Genetic interactions regulating seed phytate and oligosaccharides in soybean (Glycine max L.)

Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle

Background

Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission.

Results

The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate.

Conclusion

Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.

The Effect of Exogenous Cadmium and Zinc Applications on Cadmium, Zinc and Essential Mineral Bioaccessibility in Three Lines of Rice That Differ in Grain Cadmium Accumulation

Millions of people around the world rely on rice (Oryza sativa) for a significant portion of daily calories, but rice is a relatively poor source of essential micronutrients like iron and zinc. Rice has been shown to accumulate alarmingly high concentrations of toxic elements, such as cadmium. Cadmium in foods can lead to renal failure, bone mineral density loss, cancer, and significant neurotoxicological effects. Several strategies to limit cadmium and increase micronutrient density in staple food crops like rice have been explored, but even when cadmium concentrations are reduced by a management strategy, total cadmium levels in rice grain are an unreliable means of estimating human health risk because only a fraction of the minerals in grains are bioaccessible. The goal of this work was to assess the influence of cadmium and zinc supplied to plant roots on the bioaccessibility of cadmium and essential minerals from grains of three rice lines (GSOR 310546/low grain Cd, GSOR 311667/medium grain Cd, and GSOR 310428/high grain Cd) that differed in grain cadmium accumulation. Treatments consisted of 0 μM Cd + 2 μM Zn (c0z2), 1 μM Cd + 2 μM Zn (c1z2), or 1 μM Cd + 10 μM Zn (c1z10). Our results revealed that an increased grain cadmium concentration does not always correlate with increased cadmium bioaccessibility. Among the three rice lines tested, Cd bioaccessibility increased from 2.5% in grains from the c1z2 treatment to 17.7% in grains from the c1z10 treatment. Furthermore, Cd bioccessibility in the low-Cd-accumulating line was significantly higher than the high line in c1z10 treatment. Zinc bioaccessibility increased in the high-cadmium-accumulating line when cadmium was elevated in grains, and in the low-cadmium line when both cadmium and zinc were increased in the rice grains. Our results showed that both exogenous cadmium and elevated zinc treatments increased the bioaccessibility of other minerals from grains of the low- or high-grain cadmium lines of rice. Differences in mineral bioaccessibility were dependent on rice line. Calculations also showed that increased cadmium bioaccessibility correlated with increased risk of dietary exposure to consumers. Furthermore, our results suggest that zinc fertilization increased dietary exposure to cadmium in both high and low lines. This information can inform future experiments to analyze genotypic effects of mineral bioavailability from rice, with the goal of reducing cadmium absorption while simultaneously increasing zinc absorption from rice grains.

Quantitative Trait Loci and Candidate Genes That Control Seed Sugars Contents in the Soybean 'Forrest' by 'Williams 82' Recombinant Inbred Line Population

Soybean seed sugars are among the most abundant beneficial compounds for human and animal consumption in soybean seeds. Higher seed sugars such as sucrose are desirable as they contribute to taste and flavor in soy-based food. Therefore, the objectives of this study were to use the 'Forrest' by 'Williams 82' (F × W82) recombinant inbred line (RIL) soybean population (n = 309) to identify quantitative trait loci (QTLs) and candidate genes that control seed sugar (sucrose, stachyose, and raffinose) contents in two environments (North Carolina and Illinois) over two years (2018 and 2020). A total of 26 QTLs that control seed sugar contents were identified and mapped on 16 soybean chromosomes (chrs.). Interestingly, five QTL regions were identified in both locations, Illinois and North Carolina, in this study on chrs. 2, 5, 13, 17, and 20. Amongst 57 candidate genes identified in this study, 16 were located within 10 Megabase (MB) of the identified QTLs. Amongst them, a cluster of four genes involved in the sugars' pathway was collocated within 6 MB of two QTLs that were detected in this study on chr. 17. Further functional validation of the identified genes could be beneficial in breeding programs to produce soybean lines with high beneficial sucrose and low raffinose family oligosaccharides.

Optimizing raffinose family oligosaccharides content in plants: A tightrope walk

Plants synthesize various compounds for their growth, metabolism, and stress mitigation, and one such group of compounds is the raffinose family of oligosaccharides (RFOs). RFOs are non-reducing oligosaccharides having galactose residues attached to a sucrose moiety. They act as carbohydrate reserves in plants, assisting in seed germination, desiccation tolerance, and biotic/abiotic stress tolerance. Although legumes are among the richest sources of dietary proteins, the direct consumption of legumes is hindered by an excess of RFOs in the edible parts of the plant, which causes flatulence in humans and monogastric animals. These opposing characteristics make RFOs manipulation a complicated tradeoff. An in-depth knowledge of the chemical composition, distribution pattern, tissue mobilization, and metabolism is required to optimize the levels of RFOs. The most recent developments in our understanding of RFOs distribution, physiological function, genetic regulation of their biosynthesis, transport, and degradation in food crops have been covered in this review. Additionally, we have suggested a few strategies that can sustainably reduce RFOs in order to solve the flatulence issue in animals. The comprehensive information in this review can be a tool for researchers to precisely control the level of RFOs in crops and create low antinutrient, nutritious food with wider consumer acceptability.

Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health?

Raffinose family oligosaccharides (RFOs) are widespread across the plant kingdom, and their concentrations are related to the environment, genotype, and harvest time. RFOs are known to carry out many functions in plants and humans. In this paper, we provide a comprehensive review of RFOs, including their beneficial and anti-nutritional properties. RFOs are considered anti-nutritional factors since they cause flatulence in humans and animals. Flatulence is the single most important factor that deters consumption and utilization of legumes in human and animal diets. In plants, RFOs have been reported to impart tolerance to heat, drought, cold, salinity, and disease resistance besides regulating seed germination, vigor, and longevity. In humans, RFOs have beneficial effects in the large intestine and have shown prebiotic potential by promoting the growth of beneficial bacteria reducing pathogens and putrefactive bacteria present in the colon. In addition to their prebiotic potential, RFOs have many other biological functions in humans and animals, such as anti-allergic, anti-obesity, anti-diabetic, prevention of non-alcoholic fatty liver disease, and cryoprotection. The wide-ranging applications of RFOs make them useful in food, feed, cosmetics, health, pharmaceuticals, and plant stress tolerance; therefore, we review the composition and diversity of RFOs, describe the metabolism and genetics of RFOs, evaluate their role in plant and human health, with a primary focus in grain legumes.

Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds

The low phytic acid (lpa) trait in soybeans can be conferred by loss-of-function mutations in genes encoding myo-inositol phosphate synthase and two epistatically interacting genes encoding multidrug-resistance protein ATP-binding cassette (ABC) transporters. However, perturbations in phytic acid biosynthesis are associated with poor seed vigor. Since the benefits of the lpa trait, in terms of end-use quality and sustainability, far outweigh the negatives associated with poor seed performance, a fuller understanding of the molecular basis behind the negatives will assist crop breeders and engineers in producing variates with lpa and better germination rate. The gene regulatory network (GRN) for developing low and normal phytic acid soybean seeds was previously constructed, with genes modulating a variety of processes pertinent to phytic acid metabolism and seed viability being identified. In this study, a comparative time series analysis of low and normal phytic acid soybeans was carried out to investigate the transcriptional regulatory elements governing the transitional dynamics from dry seed to germinated seed. GRNs were reverse engineered from time series transcriptomic data of three distinct genotypic subsets composed of lpa soybean lines and their normal phytic acid sibling lines. Using a robust unsupervised network inference scheme, putative regulatory interactions were inferred for each subset of genotypes. These interactions were further validated by published regulatory interactions found in Arabidopsis thaliana and motif sequence analysis. Results indicate that lpa seeds have increased sensitivity to stress, which could be due to changes in phytic acid levels, disrupted inositol phosphate signaling, disrupted phosphate ion (Pi) homeostasis, and altered myo-inositol metabolism. Putative regulatory interactions were identified for the latter two processes. Changes in abscisic acid (ABA) signaling candidate transcription factors (TFs) putatively regulating genes in this process were identified as well. Analysis of the GRNs reveal altered regulation in processes that may be affecting the germination of lpa soybean seeds. Therefore, this work contributes to the ongoing effort to elucidate molecular mechanisms underlying altered seed viability, germination and field emergence of lpa crops, understanding of which is necessary in order to mitigate these problems.