Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.

Natural variation in Fatty Acid 9 is a determinant of fatty acid and protein content

Soybean is one of the most economically important crops worldwide and an important source of unsaturated fatty acids and protein for the human diet. Consumer demand for healthy fats and oils is increasing, and the global demand for vegetable oil is expected to double by 2050. Identification of key genes that regulate seed fatty acid content can facilitate molecular breeding of high-quality soybean varieties with enhanced fatty acid profiles. Here, we analysed the genetic architecture underlying variations in soybean seed fatty acid content using 547 accessions, including mainly landraces and cultivars from northeastern China. Through fatty acid profiling, genome re-sequencing, population genomics analyses, and GWAS, we identified a SEIPIN homologue at the FA9 locus as an important contributor to seed fatty acid content. Transgenic and multiomics analyses confirmed that FA9 was a key regulator of seed fatty acid content with pleiotropic effects on seed protein and seed size. We identified two major FA9 haplotypes in 1295 resequenced soybean accessions and assessed their phenotypic effects in a field planting of 424 accessions. Soybean accessions carrying FA9H2 had significantly higher total fatty acid contents and lower protein contents than those carrying FA9H1 . FA9H2 was absent in wild soybeans but present in 13% of landraces and 26% of cultivars, suggesting that it may have been selected during soybean post-domestication improvement. FA9 therefore represents a useful genetic resource for molecular breeding of high-quality soybean varieties with specific seed storage profiles.

Meta-Analysis and Multiomics of a Chromosome Segment Substitution Line Reveal Candidate Genes Associated with Seed Hardness in Soybean

Soybean seed hardness is a key trait that influences planting, nutritional quality, and postharvest processing, but its genetic and molecular mechanisms remain to be clarified. We used meta-analysis to detect 17 meta-quantitative trait locus (QTLs) for soybean seed hardness. We then identified a hard-seeded chromosome segment substitution line, R75, with fragments introduced from hard-seeded wild germplasm in four of the meta-QTL intervals. Observations of the seed coat ultrastructure revealed thicker palisade tissue in R75 than in its soft-seeded recurrent parent. Transcriptomics and proteomics of R75 and its recurrent parent revealed multiple candidate genes associated with seed hardness. Fifty-seven were located on homozygous introduced fragments, 26 in meta-QTL intervals, and one in both (Glyma.02G268600). Five initial candidates were selected for KASP marker development on the basis of their predicted functions and nonsynonymous SNPs. The selection efficiency of the markers was as high as 90% for nonhard lines and 43% for hard lines in the chromosome segment substitution line (CSSL) population.

The impact of GmTSA and GmALS on soybean salt tolerance: uncovering the molecular landscape of amino acid and secondary metabolism pathways

KEY MESSAGE

GmTSA and GmALS were screened out for salt stress in soybean and explore the poteintial amino acid secondary metabolism pathways. Soybean (Glycine max L.) is an oil and protein crop of global importance, and salinity has significant effects on soybean growth. Here, a population of soybean chromosome segment substitution lines was screened to identify highly salt-tolerant lines. In total, 24 quantitative trait loci (QTLs) on seven chromosomes were associated with salt tolerance, and CSSL_R71 was selected for further analysis. Although numerous genes were differentially expressed in CSSL_R71 in response to salt statically no differently, transcript levels of classical salt-response genes, including those of the salt overly sensitive pathway. Rather, salt tolerance in CSSL_R71 was associated with changes in amino acid and lipid metabolism. In particular, changes in p-coumaric acid, shikimic acid, and pyrrole-2-carboxylic acid levels accompanied salt tolerance in CSSL_R71. Eleven differentially expressed genes (DEGs) related to amino acid and secondary metabolism were identified as candidate genes on the substituted chromosome fragment. Six of these showed differences in coding sequence between the parental genotypes. Crucially, overexpression of GmTSA (Glyma.03G158400, tryptophan synthase) significantly enhanced salt tolerance in soybean hairy roots, whereas overexpression of GmALS (Glyma.13G241000, acetolactate synthase) decreased salt tolerance. Two KASP markers were developed for GmALS and used to genotype salt-tolerant and salt-sensitive lines in the CSSL population. Non-synonymous mutations were directly associated with salt tolerance. Taken together, these data provide evidence that changes in amino acid and secondary metabolism have the potential to confer salt tolerance in soybean.

Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection

N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3' end of coding sequences and in 3' UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-022-00077-2.