Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

Turquetti-Moraes, Dayana K.; Moharana, Kanhu C.; Almeida‐Silva, Fabricio; Pedrosa-Silva, Francisnei; Venâncio, Thiago M.

doi:10.1016/j.gene.2021.145976

Cited by 12 publications

(9 citation statements)

References 94 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Research showed that reducing the α-linolenic and saturated fats does not affect the concentrations of beneficial phytochemicals and antioxidants 68 . Recent discoveries on the function of key genes in fatty acids synthesis can be used to improve soy oil profile 69 . Concentrations of oleic acid higher than 70% and concentrations of α-linolenic lower than 3% improve oil stability and provide health benefits as food and feed 70 , 71 .…”

Section: Resultsmentioning

confidence: 99%

European soybean to benefit people and the environment

Rotundo,

Marshall,

McCormick

et al. 2024

Sci Rep

View full text Add to dashboard Cite

Europe imports large amounts of soybean that are predominantly used for livestock feed, mainly sourced from Brazil, USA and Argentina. In addition, the demand for GM-free soybean for human consumption is project to increase. Soybean has higher protein quality and digestibility than other legumes, along with high concentrations of isoflavones, phytosterols and minerals that enhance the nutritional value as a human food ingredient. Here, we examine the potential to increase soybean production across Europe for livestock feed and direct human consumption, and review possible effects on the environment and human health. Simulations and field data indicate rainfed soybean yields of 3.1 ± 1.2 t ha−1 from southern UK through to southern Europe (compared to a 3.5 t ha−1 average from North America). Drought-prone southern regions and cooler northern regions require breeding to incorporate stress-tolerance traits. Literature synthesized in this work evidenced soybean properties important to human nutrition, health, and traits related to food processing compared to alternative protein sources. While acknowledging the uncertainties inherent in any modelling exercise, our findings suggest that further integrating soybean into European agriculture could reduce GHG emissions by 37–291 Mt CO2e year−1 and fertiliser N use by 0.6–1.2 Mt year−1, concurrently improving human health and nutrition.

show abstract

Section: Resultsmentioning

confidence: 99%

European soybean to benefit people and the environment

Rotundo,

Marshall,

McCormick

et al. 2024

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Glyma.02G006100, Glyma.02G281500, Glyma.08G064400, Glyma.16G133700, and Glyma.20G068000) reported as candidates to improve oil quality in soybean (Niu et al 2020) (Supplementary Table 1; Supplementary Figure 1). These results indicate that the basic genetic machinery responsible for oil accumulation in soybean was already present in its last common ancestor shared with common bean, strongly suggesting that oil richness was acquired via expansions or contractions of extant gene families, mutations, and changes in transcriptional and epigenetic regulation, which were at least partially influenced by anthropogenic processes such as domestication and breeding (Turquetti-Moraes et al 2022;J. Wang et al 2020;M.…”

Section: Soybean Genes Involved In Oil Traits Belong To Families Shar...mentioning

confidence: 96%

Multiomic analysis of genes related to oil traits in legumes provide insights into lipid metabolism and oil richness in soybean

Turquetti-Moraes,

Cardoso-Silva,

Almeida-Silva

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Soybean (Glycine max) and common bean (Phaseolus vulgaris) diverged approximately 19 million years ago. While these species share a whole-genome duplication (WGD), the Glycine lineage experienced a second, independent WGD. Despite the significance of these WGDs, their impact on gene families related to oil-traits remains poorly understood. Here, we report an in-depth investigation of oil-related gene families in soybean, common bean, and twenty-eight other legume species. We adopted a systematic approach that included transcriptome and co-expression analysis, identification of orthologous groups, gene duplication modes and evolutionary rates, and family expansions and contractions. We curated a list of oil candidate genes and found that 91.5% of the families containing these genes expanded in soybean in comparison to common bean. Notably, we observed an expansion of triacylglycerol (TAG) biosynthesis (~3:1) and an erosion of TAG degradation (~1.4:1) families in soybean in comparison to common bean. In addition, TAG degradation genes were two-fold more expressed in common bean than in soybean, suggesting that oil degradation is also important for the sharply contrasting seed oil contents in these species. We found 17 transcription factor hub genes that are likely regulators of lipid metabolism. Finally, we inferred expanded and contracted families and correlated these patterns with oil content found in different legume species. In summary, our results do not only shed light on the evolution of oil metabolism genes in soybean, but also present multifactorial evidence supporting the prioritization of candidates for crop improvement.

show abstract

“…The analysis of regulatory elements in the potential promoters of RA1 and RA1-like genes identified binding motifs for TFs involved in seed germination (ABI3, [77]; ABI5, [78]; FUS3, [79]), plant development (BPC5, BPC6, [80]; TB1, [81]; ARF4, [82]; ARF16, [83]; RA1, [2]; SMZ, TGA9, [84]; bHLH130, [85]; SPL14, [86]; ATHB12, [87]; AGL27, [88]; AGL42, [89]; CDF5, [90]; ARALYDRAFT_897773, also known as TCP4, [91]; ARALYDRAFT_496250, also known as TCP5, [92]; GRF9, [93]; ANL2, [94]; PLT1, [95]; HHO3, [96]; ABF2, [97]; DOF3.6, [98]), response to abiotic stress (DREB1E, [99]; ERF008, [100]; ERF055, [101]; ERF115, [102]; NAC020, [103]; NAC045, [104]; NAC092, [105]; OsRR22, [106]), and response to biotic stress (WRKY62, [107]; WRKY75, [108]; MYB73, [109]).…”

Section: Duplication Of Sup/ra1 Correlates With Changes In the Coding...mentioning

confidence: 99%

Molecular Evolution of RAMOSA1 (RA1) in Land Plants

Bellino,

Herrera,

Rodrigues

et al. 2024

Preprint

View full text Add to dashboard Cite

RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown and the evolution in plants is partially understood. In this paper, we present a well resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein-protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, we propose that the RA1 and RA1-like gene families in grasses may have undergone subfunctionalization and neofunctionalization enabled by gene duplication.

show abstract

Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

Cited by 12 publications

References 94 publications

European soybean to benefit people and the environment

European soybean to benefit people and the environment

Multiomic analysis of genes related to oil traits in legumes provide insights into lipid metabolism and oil richness in soybean

Molecular Evolution of RAMOSA1 (RA1) in Land Plants

Contact Info

Product

Resources

About