Quantitative genetic analysis of chlorophyll a fluorescence parameters in maize in the field environments

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.

Identification of Pathogens and Evaluation of Resistance and Genetic Diversity of Maize Inbred Lines to Stalk Rot in Heilongjiang Province, China

Maize stalk rot, caused by multiple pathogens, is a serious soilborne disease worldwide. Composition of pathogens causing maize stalk rot and resistance of maize inbred lines in Heilongjiang Province, China, are not well understood. In this study, 138 fungal isolates were collected from different maize-producing areas in Heilongjiang Province, which were identified as Fusarium graminearum (23.2%), F. subglutinans (18.9%), F. cerealis (18.9%), Bipolaris zeicola (13.0%), F. brachygibbosum (13.0%), F. temperatum (7.2%), and F. proliferatum (5.8%). Among them, F. graminearum (>20%) was the predominant species among the isolates causing maize stalk rot. B. zeicola had not previously been reported causing maize stalk rot in China. Resistance of 67 maize inbred lines to maize stalk rot was assessed, and 24 lines (35.8% of them) were highly resistant or resistant, indicating that approximately 65% of these lines were susceptible to maize stalk rot. Maize inbred lines were analyzed using simple sequence repeat markers and divided into five genetic groups with 12 pairs of primers. Additionally, analysis of molecular variance indicated that 44.2% of the genetic variation in disease resistance was distributed among populations. This study provides insight into the genetic diversity of inbred maize and may contribute useful information for breeding stalk rot disease-resistant hybrids, and facilitates development of effective strategies for managing this destructive disease complex.

Crop breeding for a changing climate in the Pannonian region: towards integration of modern phenotyping tools

The Pannonian Plain, as the most productive region of Southeast Europe, has a long tradition of agronomic production as well as agronomic research and plant breeding. Many research institutions from the agri-food sector of this region have a significant impact on agriculture. Their well-developed and fruitful breeding programmes resulted in productive crop varieties highly adapted to the specific regional environmental conditions. Rapid climatic changes that occurred during the last decades led to even more investigations of complex interactions between plants and their environments and the creation of climate-smart and resilient crops. Plant phenotyping is an essential part of botanical, biological, agronomic, physiological, biochemical, genetic, and other omics approaches. Phenotyping tools and applied methods differ among these disciplines, but all of them are used to evaluate and measure complex traits related to growth, yield, quality, and adaptation to different environmental stresses (biotic and abiotic). During almost a century-long period of plant breeding in the Pannonian region, plant phenotyping methods have changed, from simple measurements in the field to modern plant phenotyping and high-throughput non-invasive and digital technologies. In this review, we present a short historical background and the most recent developments in the field of plant phenotyping, as well as the results accomplished so far in Croatia, Hungary, and Serbia. Current status and perspectives for further simultaneous regional development and modernization of plant phenotyping are also discussed.

Genetic Approaches to Enhance Multiple Stress Tolerance in Maize

The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such as simultaneous drought and heat or heavy metal exposure, or drought in combination with insect and fungal infestation. To keep up with these challenges, maize natural variation and genetic engineering are exploited. On one hand, quantitative trait loci (QTL) associated with multiple-stress tolerance are being identified by molecular breeding and genome-wide association studies (GWAS), which then could be utilized for future breeding programs of more resilient maize varieties. On the other hand, transgenic approaches in maize have already resulted in the creation of many commercial double or triple stress resistant varieties, predominantly weed-tolerant/insect-resistant and, additionally, also drought-resistant varieties. It is expected that first generation gene-editing techniques, as well as recently developed base and prime editing applications, in combination with the routine haploid induction in maize, will pave the way to pyramiding more stress tolerant alleles in elite lines/varieties on time.

The Combination of Increased Temperatures and High Irradiation Causes Changes in Photosynthetic Efficiency

Global warming and the associated climate change are imposing abiotic stress on plants. Abiotic factors are crucial for plant productivity, survival, and reproduction. Eight sunflower hybrids were tested in conditions of different water availability and with combinations of different temperatures and irradiation. The changes in the photosynthetic efficiency were measured in the morning (control conditions: 2013, 25.8 °C and 349.1 W m⁻²; 2014, 21.8 °C and 296.4 W m⁻²) and afternoon (the combination of increased temperatures and high irradiation: 2013, 34 °C and 837.9 W m⁻²; 2014, 29.4 °C and 888.9 W m⁻²) at a flowering stage in rainfed or irrigated conditions. The measurement time (morning and afternoon conditions) had a statistically significant effect on all the tested parameters. The performance index (PI_ABS) in 2013 and the maximum quantum yield of photosystem II (TR₀/ABS) in 2014 are the only parameters significantly affected by the irrigation. As a result of the combined effect of increased temperatures and high irradiation, PI_ABS values decreased by 73–92% in rainfed conditions and by 63–87% in irrigated conditions in 2013, depending on the hybrid, while in 2014, the decrease varied between 70 and 86%. The TR₀/ABS decrease was 7–17% in 2013, depending on the hybrid, and 6–12% in 2014, both in rainfed and irrigated conditions. The principal component analysis confirmed the effect of the combination of increased temperatures and high irradiation on hybrids, sorting them exclusively according to the time of measurement. All investigated parameters highly fluctuated between hybrids but without observable trends for the morning and afternoon conditions, as well as for irrigation. Plants’ reaction to the combination of increased temperatures and high irradiation manifested as a change in their photosynthetic efficiency, i.e., the photosynthetic apparatus’ functioning was impaired.

Genetic Correlations Between Photosynthetic and Yield Performance in Maize Are Different Under Two Heat Scenarios During Flowering

Chlorophyll fluorescence (ChlF) parameters are reliable early stress indicators in crops, but their relations with yield are still not clear. The aims of this study are to examine genetic correlations between photosynthetic performance of JIP-test during flowering and grain yield (GY) in maize grown under two heat scenarios in the field environments applying quantitative genetic analysis, and to compare efficiencies of indirect selection for GY through ChlF parameters and genomic selection for GY. The testcrosses of 221 intermated recombinant inbred lines (IRILs) of the IBM Syn4 population were evaluated in six environments at two geographically distinctive locations in 3 years. According to day/night temperatures and vapor pressure deficit (VPD), the two locations in Croatia and Turkey may be categorized to the mild heat and moderate heat scenarios, respectively. Mild heat scenario is characterized by daytime temperatures often exceeding 33°C and night temperatures lower than 20°C while in moderate heat scenario the daytime temperatures often exceeded 33°C and night temperatures were above 20°C. The most discernible differences among the scenarios were obtained for efficiency of electron transport beyond quinone A (Q_A) [ET/(TR-ET)], performance index on absorption basis (PI_ABS) and GY. Under the moderate heat scenario, there were tight positive genetic correlations between ET/(TR-ET) and GY (0.73), as well as between PI_ABS and GY (0.59). Associations between the traits were noticeably weaker under the mild heat scenario. Analysis of quantitative trait loci (QTL) revealed several common QTLs for photosynthetic and yield performance under the moderate heat scenario corroborating pleiotropy. Although the indirect selection with ChlF parameters is less efficient than direct selection, ET/(TR-ET) and PI_ABS could be efficient secondary breeding traits for selection under moderate heat stress since they seem to be genetically correlated with GY in the stressed environments and not associated with yield performance under non-stressed conditions predicting GY during flowering. Indirect selection through PI_ABS was also shown to be more efficient than genomic selection in moderate heat scenario.

Identification of genomic loci associated with 21chlorophyll fluorescence phenotypes by genome-wide association analysis in soybean

BACKGROUND

Photosynthesis is able to convert solar energy into chemical energy in the form of biomass, but the efficiency of photosynthetic solar energy conversion is low. Chlorophyll fluorescence measurements are rapid, non-destructive, and can provide a wealth of information about the efficiencies of the photosynthetic light reaction processes. Efforts aimed at assessing genetic variation and/or mapping of genetic loci associated with chlorophyll fluorescence phenotypes have been rather limited.

RESULTS

Evaluation of SoySNP50K iSelect SNP Beadchip data from the 189 genotypes phenotyped in this analysis identified 32,453 SNPs with a minor allele frequency (MAF) ≥ 5%. A total of 288 (non-unique) SNPs were significantly associated with one or more of the 21 chlorophyll fluorescence phenotypes. Of these, 155 were unique SNPs and 100 SNPs were only associated with a single fluorescence phenotype, while 28, 11, 2, and 14 SNPs, were associated with two, three, four and five or more fluorescence phenotypes, respectively. The 288 non-unique SNPs represent 155 unique SNPs that mark 53 loci. The 155 unique SNPs included 27 that were associated with three or more phenotypes, and thus were called multi-phenotype SNPs. These 27 multi-phenotype SNPs marked 13 multi-phenotype loci (MPL) identified by individual SNPs associated with multiple chlorophyll fluorescence phenotypes or by more than one SNP located within 0.5 MB of other multi-phenotype SNPs.

CONCLUSION

A search in the genomic regions highlighted by these 13 MPL identified genes with annotations indicating involvement in photosynthetic light dependent reactions. These, as well as loci associated with only one or two chlorophyll fluorescence traits, should be useful to develop a better understanding of the genetic basis of photosynthetic light dependent reactions as a whole as well as of specific components of the electron transport chain in soybean. Accordingly, additional genetic and physiological analyses are necessary to determine the relevance and effectiveness of the identified loci for crop improvement efforts.

Identification of genomic loci associated with 21chlorophyll fluorescence phenotypes by genome-wide association analysis in soybean

BACKGROUND

Photosynthesis is able to convert solar energy into chemical energy in the form of biomass, but the efficiency of photosynthetic solar energy conversion is low. Chlorophyll fluorescence measurements are rapid, non-destructive, and can provide a wealth of information about the efficiencies of the photosynthetic light reaction processes. Efforts aimed at assessing genetic variation and/or mapping of genetic loci associated with chlorophyll fluorescence phenotypes have been rather limited.

RESULTS

Evaluation of SoySNP50K iSelect SNP Beadchip data from the 189 genotypes phenotyped in this analysis identified 32,453 SNPs with a minor allele frequency (MAF) ≥ 5%. A total of 288 (non-unique) SNPs were significantly associated with one or more of the 21 chlorophyll fluorescence phenotypes. Of these, 155 were unique SNPs and 100 SNPs were only associated with a single fluorescence phenotype, while 28, 11, 2, and 14 SNPs, were associated with two, three, four and five or more fluorescence phenotypes, respectively. The 288 non-unique SNPs represent 155 unique SNPs that mark 53 loci. The 155 unique SNPs included 27 that were associated with three or more phenotypes, and thus were called multi-phenotype SNPs. These 27 multi-phenotype SNPs marked 13 multi-phenotype loci (MPL) identified by individual SNPs associated with multiple chlorophyll fluorescence phenotypes or by more than one SNP located within 0.5 MB of other multi-phenotype SNPs.

CONCLUSION

A search in the genomic regions highlighted by these 13 MPL identified genes with annotations indicating involvement in photosynthetic light dependent reactions. These, as well as loci associated with only one or two chlorophyll fluorescence traits, should be useful to develop a better understanding of the genetic basis of photosynthetic light dependent reactions as a whole as well as of specific components of the electron transport chain in soybean. Accordingly, additional genetic and physiological analyses are necessary to determine the relevance and effectiveness of the identified loci for crop improvement efforts.

Frequently asked questions about chlorophyll fluorescence, the sequel

Using chlorophyll (Chl) a fluorescence many aspects of the photosynthetic apparatus can be studied, both in vitro and, noninvasively, in vivo. Complementary techniques can help to interpret changes in the Chl a fluorescence kinetics. Kalaji et al. (Photosynth Res 122:121-158, 2014a) addressed several questions about instruments, methods and applications based on Chl a fluorescence. Here, additional Chl a fluorescence-related topics are discussed again in a question and answer format. Examples are the effect of connectivity on photochemical quenching, the correction of F V /F M values for PSI fluorescence, the energy partitioning concept, the interpretation of the complementary area, probing the donor side of PSII, the assignment of bands of 77 K fluorescence emission spectra to fluorescence emitters, the relationship between prompt and delayed fluorescence, potential problems when sampling tree canopies, the use of fluorescence parameters in QTL studies, the use of Chl a fluorescence in biosensor applications and the application of neural network approaches for the analysis of fluorescence measurements. The answers draw on knowledge from different Chl a fluorescence analysis domains, yielding in several cases new insights.

Genetic variability and heritability of chlorophyll a fluorescence parameters in Scots pine (Pinus sylvestris L.)

Current knowledge of the genetic mechanisms underlying the inheritance of photosynthetic activity in forest trees is generally limited, yet it is essential both for various practical forestry purposes and for better understanding of broader evolutionary mechanisms. In this study, we investigated genetic variation underlying selected chlorophyll a fluorescence (ChlF) parameters in structured populations of Scots pine (Pinus sylvestris L.) grown on two sites under non-stress conditions. These parameters were derived from the OJIP part of the ChlF kinetics curve and characterize individual parts of primary photosynthetic processes associated, for example, with the exciton trapping by light-harvesting antennae, energy utilization in photosystem II (PSII) reaction centers (RCs) and its transfer further down the photosynthetic electron-transport chain. An additive relationship matrix was estimated based on pedigree reconstruction, utilizing a set of highly polymorphic single sequence repeat markers. Variance decomposition was conducted using the animal genetic evaluation mixed-linear model. The majority of ChlF parameters in the analyzed pine populations showed significant additive genetic variation. Statistically significant heritability estimates were obtained for most ChlF indices, with the exception of DI0/RC, φD0 and φP0 (Fv/Fm) parameters. Estimated heritabilities varied around the value of 0.15 with the maximal value of 0.23 in the ET0/RC parameter, which indicates electron-transport flux from QA to QB per PSII RC. No significant correlation was found between these indices and selected growth traits. Moreover, no genotype × environment interaction (G × E) was detected, i.e., no differences in genotypes' performance between sites. The absence of significant G × E in our study is interesting, given the relatively low heritability found for the majority of parameters analyzed. Therefore, we infer that polygenic variability of these indices is selectively neutral.

Effects of bisphenol A on chlorophyll fluorescence in five plants

The aim of this study was to evaluate the effects of bisphenol A (BPA) on plant photosynthesis and determine whether the photosynthetic response to BPA exposure varies in different plants. Chlorophyll fluorescence techniques were used to investigate the effects of BPA on chlorophyll fluorescence parameters in tomato (Lycopersicum esculentum), lettuce (Lactuca sativa), soybean (Glycine max), maize (Zea mays), and rice (Oryza sativa) seedlings. Low-dose (1.5 or 3.0 mg L(-1)) BPA exposure improved photosystem II efficiency, increased the absorption and conversion efficiency of primary light energy, and accelerated photosynthetic electron transport in each plant, all of which increased photosynthesis. These effects weakened or disappeared after the withdrawal of BPA. High-dose (10.0 mg L(-1)) BPA exposure damaged the photosystem II reaction center, inhibited the photochemical reaction, and caused excess energy to be released as heat. These effects were more evident after the highest BPA dose (17.2 mg L(-1)), but they weakened after the withdrawal of BPA. The magnitude of BPA exposure effects on the chlorophyll fluorescence parameters in the five plants followed the order: lettuce > tomato > soybean > maize > rice. The opposite order was observed following the removal of BPA. In conclusion, the chlorophyll fluorescence response in plants exposed to BPA depended on BPA dose and plant species.