Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis

Introduction

An important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security.

Methods

In this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in two watering regimes [well-watered (WW) and drought stress (DS)] for 3 years. In the DS treatment, irrigation continued till the 50% pod development stage, whereas in the WW condition, it was performed throughout the whole growing season.

Results

The results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288-kbps LD decay distance analysis revealed 2,232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 were involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight, and grain yield in drought conditions. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation.

Discussion

The results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.

An atypical heterotrimeric Gα and its interactome suggest an extra-large role in overcoming abiotic and biotic stress

Canonical heterotrimeric G-proteins (G-proteins) are comprised of Gα, Gβ, and Gγ subunits. G-proteins regulate multiple crucial plant growth and development processes, incorporating environmental responses. Besides Gα, Gβ and Gγ, the discovery of atypical Gα subunits termed as extra-large G-proteins or extra-large GTP-binding proteins (XLGs) makes G-protein signaling unique in plants. The C-terminus of XLG shares similarities with the canonical Gα subunits; the N-terminus harbors a nuclear localization signal (NLS) and is rich in cysteine. The earlier explorations suggest XLG's role in flowering, the development of embryos and seedlings, root morphogenesis, stamen development, cytokinin-induced development, stomatal opening and regulation of rice grain filling. The XLGs are also known to initiate signaling cascades that prime plants against a variety of abiotic and biotic stresses. They are also engaged in controlling several agronomic parameters such as rice panicle length, grain filling, grain size, and biomass, highlighting their potential contribution to crop improvement. The present review explores the remarkable properties of non-canonical Gα subunits (XLGs) and reflects on the various developmental, abiotic and biotic stress signaling pathways controlled by them. Moreover, the bottleneck dilemma of how a tiny handful of XLGs control a multiplicity of stress-responsive activities is partially resolved in this review by addressing the interaction of XLGs with different interacting proteins. XLG proteins presented in this review can be exploited to gain access to highly productive and stress-tolerant plants.

Molecular Identification of the G-Protein Genes and Their Expression Profiles in Response to Nitrogen Deprivation in Brassica napus

Heterotrimeric guanine nucleotide binding protein (G-protein) consisting of Gα, Gβ, and Gγ subunits is one of the key signal transducers in plants. Recent studies indicated that G-protein has been proposed as an important mediator of nitrogen responses in rice, wheat, and Arabidopsis. However, little is known about these G-proteins in Brassica napus (B. napus), except for three identified G-proteins, BnGA1, BnGB1, and BnGG2. Therefore, the aim of the present study is to characterize the members of the G-protein gene family in allotetraploid B. napus and to analyze their expression profiles in response to nitrogen deprivation. In total, 21 G-protein family members were identified in B. napus, encoding two Gα, six Gβ, and 13 Gγ. Sequence and phylogenetic analyses showed that although genome-wide triploid events increased the number of genes encoding Gα, Gβ, and Gγ subunits, the gene structure and protein properties of the genes encoding each G-protein subunit were extremely conserved. Collinearity analysis showed that most G-protein genes in B. napus had syntenic relationships with G-protein members of Arabidopsis, Brassica rape (B. rapa), and Brassica oleracea (B. oleracea). Expression profile analysis indicated that Gα and C-type Gγ genes (except BnGG10 and BnGG12 were highly expressed in flower and ovule) were barely expressed in most organs, whereas most Gβ and A-type Gγ genes tended to be highly expressed in most organs. G-protein genes also showed various expression patterns in response to nitrogen-deficient conditions. Under nitrogen deficiency, Gα and five C-type Gγ genes were upregulated initially in roots, while in leaves, Gα was downregulated initially and five C-type Gγ genes were highly expressed in different times. These results provide a complex genetic dissection of G-protein genes in B. napus, and insight into the biological functions of G-protein genes in response to nitrogen deficiency.

Interacting partners of Brassica juncea Regulator of G-protein Signaling protein suggest its role in cell wall metabolism and cellular signaling

Heterotrimeric G-proteins interact with various upstream and downstream effectors to regulate various aspects of plant growth and development. G-protein effectors have been recently reported in Arabidopsis thaliana; however, less information is available from polyploid crop species having complex networks of G-protein components. Regulator of G-protein signaling (RGS) is a well-characterized GTPase accelerating protein, which plays an important role in the regulation of the G-protein cycle in plants. In the present study, four homologs encoding RGS proteins were isolated from the allotetraploid Brassica juncea, a globally important oilseed, vegetable, and condiment crop. The B. juncea RGS proteins were grouped into distinct BjuRGS1 and BjuRGS2 orthologous clades, and the expression of BjuRGS1 homologs was predominantly higher than BjuRGS2 homologs across the tested tissue types of B. juncea. Utilizing B. juncea Y2H library screening, a total of 30 nonredundant interacting proteins with the RGS-domain of the highly expressed BjuA.RGS1 was identified. Gene ontology analysis indicated that these effectors exerted various molecular, cellular, and physiological functions. Many of them were known to regulate cell wall metabolism (BjuEXP6, Bju-α-MAN, BjuPGU4, BjuRMS3) and phosphorylation-mediated cell signaling (BjuMEK4, BjuDGK3, and BjuKinase). Furthermore, transcript analysis indicated that the identified interacting proteins have a coexpression pattern with the BjuRGS homologs. These findings increase our knowledge about the novel targets of G-protein components from a globally cultivated Brassica crop and provide an important resource for developing a plant G-protein interactome network.

The multifaceted roles of heterotrimeric G-proteins: lessons from models and crops

The review summarizes our advanced understanding of the heterotrimeric G-protein research from model plants and their emerging roles in modulating various plant architecture and agronomical traits in crop species. Heterotrimeric G-proteins (hereafter G-proteins), consisting of G-alpha (Gα), G-beta (Gβ) and G-gamma (Gγ) subunits, are key signal transducers conserved across different forms of life. The discovery of plant lineage-specific G-protein components (extra-large G-proteins and type-C Gγ subunits), inherent polyploidy in angiosperms, and unique modes of G-protein cycle regulation in plants pointed out to a few fundamental differences of plant G-protein signaling from its animal counterpart. Over the last 2 decades, extensive studies in the model plant Arabidopsis thaliana have confirmed the involvement of G-proteins in a wide range of plant growth and development, and stress adaptation processes. The G-protein research in crop species, however, is still in its infancy, and a handful of studies suggest important roles of G-proteins in regulating plant architectural and key agronomical traits including plant's response to abiotic and biotic factors. We propose that the advancement made in plant G-proteins research will facilitate the development of novel approaches to manage plant yield and fitness in changing environments.

Extra-large G-proteins influence plant response to Sclerotinia sclerotiorum by regulating glucosinolate metabolism in Brassica juncea

Heterotrimeric G-proteins are one of the highly conserved signal transducers across phyla. Despite the obvious importance of G-proteins in controlling various plant growth and environmental responses, there is no information describing the regulatory complexity of G-protein networks during pathogen response in a polyploid crop. Here, we investigated the role of extra-large G-proteins (XLGs) in the oilseed crop Brassica juncea, which has inherent susceptibility to the necrotrophic fungal pathogen Sclerotinia sclerotiorum. The allotetraploid B. juncea genome contains multiple homologs of three XLG genes (two BjuXLG1, five BjuXLG2, and three BjuXLG3), sharing a high level of sequence identity, gene structure organization, and phylogenetic relationship with the progenitors' orthologs. Quantitative reverse transcription PCR analysis revealed that BjuXLGs have retained distinct expression patterns across plant developmental stages and on S. sclerotiorum infection. To determine the role of BjuXLG genes in the B. juncea defence response against S. sclerotiorum, RNAi-based suppression was performed. Disease progression analysis showed more rapid lesion expansion and fungal accumulation in BjuXLG-RNAi lines compared to the vector control plants, wherein suppression of BjuXLG3 homologs displayed more compromised defence response at the later time point. Knocking down BjuXLGs caused impairment of the host resistance mechanism to S. sclerotiorum, as indicated by reduced expression of defence marker genes PDF1.2 and WRKY33 on pathogen infection. Furthermore, BjuXLG-RNAi lines showed reduced accumulation of leaf glucosinolates on S. sclerotiorum infection, wherein aliphatic glucosinolates were significantly compromised. Overall, our data suggest that B. juncea XLG genes are important signalling nodes modulating the host defence pathways in response to this necrotrophic pathogen.

A complex interplay of Gβ and Gγ proteins regulates plant growth and defence traits in the allotetraploid Brassica juncea

Gene expression analysis coupled with in-planta studies showed that specific Gβγ combination regulates plant growth and defence traits in the allotetraploid Brassica juncea. Plant heterotrimeric G-proteins regulate a wide range of responses despite their limited repertoire of core components. The roles and functional interactions between different G-protein subunits are quite perplexing, which get further complicated with polyploidy. Here, we show that the allotetraploid Brassica juncea comprises multiple homologs of G-protein genes, encoding six BjuGβ and ten highly divergent BjuGγ subunit proteins, later being classified into type-A1, type-A2 and type-C Gγ proteins. The encoded BjuGβ and BjuGγ proteins shared close evolutionary relationship and have retained distinct spatio-temporal expression patterns during plant developmental stages and in response to the necrotrophic pathogen, Sclerotinia sclerotiorum. RNAi based suppression of BjuGβ and BjuGγ genes suggested functional overlap and selectivity of BjuGβs with three distinct BjuGγ type subunits, to regulate plant height (BjuGβγA2 and BjuGβγC), seed weight (BjuGβGγA1 and BjuGβGγC), silique size (BjuGβGγC) and pathogen response (BjuGβGγA1 and BjuGβGγC). Further, the triplicated BjuGβ genes, formed due to Brassica specific whole-genome-triplication event, showed differential involvement during pathogen response, wherein overexpression of BjuGβ2 displayed higher resistance to Sclerotinia infection. Taken together, our study demonstrates that multiple BjuGβ and BjuGγ proteins have retained distinct spatio-temporal expression and functional selectivity to regulate specific plant growth and defence traits in the oilseed B. juncea.

Genome-wide identification of genes involved in heterotrimeric G-protein signaling in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating fruit development

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an economical crop with excellent edible, nutritional, and medicinal values. However, the production of Tartary buckwheat is very low and it is urgent to breed high-yield varieties for satisfying the increasing market demand. Heterotrimeric G-protein signaling involves in the regulation of agronomical traits and fruit development in several plant species. In this study, fifteen genes involved in G-protein signaling were characterized in Tartary buckwheat and their potential roles in fruit development were revealed by expression analysis. The exon-intron organization and conserved motif of Tartary buckwheat G-protein signaling genes were similar to those in other dicot plants. All these genes were ubiquitously and differently expressed in five tissues. The expression patterns of Tartary buckwheat G-protein signaling genes in fruit suggested they may play important roles in the fruit at early development stage, which was supported by meta-analysis of G-protein signaling genes' expression in the fruits from different species. Furthermore, we found the expression of G-protein signaling genes in fruit showed high correlation with 178 transcription factors, which indicated a transcriptional regulatory loop moderating G-protein signaling genes' expression during fruit development. This paper provides new insights into the physiological functions of G-protein signaling in fruit.

Heterotrimeric Gα subunit regulates plant architecture, organ size and seed weight in the oilseed Brassica juncea

Two BjuGα proteins exhibit conserved GTP-binding and GTP-hydrolysis activities, and function in maintaining overall plant architecture and controlling multiple yield-related traits in the oilseed Brassica juncea. Heterotrimeric G-protein (Gα, Gβ and Gγ) are key signal transducers, well characterized in model plants Arabidopsis and rice. However, our knowledge about the roles played by G-proteins in regulating various growth and developmental traits in polyploid crops, having a complex G-protein signalling network, is quite sparse. In the present study, two Gα encoding genes (BjuA.Gα1 and BjuB.Gα1) were isolated from the allotetraploid Brassica juncea, a globally cultivated oilseed crop of the Brassicaceae family. BjuGα1 genes share a close evolutionary relationship, and the encoded proteins exhibit highly conserved G-protein activities while showing expression differentiation, wherein BjuA.Gα1 was the highly abundant transcript during plant growth and developmental stages. RNAi based suppression of BjuGα1 displayed compromised effects on most of the tested vegetative and reproductive parameters, particularly plant height (32-58%), flower and siliques dimensions, and seed weight (11-13%). Further, over-expression of a constitutively active Gα, lacking the GTPase activity, produced plants with increased height, organ size and seed weight (7-25%), without altering seed quality traits like fatty acid composition, glucosinolates, oil and protein contents. Our study demonstrates that BjuGα1 proteins control overall plant architecture and multiple yield-related traits in the oilseed B. juncea, suggesting that BjuGα1 could be a promising target for crop improvement.

Duplicated RGS (Regulator of G-protein signaling) proteins exhibit conserved biochemical but differential transcriptional regulation of heterotrimeric G-protein signaling in Brassica species

G-alpha (Gα) and ‘Regulator of G-protein Signaling (RGS)’ proteins are the two key components primarily involved in regulation of heterotrimeric G-proteins signaling across phyla. Unlike Arabidopsis thaliana, our knowledge about G-protein regulation in polyploid Brassica species is sparse. In this study, we identified one Gα and two RGS genes each from three species of Brassica ‘U’ triangle and assessed the effects of whole genome triplication on the divergence of gene sequence and structure, protein-protein interaction, biochemical activities, and gene expression. Sequence and phylogenetic analysis revealed that the deduced Gα and RGS proteins are evolutionarily conserved across Brassica species. The duplicated RGS proteins of each Brassica species interacted with their cognate Gα but displayed varying levels of interaction strength. The Gα and the duplicated RGS proteins of Brassica species exhibited highly conserved G-protein activities when tested under in-vitro conditions. Expression analysis of the B. rapa RGS genes revealed a high degree of transcriptional differentiation across the tested tissue types and in response to various elicitors, particularly under D-glucose, salt and phytohormone treatments. Taken together, our results suggest that the RGS-mediated regulation of G-protein signaling in Brassica species is predominantly governed by stage and condition-specific expression differentiation of the duplicated RGS genes.

Pattern of expression and interaction specificity of multiple G-protein beta (Gβ) subunit isoforms with their potential target proteins reveal functional dominance of BjuGβ1 in the allotetraploid Brassica juncea

Heterotrimeric G-protein, consisting Gα, Gβ and Gγ subunits, interacts with various upstream and downstream effector (target) proteins to regulate a large array of conserved and species-specific biological functions. The targets of G-protein components are recently reported in model plant Arabidopsis thaliana; however limited information is available from crop species. In this study, we utilized yeast two-hybrid (Y2H) assay to screen the diversity of interacting partners of multiple Gβ subunit isoforms from allotetraploid Brassica juncea, a globally important oilseed and vegetable crop. The three BjuGβ genes (BjuGβ1-3), resulted from whole genome triplication event in Brassica lineage, showed distinct expression profile during plant developmental stages with maximal transcript abundance during reproductive stages. Protein-protein interaction of three BjuGβ proteins (bait) against the Y2H cDNA library (prey) identified a total of 14 and 1 non-redundant targets for BjuGβ1 and BjuGβ2, whereas BjuGβ3 screening surprisingly did not yield any genuine target, thereby suggesting functional dominance of BjuGβ1. The triplicated BjuGβ isoforms showed a high degree of interaction strength and specificity with the identified target proteins, which are known to be involved in diverse biological functions in plants. qRT-PCR analysis further indicated that the expression of BjuGβ-target genes was developmentally regulated under various tissue types studied and showed a high degree of co-expression pattern with the BjuGβ genes, particularly during flower and silique development in B. juncea. Taken together, our data provides novel insights on pattern of expression and interaction specificity governing functional divergence of multiple Gβ subunit proteins in polyploid B. juncea.

Class-Specific Evolution and Transcriptional Differentiation of 14-3-3 Family Members in Mesohexaploid Brassica rapa

14-3-3s are highly conserved, multigene family proteins that have been implicated in modulating various biological processes. The presence of inherent polyploidy and genome complexity has limited the identification and characterization of 14-3-3 proteins from globally important Brassica crops. Through data mining of Brassica rapa, the model Brassica genome, we identified 21 members encoding 14-3-3 proteins namely, BraA.GRF14.a to BraA.GRF14.u. Phylogenetic analysis indicated that B. rapa contains both ε (epsilon) and non-ε 14-3-3 isoforms, having distinct intron-exon structural organization patterns. The non-ε isoforms showed lower divergence rate (Ks < 0.45) compared to ε protein isoforms (Ks > 0.48), suggesting class-specific divergence pattern. Synteny analysis revealed that mesohexaploid B. rapa genome has retained 1-5 orthologs of each Arabidopsis 14-3-3 gene, interspersed across its three fragmented sub-genomes. qRT-PCR analysis showed that 14 of the 21 BraA.GRF14 were expressed, wherein a higher abundance of non-ε transcripts was observed compared to the ε genes, indicating class-specific transcriptional bias. The BraA.GRF14 genes showed distinct expression pattern during plant developmental stages and in response to abiotic stress, phytohormone treatments, and nutrient deprivation conditions. Together, the distinct expression pattern and differential regulation of BraA.GRF14 genes indicated the occurrence of functional divergence of B. rapa 14-3-3 proteins during plant development and stress responses.

Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control

Stomata control the concomitant exchange of CO2 and transpiration in land plants. While a constant supply of CO2 is need to maintain the rate of photosynthesis, the accompanying water losses must be tightly regulated to prevent dehydration and undesired metabolic changes. The factors affecting stomatal movement are directly coupled with the cellular networks of guard cells. Although the guard cell has been used as a model for characterization of signaling pathways, several important questions about its functioning remain elusive. Current modeling approaches describe the stomatal conductance in terms of relatively few easy-to-measure variables being unsuitable for in silico design of genetic manipulation strategies. Here, we argue that a system biology approach, combining modeling and high-throughput experiments, may be used to elucidate the mechanisms underlying stomata control and to determine targets for modulation of stomatal responses to environment. In support of our opinion, we review studies demonstrating how high-throughput approaches have provided a systems-view of guard cells. Finally, we emphasize the opportunities and challenges of genome-scale modeling and large-scale data integration for in silico manipulation of guard cell functions to improve crop yields, particularly under stress conditions which are of pertinence both to climate change and water use efficiency.