New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS

Lysine is an essential amino acid that cannot be synthesized in humans. Rice is a global staple food for humans but has a rather low lysine content. Identification of the quantitative trait nucleotides (QTNs) and genes underlying lysine content is crucial to increase lysine accumulation. In this study, five grain and three leaf lysine content datasets and 4,630,367 single nucleotide polymorphisms (SNPs) of 387 rice accessions were used to perform a genome-wide association study (GWAS) by ten statistical models. A total of 248 and 71 common QTNs associated with grain/leaf lysine content were identified. The accuracy of genomic selection/prediction RR-BLUP models was up to 0.85, and the significant correlation between the number of favorable alleles per accession and lysine content was up to 0.71, which validated the reliability and additive effects of these QTNs. Several key genes were uncovered for fine-tuning lysine accumulation. Additionally, 20 and 30 QTN-by-environment interactions (QEIs) were detected in grains/leaves. The QEI-sf0111954416 candidate gene LOC_Os01g21380 putatively accounted for gene-by-environment interaction was identified in grains. These findings suggested the application of multi-model GWAS facilitates a better understanding of lysine accumulation in rice. The identified QTNs and genes hold the potential for lysine-rich rice with a normal phenotype.

A metabolomics study in citrus provides insight into bioactive phenylpropanoid metabolism

Citrus fruits are widely consumed worldwide in juices or as fresh and provide a broad range of phytonutrients that are important for human health. Here, a citrus multi-omics resource is presented: comprehensive metabolic profiling of various citrus species was performed and metabolic profiles were compared among species, with a focus on the phenylpropanoid metabolic pathway. A metabolite-based genome-wide association analysis (mGWAS) of 154 pummelo accessions was performed using factored spectrally transformed linear mixed models (FaST-LMM) and efficient mixed-model association eXpedited (EMMAX), and the genetic and biochemical basis of metabolomic variation was comprehensively analysed. A metabolite-single nucleotide polymorphism-gene (metabolite-SNP-gene) interaction network was constructed for pummelo, and many candidate loci controlling the synthesis and regulation of bioactive compounds were identified; among these loci, three BAHD malonyltransferases were involved in the malonylation of flavonoid glycosides. Further investigation revealed that an R2R3-MYB transcription factor CgMYB1 positively controls the metabolism of phenylpropanoid molecules, particularly the flavonoid derivatives. This study provides valuable data resources on the metabolic regulatory networks of bioactive components in citrus, in addition to demonstrating an efficient method for metabolic pathway dissection and providing targets for future breeding work with the aim of improving nutritional value.

Genome-Wide Identification and Expression Analysis of the SUT Family from Three Species of Sapindaceae Revealed Their Role in the Accumulation of Sugars in Fruits

Sapindaceae is an economically important family of Sapindales and includes many fruit crops. The dominant transport and storage form of photoassimilates in higher plants is sucrose. Sucrose transporter proteins play an irreplaceable role in the loading, transportation, unloading, and distribution of sucrose. A few SUT (sugar transporter) family genes have been identified and characterized in various plant species. In this study, 15, 15, and 10 genes were identified in litchi, longan, and rambutan, respectively, via genome-wide screening. These genes were divided into four subgroups based on phylogenetics. Gene duplication analysis suggested these genes underwent potent purifying selection and tandem duplications during evolution. The expression levels of SlSut01 and SlSut08 were significantly increased in the fruits of Sapindaceae members. The homologs of these two genes in longan and rambutan were also highly expressed in the fruits. The expression pattern of SUTs in three organs of the two varieties was also explored. Subcellular colocalization experiments revealed that the proteins encoded by both genes were present in the plasma membrane. This report provides data for the functional study of SUTs in litchi and provides a basis for screening sugar accumulation-related genes in fruits of Sapindaceae.

In situ 15 N-N2 O site preference and O2 concentration dynamics disclose the complexity of N2 O production processes in agricultural soil

Arable soil continues to be the dominant anthropogenic source of nitrous oxide (N2 O) emissions owing to application of nitrogen (N) fertilizers and manures across the world. Using laboratory and in situ studies to elucidate the key factors controlling soil N2 O emissions remains challenging due to the potential importance of multiple complex processes. We examined soil surface N2 O fluxes in an arable soil, combined with in situ high-frequency measurements of soil matrix oxygen (O2 ) and N2 O concentrations, in situ 15 N labeling, and N2 O 15 N site preference (SP). The in situ O2 concentration and further microcosm visualized spatiotemporal distribution of O2 both suggested that O2 dynamics were the proximal determining factor to matrix N2 O concentration and fluxes due to quick O2 depletion after N fertilization. Further SP analysis and in situ 15 N labeling experiment revealed that the main source for N2 O emissions was bacterial denitrification during the hot-wet summer with lower soil O2 concentration, while nitrification or fungal denitrification contributed about 50.0% to total emissions during the cold-dry winter with higher soil O2 concentration. The robust positive correlation between O2 concentration and SP values underpinned that the O2 dynamics were the key factor to differentiate the composite processes of N2 O production in in situ structured soil. Our findings deciphered the complexity of N2 O production processes in real field conditions, and suggest that O2 dynamics rather than stimulation of functional gene abundances play a key role in controlling soil N2 O production processes in undisturbed structure soils. Our results help to develop targeted N2 O mitigation measures and to improve process models for constraining global N2 O budget.

Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains

Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.

SlERF.H6 mediates the orchestration of ethylene and gibberellin signaling that suppresses bitter-SGA biosynthesis in tomato

Steroidal glycoalkaloids (SGAs) constitute a characteristic class of antinutritional metabolites that are found in certain Solanum species. Despite the considerable studies on SGA biosynthesis, the mechanisms of crosstalk between hormone signaling pathways that regulate SGA content still remain to be elucidated. Here, we performed a metabolic genome-wide association study (mGWAS) based on the levels of SGA metabolites and identified SlERF.H6 as a negative regulator of bitter-SGA biosynthesis. SlERF.H6 repressed the expression of SGA biosynthetic glycoalkaloid metabolism (GAME) genes and caused a subsequent decrease in the abundance of bitter SGAs. Furthermore, SlERF.H6 were shown to act downstream of GAME9, a regulator of SGA biosynthesis in tomato. We also uncovered the interplay between ethylene and gibberellin (GA) signaling in regulating SGA biosynthesis. SlERF.H6, acting as a downstream component in ethylene signaling, modulated GA content by inhibiting SlGA2ox12 expression. Increasing levels of endogenous GA₁₂ and GA₅₃ in SlERF.H6-OE could inhibit of GA on SGA biosynthesis. Additionally, 1-aminocyclopropane-1-carboxylic acid (ACC) treatment decreased the stability of SlERF.H6, weakening its inhibition on GAME genes and SlGA2ox12, and caused bitter-SGA accumulation. Our findings reveal a key role of SlERF.H6 in the regulation of SGA biosynthesis through the coordinated ethylene-gibberellin signaling.

Comprehensive Analysis of Metabolome and Transcriptome Reveals the Regulatory Network of Coconut Nutrients

Coconut flesh is widely consumed in the market for its good flavor. However, a comprehensive and dynamic assessment of the nutrients in coconut flesh and their molecular regulatory mechanisms is lacking. In this study, the metabolite accumulation and gene expression of three representative coconut cultivars belonging to two subspecies were investigated using ultra performance liquid chromatography/tandem mass spectrometry. A total of 6101 features were detected, of which 52, 8, and 158 were identified as amino acids and derivatives, polyamines, and lipids, respectively. The analysis of the metabolite pathway showed that glutathione and α-linolenate were the main differential metabolites. Transcriptome data revealed significant differences in the expression of five glutathione structural genes and thirteen polyamine-regulated genes, consistent with trends in metabolite accumulation. Weighted correlation network and co-expression analyses showed that a novel gene WRKY28 was implicated in the regulation of lipid synthesis. These results broaden our understanding of coconut nutrition metabolism and provide new insights into the molecular basis of coconut nutrition metabolism.