic analysis (Fig. 5a). We found that, although the ratios of H_I to H_II and H_I to H_III were greatly decreased from wild soybeans to cultivated soybeans (Fig. 5b), GmSWEET10b did not show significantly artificial selection during soybean domestication at the genome-wide level (Fig. 5c). However, similarly to GmSWEET10a, the haplotypes mainly present in cultivated soybeans exhibited significantly higher seed size and oil content but lower protein content than the haplotype mainly present in wild soybeans (Fig. 5d–f), suggesting that GmSWEET10b may still be undergoing selection.

13Previous studies have shown that SWEET proteins can transport either mono- or disaccharides or both. To first test the sugar-transport activities of GmSWEET10a and GmSWEET10b, we used a newly improved, high-affinity sensor named FLIPsuc-2-10μ with new N-terminal and C-terminal linkers and constructs with the 5’UTRs and codons optimized for humans. When this sensor was co-expressed with GmSWEET10a or GmSWEET10b in the human embryonic kidney line HEK293T, weak sucrose transport activity was detected (as a negative ratio change) when 40 mM sucrose was supplied (Fig. 6a). Sucrose transport by GmSWEET10a and GmSWEET10b was further confirmed by 14C-sucrose radiotracer uptake experiments in Xenopus oocytes (Fig. 6b). GmSWEET10a and GmSWEET10b can also uptake glucose and fructose in oocytes.

14It is possible that the reduced seed weight in the double sw10a;10b mutant is caused by the low availability of sugars in embryos, similar to what is observed in atsweet11;12;15. To investigate this, sugar levels were measured in isolated seed coats and embryos at the end of the transition phase (14–16 DAF) and storage phase I (20–22 DAF) in WT (Williams 82) and sw10a;10b mutants. In the embryos of the sw10a;10b mutants, the glucose, fructose and sucrose levels were significantly lower at both stages compared to those of WT (Fig. 6c and d). In contrast, in the seed coat of the sw10a;10b mutants, the sucrose content was significantly higher at 14–16 DAF and the hexose content was significantly higher at 20–22 DAF compared with those of WT. Our results indicated that the transport of these three forms of sugar from the seed coat to the embryo are impaired in the sw10a;10b mutant (Fig. 6c and d). This suggests that GmSWEET10a and GmSWEET10b largely determine sugar partitioning between the seed coat and the embryo.

15Previous studies showed that sugar allocation affects embryo development and regulates both fatty-acid biosynthesis and protein biosynthesis. Thus, we speculated that the increased seed size and higher oil content that arose through soybean domestication might be caused by increasing the sugar content in the embryo through the selection of elite GmSWEET10a alleles.

16Seed size, oil content and protein content are essential factors for soybean yield and quality. Each of these quantitative traits is controlled by multiple genetic loci. At least 267, 299 and 225 QTLs have been reported to be responsible for the seed size, oil content and protein content in soybean, respectively (retrieved from SoyBase, https://soybase.org/). In the study, we have shown that GmSWEET10a and GmSWEET10b are specifically expressed in the seed coat, likely transport sugars from seed coats to embryos and genetically regulate seed size and composition. GmSWEET10a is a QTL that genetically regulates seed size and composition simultaneously, and was subjected to strong artificial selection during soybean domestication. However, plots of the 100-seed weight against the fatty-acid content and the protein content from the natural population showed that there are cultivated soybeans combining the traits of large seed and high oil content or the traits of large seeds and high protein content (Supplementary Fig. 1d and e). Thus, selections on other genes that do not have pleiotropic effects on these three traits likely occur.

17A working model of GmSWEET10a and GmSWEET10b function and their contribution to soybean domestication is proposed (Fig. 6e). At the seed-storage stage, sucrose, as the major carbon source, is delivered to the seed coat via the funicular phloem. Then sucrose, together with a few hexoses (including glucose and fructose) presumably hydrolysed from sucrose, is exported into the cell-wall space via GmSWEET10a and GmSWEET10b, and subsequently imported into the embryo by other sugar transporters. Imported sugars are metabolized for energy generation and carbon skeleton supply for the synthesis of storage compounds including lipids, proteins and starch.

18Sucrose concentrations in seed coats and embryos reach a high and steady level at the rapid-seed-growth stage. Thus, sucrose flux across seed coats is particularly important to meet the increasing demand for a carbon source for a high rate of seed growth. Haplotype III of GmSWEET10a was selected during soybean domestication (from G. soja to G. max) because it confers a relatively higher expression of GmSWEET10a, which allows more sucrose to flux to the developing embryos at the rapid-seed-growth stage, and consequently leads to a higher seed-growth rate, larger seed and higher oil content. The selection of GmSWEET10b is currently ongoing and presumably leads to a selected function in contributing to seed-size-storage components, like GmSWEET10a.

19The positive contribution of GmSWEET10a and 10b to seed size and oil content can be attributed to the following reasons. First, the elevated expression of the sugar transporter GmSWEET10a or GmSWEET10b can lead to the flux of more sugars into embryos from maternal tissues. It may trigger embryo cell division and expansion, and consequently larger seeds. Second, the increased transport of sugars into the embryos would result in an increase in the carbon resources for lipid synthesis. Some intermediates derived from glycolysis are directly or indirectly shared by lipid- and protein-synthesis pathways. Lipid synthesis may be enhanced due to more precursor of acetyl-CoA available from glycolysis and thus more lipid can be produced and accumulate. On the other hand, protein synthesis depends on both carbon and nitrogen availability. As GmSWEET10a or GmSWEET10b sugar-transporter activities increase, the nitrogen availability may become a limiting factor and thereby decrease the relative protein contents.

20The knocking out of GmSWEET10a resulted in a 7.4% and 7.2% decrease in the 100-seed weight and fatty-acid content, but a 6.4% increase in the protein content (Fig. 3d–f). A similar effect was observed for its homologue GmSWEET10b (Fig. 4h–j). When both GmSWEET10a and GmSWEET10b were knocked out, the impact on these parameters increased to –40.2%, –40.7% and +32.1%, respectively (Supplemental Fig. 4b–d and f–h). These seed phenotypes supported that GmSWEET10a and GmSWEET10b are essential sugar transporters for sugar unloading from the soybean-seed coat to the embryos. It is worth noting that the knockout of GmSWEET10b has a stronger impact on the seed weight, as well as the oil and protein content, compared with GmSWEET10a (Figs 3d–f and 4h–j). This indeed is consistent with the transcript-level difference in their transcript abundance (Figs 1c and 4b), although not proportionate to the 10-fold difference at their transcript levels. It requires further study to determine whether their protein abundance and transporter activities correspond to their transcript abundance.

21In addition to that, we retrieved the expression data of all the members of the SWEET and SUT/SUF family, which includes genes that have been implicated in exporting sucrose from the seed coat in pea and bean in the seed coats from Gene Networks in Seed Development (Supplemental Table 2). Among the 27 SWEET and SUT/SUF genes analysed, only GmSWEET10s, GmSWEET13s and GmSWEET14s were expressed in seed coats. RT-qPCR showed that GmSWEET13s and GmSWEET14s were indeed expressed in seed coats, although at a lower level than in GmSWEET10a and GmSWEET10b (Supplemental Fig. 5a and b). Thus, whereas we speculate that, while GmSWEET10a and GmSWEET10b play essential roles in sugar unloading from the seed coats to the embryos, other uncharacterized sugar transporters, such as GmSWEET13s and GmSWEET14s, may also play roles, either due to their inherent function or as a compensation mechanism in the absence of GmSWEET10a and GmSWEET10b.

22Introduction of an additional genomic copy of either GmSWEET10a or GmSWEET10b into soybean led to significant increases in yield, ranging from 11% to 20%, without the compromise of other agronomic traits (Supplementary Fig. 6). Genome editing is a powerful approach for targeted mutagenesis and has been successfully used for crop-trait improvement. A recent study found that disruption of MIR396e and MIR396f by CRISPR/Cas9 significantly improves rice yield under nitrogen-deficient conditions. We speculate that alteration of the expression of GmSWEET10a and GmSWEET10b by precise genome editing may enhance seed and oil yield in soybean. Furthermore, since GmSWEET10b has not yet been fixed in cultivated soybeans, the further discovery and utilization of elite allele(s) of GmSWEET10b may provide a new avenue for future soybean breeding. Another member of the SWEET family, SWEET4, was found to be likely selected during the domestication of both maize and rice, indicating that a parallel selection of the SWEET family members may exist across different crop species during domestication. Identification of these genes would facilitate the improvement of current crops. Thus, SWEET genes should be priority targets across a wide range of species for the improvement of crops and possibly even underused or undomesticated plants.

23For details, please see Supplementary data.