Integrated Transcriptomic and Bioinformatics Analyses Reveal the Molecular Mechanisms for the Differences in Seed Oil and Starch Content Between Glycine max and Cicer arietinum

Abstract

The seed oil and starch content of soybean are significantly different from that of chickpea. However, there are limited studies on its molecular mechanisms. To address this issue, we conducted integrated transcriptomic and bioinformatics analyses for species-specific genes and acyl-lipid-, starch-, and carbon metabolism-related genes. Among seven expressional patterns of soybean-specific genes, four were highly expressed at the middle- and late oil accumulation stages; these genes significantly enriched fatty acid synthesis and carbon metabolism, and along with common acetyl CoA carboxylase (ACCase) highly expressed at soybean middle seed development stage, common starch-degrading enzyme beta-amylase-5 (BAM5) was highly expressed at soybean early seed development stage and oil synthesis-related genes ACCase, KAS, KAR, ACP, and long-chain acyl-CoA synthetase (LACS) were co-expressed with WRI1, which may result in high seed oil content and low seed starch content in soybean. The common ADP-glucose pyrophosphorylase (AGPase) was highly expressed at chickpea middle seed development stage, along with more starch biosynthesis genes co-expressed with four-transcription-factor homologous genes in chickpea than in soybean, and the common WRI1 was not co-expressed with oil synthesis genes in chickpea, which may result in high seed starch content and low seed oil content in chickpea. The above results may be used to improve chickpea seed oil content in two ways. One is to edit CaWRI1 to co-express with oil synthesis-related genes, which may increase carbon metabolites flowing to oil synthesis, and another is to increase the expression levels of miRNA159 and miRNA319 to inhibit the expression of MYB33, which may downregulate starch synthesis-related genes, making more carbon metabolites flow into oil synthesis. Our study will provide a basis for future breeding efforts to increase the oil content of chickpea seeds.

Integrated Bioinformatics and Multi-Omics Analyses Reveal Possible Molecular Mechanisms for Seed Starch Content Differences between Glycine max and Cicer arietinum

“…Similar results were also found in low-starch and high-starch pea in Liu et al [67]. Third, we observed that starch synthesis-related genes in chickpea are highly expressed in the later stages of seed development, which is consistent with the main stages (mid-to-late stages) of nutrient accumulation in Steven et al [35], Garg et al [34], and Cheng et al [28]. This is more favorable for seed starch synthesis in chickpea.…”

“…Fourth, Scheidig et al [68] and Zeeman et al [69] showed that BMY activity is positively correlated with the extent of starch degradation, while Andriotis et al [70] found that reduced starch degradation rates in bmy mutants led to increased seed starch content in Arabidopsis. Finally, Cheng et al [28] found that high expression levels of starch synthesis-related genes APS (Ca_07632), APL (Ca_04774), GBSS (Ca_22418), and SSII (Ca_10512) in chickpea during the rapid synthesis stages of storage materials, and high expression levels of starch degradation-related gene BAM during the soybean seed development stages, resulted in higher seed starch content in chickpea compared to soybean. This is consistent with our findings in this study.…”

“…Meanwhile, GmPHS was positively regulated by ERF, bHLH, bZIP, MYB, WRKY, HD-ZIP, and TCP (Figure 5), although there have been no references to the regulation of TFs for PHS [81]. In addition, Cheng et al [28] discovered that the starch synthesis-related gene AGP was highly expressed in chickpea, and more starch biosynthesis genes were co-expressed with TFs in chickpea than in soybean, which may result in higher seed starch content in chickpea. Similarly, in this study, BMY and PHS showed high expression levels in soybean, and GmBMY and GmPHS had more co-expressed TFs, which may result in lower seed starch content in soybean.…”

“…This study aims to fill this knowledge gap by employing multi-omics and bioinformatics analyses to provide an in-depth exploration of the possible molecular mechanisms governing seed starch content in both species. Based on the sucrose and starch metabolism-related genes in Arabidopsis and in Cheng et al [28], this study first used a comparative genomics approach to identify homologous sucrose and starch metabolism-related genes in cultivated soybean and cultivated chickpea. Then, multi-omics datasets from soybean and chickpea were used to investigate their expression patterns, protein interaction networks, the co-expression networks of the above genes and TFs, and the regulatory relationships between miRNAs and genes.…”

Integrated Bioinformatics Analyses of PIN1, CKX, and Yield-Related Genes Reveals the Molecular Mechanisms for the Difference of Seed Number Per Pod Between Soybean and Cowpea

“…The expression patterns of genes in flower, leaf, stem, root, pod, and seed in soybean, cowpea, and kidney bean were analyzed via standardized expression levels, log 2 ( y + 1), where y was real expression level. Relative expression levels were defined as the ratio of the expression level of one gene to average expression level of all the genes in the species (deleting the genes with expression level less than 1.0) ( Zhang et al, 2018 ; Zhou et al, 2019 ; Cheng et al, 2021 ) and used to compare the differences of expression levels of genes in the flowers of soybean and cowpea. The TBtools and SigmaPlot software packages were used to draw HeatMap and relative expression levels, respectively.…”