Genome-wide association study identifies variation of glucosidase being linked to natural variation of the maximal quantum yield of photosystem II

Identification of genetic loci and candidate genes regulating photosynthesis and leaf morphology through genome-wide association study in Brassica napus L

Rapeseed (Brassica napus L.) is a major agricultural crop with diverse applications, particularly in the production of seed oil for both culinary use and biodiesel. However, its photosynthetic efficiency, a pivotal determinant of yield, remains relatively low compared with other C3 plants such as rice and soybean, highlighting the necessity of identifying the genetic loci and genes regulating photosynthesis in rapeseed. In this study, we investigated 5 photosynthesis traits and 5 leaf morphology traits in a natural population of rapeseed, and conducted a genome-wide association study (GWAS) to identify significantly associated loci and genes. The results showed that the gas-exchange parameters of the dark reactions in photosynthesis exhibited a significant positive correlation with the chlorophyll content, whereas they showed a weaker negative correlation with the leaf area. By GWAS, a total of 538 quantitative trait nucleotides (QTNs) were identified as significantly associated with traits related to both leaf morphology and photosynthesis. These QTNs were classified into 84 QTL clusters, of which, 21 clusters exhibited remarkable stability across different traits and environmental conditions. In addition, a total of 3,129 potential candidate genes were identified to be significantly associated with the above-mentioned 10 traits, most of which were shared by certain traits, further indicating the reliability of the findings. By integrating GWAS data with GO enrichment analysis and gene expression analysis, we further identified 8 key candidate genes that are associated with the regulation of photosynthesis, chlorophyll content, leaf area, and leaf petiole angle. Taken together, this study identified key genetic loci and candidate genes with the potential to improve photosynthetic efficiency in rapeseed. These findings provide a theoretical framework for breeding new rapeseed varieties with enhanced photosynthetic capabilities.

Genome-wide association analysis identifies candidates of three bulb traits in garlic

Garlic bulbs generally possess several swelling cloves, and the swelling degree of the bulbs determines its yield and appearance quality. However, the genetic basis underlying bulb traits remains poorly known. To address this issue, we performed a genome-wide association analysis for three bulb traits: bulb weight, diameter, and height. It resulted in the identification of 51 significant associated signals from 38 genomic regions. Twelve genes from the associated regions, whose transcript abundances in the developmental bulb showed significant correlations with the investigated traits in 81 garlic accessions, were considered the candidates of the corresponding locus. We focused on five of these candidates and their variations and revealed that the promoter variations of fructose-bisphosphate aldolase-encoding Asa8G05696.1 and beta-fructofuranosidase-encoding Asa6G01167.1 are responsible for the functional diversity of these two genes in garlic population. Interestingly, our results revealed that all candidates we focused on experienced a degree of selection during garlic evolutionary history, and different genotypes of them were retained in two China-cultivated garlic groups. Taken together, these results suggest a potential involvement of those candidates in the parallel evolution of garlic bulb organs in two China-cultivated garlic groups. This study provides important insights into the genetic basis of garlic bulb traits and their evolution.

Photosynthesis: Genetic Strategies Adopted to Gain Higher Efficiency

The global challenge of feeding an ever-increasing population to maintain food security requires novel approaches to increase crop yields. Photosynthesis, the fundamental energy and material basis for plant life on Earth, is highly responsive to environmental conditions. Evaluating the operational status of the photosynthetic mechanism provides insights into plants' capacity to adapt to their surroundings. Despite immense effort, photosynthesis still falls short of its theoretical maximum efficiency, indicating significant potential for improvement. In this review, we provide background information on the various genetic aspects of photosynthesis, explain its complexity, and survey relevant genetic engineering approaches employed to improve the efficiency of photosynthesis. We discuss the latest success stories of gene-editing tools like CRISPR-Cas9 and synthetic biology in achieving precise refinements in targeted photosynthesis pathways, such as the Calvin-Benson cycle, electron transport chain, and photorespiration. We also discuss the genetic markers crucial for mitigating the impact of rapidly changing environmental conditions, such as extreme temperatures or drought, on photosynthesis and growth. This review aims to pinpoint optimization opportunities for photosynthesis, discuss recent advancements, and address the challenges in improving this critical process, fostering a globally food-secure future through sustainable food crop production.

Integrated transcriptome and metabolism unravel critical roles of carbon metabolism and oxidoreductase in mushroom with Korshinsk peashrub substrates

Edible fungi cultivation serves as an efficient biological approach to transforming agroforestry byproducts, particularly Korshinsk peashrub (KP) branches into valuable mushroom (Lentinus edodes) products. Despite the widespread use of KP, the molecular mechanisms underlying its regulation of mushroom development remain largely unknown. In this study, we conducted a combined analysis of transcriptome and metabolism of mushroom fruiting bodies cultivated on KP substrates compared to those on apple wood sawdust (AWS) substrate. Our aim was to identify key metabolic pathways and genes that respond to the effects of KP substrates on mushrooms. The results revealed that KP induced at least a 1.5-fold increase in protein and fat content relative to AWS, with 15% increase in polysaccharide and total sugar content in mushroom fruiting bodies. There are 1196 differentially expressed genes (DEGs) between mushrooms treated with KP relative to AWS. Bioinformatic analysis show significant enrichments in amino acid metabolic process, oxidase activity, malic enzyme activity and carbon metabolism among the 698 up-regulated DEGs induced by KP against AWS. Additionally, pathways associated with organic acid transport and methane metabolism were significantly enriched among the 498 down-regulated DEGs. Metabolomic analysis identified 439 differentially abundant metabolites (DAMs) in mushrooms treated with KP compared to AWS. Consistent with the transcriptome data, KEGG analysis on metabolomic dataset suggested significant enrichments in carbon metabolism, alanine, aspartate and glutamate metabolism among the up-regulated DAMs by KP. In particular, some DAMs were enhanced by 1.5-fold, including D-glutamine, L-glutamate, glucose and pyruvate in mushroom samples treated with KP relative to AWS. Targeted metabolomic analysis confirmed the contents of DAMs related to glutamate metabolism and energy metabolism. In conclusion, our findings suggest that reprogrammed carbon metabolism and oxidoreductase pathways act critical roles in the enhanced response of mushroom to KP substrates.

From leaf to multiscale models of photosynthesis: applications and challenges for crop improvement

To keep up with the growth of human population and to circumvent deleterious effects of global climate change, it is essential to enhance crop yield to achieve higher production. Here we review mathematical models of oxygenic photosynthesis that are extensively used, and discuss in depth a subset that accounts for diverse approaches providing solutions to our objective. These include models (1) to study different ways to enhance photosynthesis, such as fine-tuning antenna size, photoprotection and electron transport; (2) to bioengineer carbon metabolism; and (3) to evaluate the interactions between the process of photosynthesis and the seasonal crop dynamics, or those that have included statistical whole-genome prediction methods to quantify the impact of photosynthesis traits on the improvement of crop yield. We conclude by emphasizing that the results obtained in these studies clearly demonstrate that mathematical modelling is a key tool to examine different approaches to improve photosynthesis for better productivity, while effective multiscale crop models, especially those that also include remote sensing data, are indispensable to verify different strategies to obtain maximized crop yields.

Deciphering the genetic landscape of seedling drought stress tolerance in wheat (Triticum aestivum L.) through genome-wide association studies

Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic basis of stress tolerance is important to develop drought resilient, high-yielding wheat cultivars. In this study, we investigated the effects of drought stress on seedling characteristics in an association panel consisting of 198 germplasm lines. Our findings revealed that drought stress had a detrimental effect on all the seedling characteristics under investigation with a maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain a deeper understanding, we conducted a genome-wide association analysis using 12,511 single nucleotide polymorphisms (SNPs), which led to the identification of 39 marker-trait associations (MTAs). Of these 39 MTAs, 13 were particularly noteworthy as they accounted for >10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were further utilized to extract 216 candidate gene (CGs) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with functional relevance to drought stress. These genes encoded the WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, Protein kinase domain, Cytochrome P450, Leucine-rich repeat domain superfamily, BURP domain, Calmodulin-binding protein60, Ubiquitin-like domain, etc. Findings from this study hold significant promise for wheat breeders as they provide direct assistance in selecting lines harboring favorable alleles for improved drought stress tolerance. Additionally, the identified SNPs and CGs will enable marker-assisted selection of potential genomic regions associated with enhanced drought stress tolerance in wheat.

Genome-wide association study unravels genomic regions associated with chlorophyll fluorescence parameters in wheat (Triticum aestivum L.) under different sowing conditions

KEY MESSAGE

Genome-wide association study identified 205 significant marker-trait associations for chlorophyll fluorescence parameters in wheat. Candidate gene mining, in silico expression, and promoter analyses revealed the potential candidate genes associated with the studied parameters. The present study investigated the effect of varied sowing conditions (viz., early, timely, and late) on different chlorophyll fluorescence parameters in diverse wheat germplasm set comprising of 198 lines over two cropping seasons (2020-2021 and 2021-2022). Further, a genome-wide association study was conducted to identify potential genomic regions associated with these parameters. The results revealed significant impacts of sowing conditions on all fluorescence parameters, with the maximum and minimum effects on FI (26.64%) and FV/FM (2.12%), respectively. Among the 205 marker-trait associations (MTAs) identified, 11 high-confidence MTAs were chosen, exhibiting substantial effects on multiple fluorescence parameters, and each explaining more than 10% of the phenotypic variation. Through gene mining of genomic regions encompassing high-confidence MTAs, we identified a total of 626 unique gene models. In silico expression analysis revealed 42 genes with an expression value exceeding 2 TPM. Among them, 10 genes were identified as potential candidate genes with functional relevance to enhanced photosynthetic efficiency. These genes mainly encoded for the following important proteins/products-ankyrin repeat protein, 2Fe-2S ferredoxin-type iron-sulfur-binding domain, NADH-ubiquinone reductase complex-1 MLRQ subunit, oxidoreductase FAD/NAD(P)-binding, photosystem-I PsaF, and protein kinases. Promoter analysis revealed the presence of light-responsive (viz., GT1-motif, TCCC-motif, I-box, GT1-motif, TCT-motif, and SP-1) and stress-responsive (viz., ABRE, AuxRR-core, GARE-motif, and ARE) cis-regulatory elements, which may be involved in the regulation of identified putative candidate genes. Findings from this study could directly help wheat breeders in selecting lines with favorable alleles for chlorophyll fluorescence, while the identified markers will facilitate marker-assisted selection of potential genomic regions for improved photosynthesis.

The Molecular Mechanism of GhbHLH121 in Response to Iron Deficiency in Cotton Seedlings

Iron deficiency caused by high pH of saline-alkali soil is a major source of abiotic stress affecting plant growth. However, the molecular mechanism underlying the iron deficiency response in cotton (Gossypium hirsutum) is poorly understood. In this study, we investigated the impacts of iron deficiency at the cotton seedling stage and elucidated the corresponding molecular regulation network, which centered on a hub gene GhbHLH121. Iron deficiency induced the expression of genes with roles in the response to iron deficiency, especially GhbHLH121. The suppression of GhbHLH121 with virus-induced gene silence technology reduced seedlings' tolerance to iron deficiency, with low photosynthetic efficiency and severe damage to the structure of the chloroplast. Contrarily, ectopic expression of GhbHLH121 in Arabidopsis enhanced tolerance to iron deficiency. Further analysis of protein/protein interactions revealed that GhbHLH121 can interact with GhbHLH IVc and GhPYE. In addition, GhbHLH121 can directly activate the expression of GhbHLH38, GhFIT, and GhPYE independent of GhbHLH IVc. All told, GhbHLH121 is a positive regulator of the response to iron deficiency in cotton, directly regulating iron uptake as the upstream gene of GhFIT. Our results provide insight into the complex network of the iron deficiency response in cotton.

Integrative analysis of transcriptome and metabolism reveals potential roles of carbon fixation and photorespiratory metabolism in response to drought in Shanlan upland rice

Shanlan upland rice is an important landrace rice resource and is characterized with high drought stress (DS) tolerance relative to cultivated rice. However, the molecular mechanism of DS response in Shanlan upland rice remains unclear. In this study, we performed an integrated analysis of transcriptome and targeted metabolism to decipher the key biological pathways that responded to drought tolerance using two Shanlan upland rice lines. Results show that SL10 possesses 64% higher photosynthetic efficiency (Pn) and 2-fold higher water use efficiency (WUE) than that in SL1 exposed to DS. The decrease in Pn by DS is not due to stomatal limitation effects for SL1. Transcriptome analysis suggests photosynthesis relevant pathways (photosynthesis-antenna proteins and carbon fixation) and photorespiration relevant pathway (glycine, serine and threonine metabolism) in SL1 under DS were significantly enriched in the down-regulated and up-regulated DEGs list, respectively. There are 412 up-regulated and 233 down-regulated drought responsive genes (DRGs) in SL10 relative to SL1 induced by DS. Targeted metabolism results suggest that the contents across five metabolites related to carbon fixation pathway were declined by 36 and 8% in SL1 and SL10 caused by DS, respectively. We finally summarized the both gene expression and metabolites involved in photorespiration and carbon fixation pathways in response to DS in both rice lines. This study provides valuable information for better understanding the molecular mechanism underlying drought tolerance in Shanlan rice.

Natural variation in the fast phase of chlorophyll a fluorescence induction curve (OJIP) in a global rice minicore panel

Photosynthesis can be probed through Chlorophyll a fluorescence induction (FI), which provides detailed insight into the electron transfer process in Photosystem II, and beyond. Here, we have systematically studied the natural variation of the fast phase of the FI, i.e. the OJIP phase, in rice. The OJIP phase of the Chl a fluorescence induction curve is referred to as "fast transient" lasting for less than a second; it is obtained after a dark-adapted sample is exposed to saturating light. In the OJIP curve, "O" stands for "origin" (minimal fluorescence), "P" for "peak" (maximum fluorescence), and J and I for inflection points between the O and P levels. Further, F_o is the fluorescence intensity at the "O" level, whereas F_m is the intensity at the P level, and F_v (= F_m - F_o) is the variable fluorescence. We surveyed a set of quantitative parameters derived from the FI curves of 199 rice accessions, grown under both field condition (FC) and growth room condition (GC). Our results show a significant variation between Japonica (JAP) and Indica (IND) subgroups, under both the growth conditions, in almost all the parameters derived from the OJIP curves. The ratio of the variable to the maximum (F_v/F_m) and of the variable to the minimum (F_v/F_o) fluorescence, the performance index (PI_abs), as well as the amplitude of the I-P phase (A_I-P) show higher values in JAP compared to that in the IND subpopulation. In contrast, the amplitude of the O-J phase (A_O-J) and the normalized area above the OJIP curve (S_m) show an opposite trend. The performed genetic analysis shows that plants grown under GC appear much more affected by environmental factors than those grown in the field. We further conducted a genome-wide association study (GWAS) using 11 parameters derived from plants grown in the field. In total, 596 non-unique significant loci based on these parameters were identified by GWAS. Several photosynthesis-related proteins were identified to be associated with different OJIP parameters. We found that traits with high correlation are usually associated with similar genomic regions. Specifically, the thermal phase of FI, which includes the amplitudes of the J-I and I-P subphases (A_J-I and A_I-P) of the OJIP curve, is, in turn, associated with certain common genomic regions. Our study is the first one dealing with the natural variations in rice, with the aim to characterize potential candidate genes controlling the magnitude and half-time of each of the phases in the OJIP FI curve.

Identification of soybean phosphorous efficiency QTLs and genes using chlorophyll fluorescence parameters through GWAS and RNA-seq

MAIN CONCLUSION

Soybean phosphorous efficiency QTLs were identified and candidate genes were predicted using chlorophyll fluorescence parameters through GWAS and RNA-seq. Phosphorus (P) is an essential nutrient element for crop growth and development, lack of P uptake seriously affects yield in various crops. Photosynthesis is the basis of crop production, while it is very sensitive to P deficiency. It is of great importance to study the genetic relationship between photosynthesis and P efficiency to provide genetic insight for soybean improvement. In this study, a genome-wide association study (GWAS) was performed using 292,035 SNPs and the ratios of four main chlorophyll fluorescence parameters of 219 diverse soybean accessions under P deficiency and normal P across three experiments. In total, 52 SNPs in 12 genomic regions were detected in association with the four main chlorophyll fluorescence parameters under sufficient or deficient P levels. Combined it with RNA-seq analysis, we predicted three candidate genes for the significant genomic regions. For example, the expression level of the candidate gene (Glyma.18g092900) in P deficiency tolerant accession was three times higher than that of P deficiency sensitive one under phosphorous deficiency condition. This study provides insight into genetic links between photosynthetic and phosphorous efficiency and further functional analysis will provide valuable information for understanding the underlying genetic mechanism to facilitate marker-assisted breeding in soybean.

Identification of Sorghum (Sorghum bicolor (L.) Moench) Genotypes with Potential for Hydric and Heat Stress Tolerance in Northeastern Mexico

Sorghum (Sorghum bicolor (L.) Moench) is cultivated in regions with frequent drought periods and high temperatures, conditions that have intensified in the last decades. One of the most important photosynthetic components, sensible to hydric stress, is maximum quantum yield for photosystem II (PSII, or Fv/Fm). The objective of the present study was to identify sorghum genotypes with tolerance to hydric and heat stress. The treatments were hydric status (hydric stress or non-hydric stress (irrigation)), the plant's developmental stages (pre or post-anthesis), and six genotypes. The response variables were Fv/Fm; photosynthetic rate (P_N); stomatal conductance (g_s); transpiration rate (E); relative water content (RWC); damage to cell membrane (DCM) at temperatures of 40 and 45 °C; and agronomic variables. The experiment was conducted in pots in open sky in Marín, N.L., in the dry and hot northeast Mexico. The treatment design was a split-split plot design, with three factors. Hydric stress diminished the functioning of the photosynthetic apparatus by 63%, due to damage caused to PSII. Pre-anthesis was the most vulnerable stage to hydric stress as it decreased the weight of grains per panicle (85%), number of grains per panicle (69%), and weight of 100 grains (46%). Genotypes LER 1 and LER 2 were identified as tolerant to hydric stress, as they had lower damage to PSII; LER 1 and LEB 2 for their superior RWC; and LER 1 as a thermo tolerant genotype, due to its lower DCM at 45 °C. It was concluded that LER 1 could have the potential for both hydric and heat stress tolerance in the arid northeast Mexico.

Gibberellin Metabolism and Signaling: Targets for Improving Agronomic Performance of Crops

Gibberellins (GAs) are a class of tetracyclic diterpenoid phytohormones that regulate many aspects of plant development, including seed germination, stem elongation, leaf expansion, pollen maturation, and the development of flowers, fruits and seeds. During the past decades, the primary objective of crop breeding programs has been to increase productivity or yields. 'Green Revolution' genes that can produce semidwarf, high-yielding crops were identified as GA synthesis or response genes, confirming the value of research on GAs in improving crop productivity. The manipulation of GA status either by genetic alteration or by exogenous application of GA or GA biosynthesis inhibitors is often used to optimize plant growth and yields. In this review, we summarize the roles of GAs in major aspects of crop growth and development and present the possible targets for the fine-tuning of GA metabolism and signaling as a promising strategy for crop improvement.

Alterations in stomatal response to fluctuating light increase biomass and yield of rice under drought conditions

The acceleration of stomatal closure upon high to low light transition could improve plant water use efficiency and drought tolerance. Herein, using genome-wide association study, we showed that the genetic variation in OsNHX1 was strongly associated with the changes in τ_cl , the time constant of stomatal closure, in 206 rice accessions. OsNHX1 overexpression in rice resulted in a decrease in τ_cl , and an increase in biomass, grain yield under drought. Conversely, OsNHX1 knockout by CRISPR/CAS9 shows opposite trends for these traits. We further found three haplotypes spanning the OsNHX1 promoter and CDS regions. Two among them, HapII and HapIII, were found to be associated with a high and low τ_cl , respectively. A near-isogenic line (NIL, S464) was developed through replacing the genomic region harboring HapII (~10 kb) from MH63 (recipient) rice cultivar by the same sized genomic region containing Hap III from 02428 (donor). Compared with MH63, S464 shows a reduction by 35% in τ_cl and an increase by 40% in the grain yield under drought. However, under normal conditions, S464 maintains closely similar grain yield as MH63. The global distribution of the two OsNHX1 haplotypes is associated with the local precipitation. Taken together, the natural variation in OsNHX1 could be utilized to manipulate the stomatal dynamics for an improved rice drought tolerance.

Overexpression of maize transcription factor mEmBP-1 increases photosynthesis, biomass, and yield in rice

Identifying new options to improve photosynthetic capacity is a major approach to improve crop yield potential. Here we report that overexpression of the gene encoding the transcription factor mEmBP-1 led to simultaneously increased expression of many genes in photosynthesis, including genes encoding Chl a,b-binding proteins (Lhca and Lhcb), PSII (PsbR3 and PsbW) and PSI reaction center subunits (PsaK and PsaN), chloroplast ATP synthase subunit, electron transport reaction components (Fd1 and PC), and also major genes in the Calvin-Benson-Bassham cycle, including those encoding Rubisco, glyceraldehyde phosphate dehydrogenase, fructose bisphosphate aldolase, transketolase, and phosphoribulokinase. These increased expression of photosynthesis genes resulted in increased leaf chlorophyll pigment, photosynthetic rate, biomass growth, and grain yield both in the greenhouse and in the field. Using EMSA experiments, we showed that mEmBP-1a protein can directly bind to the promoter region of photosynthesis genes, suggesting that the direct binding of mEmBP-1a to the G-box domain of photosynthetic genes up-regulates expression of these genes. Altogether, our results show that mEmBP-1a is a major regulator of photosynthesis, which can be used to increase rice photosynthesis and yield in the field.

Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.)

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (Rd) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with Rd. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that Rd shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. Rd also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of Rd collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high Rd. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% Rd of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of Rd in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.