Trait and Marker Associations in Oryza nivara and O. rufipogon Derived Rice Lines under Two Different Heat Stress Conditions

Strategies to fortify the nutritional values of polished rice by implanting selective traits from brown rice: A nutrigenomics-based approach

Whole-grain cereals are important components of a healthy diet. It reduces the risk of many deadly diseases like cardiovascular diseases, diabetes, cancer, etc. Brown rice is an example of whole grain food, which is highly nutritious due to the presence of various bioactive compounds (flavonoids, phenolics, vitamins, phytosterols, oils, etc.) associated with the rice bran layer of brown rice. White rice is devoid of the nutritious rice bran layer and thus lacks the bioactive compounds which are the major attractants of brown rice. Therefore, to confer health benefits to the public at large, the nutrigenomic potential of white rice may be improved by integrating the phytochemicals associated with the rice bran layer of brown rice into it via biofortification processes like conventional breeding, agronomic practices, metabolic engineering, CRISPR/Cas9 technology, and RNAi techniques. Thus, this review article focuses on improving the nutritional qualities of white/polished rice through biofortification processes, utilizing new breeding technologies (NBTs).

Unlocking the Multifaceted Mechanisms of Bud Outgrowth: Advances in Understanding Shoot Branching

Shoot branching is a complex and tightly regulated developmental process that is essential for determining plant architecture and crop yields. The outgrowth of tiller buds is a crucial step in shoot branching, and it is influenced by a variety of internal and external cues. This review provides an extensive overview of the genetic, plant hormonal, and environmental factors that regulate shoot branching in several plant species, including rice, Arabidopsis, tomato, and wheat. We especially highlight the central role of TEOSINTE BRANCHED 1 (TB1), a key gene in orchestrating bud outgrowth. In addition, we discuss how the phytohormones cytokinins, strigolactones, and auxin interact to regulate tillering/branching. We also shed light on the involvement of sugar, an integral component of plant development, which can impact bud outgrowth in both trophic and signaling ways. Finally, we emphasize the substantial influence of environmental factors, such as light, temperature, water availability, biotic stresses, and nutrients, on shoot branching. In summary, this review offers a comprehensive evaluation of the multifaced regulatory mechanisms that underpin shoot branching and highlights the adaptable nature of plants to survive and persist in fluctuating environmental conditions.

Epigenetic and transcription factors synergistically promote the high temperature response in plants

Temperature is one of the main environmental cues affecting plant growth and development, and plants have evolved multiple mechanisms to sense and acclimate to high temperature. Emerging research has shown that transcription factors, epigenetic factors, and their coordination are essential for plant temperature responses and the resulting phenological adaptation. Here, we summarize recent advances in molecular and cellular mechanisms to understand how plants acclimate to high temperature and describe how plant meristems sense and integrate environmental signals. Furthermore, we lay out future directions for new technologies to reveal heterogeneous responses in different cell types thus improving plant environmental plasticity.

Meta-Analysis of Microarray Data and Their Utility in Dissecting the Mapped QTLs for Heat Acclimation in Rice

In the current global warming scenario, it is imperative to develop crops with improved heat tolerance or acclimation, for which knowledge of major heat stress-tolerant genes or genomic regions is a prerequisite. Though several quantitative trait loci (QTLs) for heat tolerance have been mapped in rice, candidate genes from these QTLs have not been reported yet. The meta-analysis of microarray datasets for heat stress in rice can give us a better genomic resource for the dissection of QTLs and the identification of major candidate genes for heat stress tolerance. In the present study, a database, RiceMetaSys-H, comprising 4227 heat stress-responsive genes (HRGs), was created using seven publicly available microarray datasets. This included in-house-generated microarray datasets of Nagina 22 (N22) and IR64 subjected to 8 days of heat stress. The database has provisions for searching the HRGs through genotypes, growth stages, tissues, and physical intervals in the genome, as well as Locus IDs, which provide complete information on the HRGs with their annotations and fold changes, along with the experimental material used for the analysis. The up-regulation of genes involved in hormone biosynthesis and signalling, sugar metabolism, carbon fixation, and the ROS pathway were found to be the key mechanisms of enhanced heat tolerance. Integrating variant and expression analysis, the database was used for the dissection of the major effect of QTLs on chromosomes 4, 5, and 9 from the IR64/N22 mapping population. Out of the 18, 54, and 62 genes in these three QTLs, 5, 15, and 12 genes harboured non-synonymous substitutions. Fifty-seven interacting genes of the selected QTLs were identified by a network analysis of the HRGs in the QTL regions. Variant analysis revealed that the proportion of unique amino acid substitutions (between N22/IR64) in the QTL-specific genes was much higher than the common substitutions, i.e., 2.58:0.88 (2.93-fold), compared to the network genes at a 0.88:0.67 (1.313-fold) ratio. An expression analysis of these 89 genes showed 43 DEGs between IR64/N22. By integrating the expression profiles, allelic variations, and the database, four robust candidates (LOC_Os05g43870, LOC_Os09g27830, LOC_Os09g27650, andLOC_Os09g28000) for enhanced heat stress tolerance were identified. The database thus developed in rice can be used in breeding to combat high-temperature stress.

Changes in physiological traits and expression of key genes involved in sugar signaling pathway in rice under high temperature stress

Efficient assimilate partitioning between the source and sink organs to achieve increased grain weight is coordinated by the sugar signaling mechanism. The expression of the genes involved in sugar signaling mainly hexokinases 2 (OsHXK2), Sucrose-nonfermentation1-related protein kinase1 (OsSnRK1), trehalose-6-phosphate synthase 1 (OsTPS1) and target of rapamycin (OsTOR) under high temperature stress was examined in tolerant (NL-44) and susceptible (Vandana) varieties of rice. The photosynthetic rate, stomatal conductance, water-use efficiency, photochemical efficiency (Fv/Fm), quantum yield (ϕPSII), pollen viability, spikelet fertility and 1000 grain weight were significantly higher in NL-44 compared to Vandana under stress. The difference in the gene expression levels in the vegetative and grain-filling phases as well as between the tolerant and susceptible varieties, revealed unique pathways of sugar signaling under heat stress. In the vegetative phase, the expression of OsTOR seems to be the difference between NL-44 and Vandana for their differed heat stress tolerance whereas, in the grain-filling phase, the difference between the varieties lay in the regulation of OsHXK2. The comparative changes in the expression levels between the genes under the varying conditions indicate the sugar status in the source and sink organs that are available for translocation or remobilization.

Ectopic expression of human apolipoprotein D in Arabidopsis plants lacking chloroplastic lipocalin partially rescues sensitivity to drought and oxidative stress

The chloroplastic lipocalin (LCNP) is induced in response to various abiotic stresses including high light, dehydration and low temperature. It contributes to protection against oxidative damage promoted by adverse conditions by preventing accumulation of fatty acid hydroperoxides and lipid peroxidation. In contrast to animal lipocalins, LCNP is poorly characterized and the molecular mechanism by which it exerts protective effects during oxidative stress is largely unknown. LCNP is considered the ortholog of human apolipoprotein D (APOD), a protein whose lipid antioxidant function has been characterized. Here, we investigated whether APOD could functionally replace LCNP in Arabidopsis thaliana. We introduced APOD cDNA fused to a chloroplast transit peptide encoding sequence in an Arabidopsis LCNP KO mutant line and challenged the transgenic plants with different abiotic stresses. We demonstrated that expression of human APOD in Arabidopsis can partially compensate for the lack of the plastid lipocalin. The results are consistent with a conserved function of APOD and LCNP under stressful conditions. However, if the results obtained with the drought and oxidative stresses point to the protective effect of constitutive expression of APOD in plants lacking LCNP, this effect is not as effective as that conferred by LCNP overexpression. Moreover, when investigating APOD function in thylakoids after high light stress at low temperature, it appeared that APOD could not contribute to qH, a slowly reversible form of non-photochemical chlorophyll fluorescence quenching, as described for LCNP. This work provides a base of understanding the molecular mechanism underlying LCNP protective function.

Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice (Oryza sativa L.) landraces

A core set of 190 rice landraces were used to decipher the genetic structure and to discover the chromosomal regions containing QTLs, affecting the grain micro-nutrients, fatty acids, and yield-related traits by using 148 molecular markers in this study. Landraces were categorized into three sub-groups based on population stratification study and followed by neighbor-joining tree and principal component analysis. Analysis of variance revealed abundant variations among the landraces for studied traits with less influence of environmental factors. Genome Wide Association Studies (GWAS) revealed 22 significant and consistent QTLs through marker trait association (MTAs) for 12 traits based on 2 years and pooled analysis. Out of 22 QTLs, three have been reported earlier while 19 QTLs are novel. Interestingly, 13 QTLs out of 22 were explained more than 10% phenotypic variance. Association of RM1148 and RM205 with Days to 50% flowering was comparable with flowering control genes Ghd8/qDTH8 and qDTH9, respectively. Similarly, Zn content was associated with RM44, which is situated within the QTL qZn8-1. Moreover, significant association of RM25 with oleic acid content was closely positioned with QTL qOle8. Association of RM7434 with grain yield/plant; RM184 with spikelet fertility %; R3M10, R9M42 with hundred seed weight; RM536, RM17467, RM484, RM26063 with Fe content; RM44, RM6839 with Zn content are the major outcomes of this study. In addition, association of R11M23 with days to 50% flowering, panicle length and total spikelets per panicle are explained the possible occurrence of pleiotropism among these traits. Prominent rice landraces viz., Anjani (early maturity); Sihar (extra dwarf); Gangabaru (highest grain yield/plant); Karhani (highest iron content); Byalo-2 (highest zinc content) and Kadamphool (highest oleic acid) were identified through this study. The present study will open many avenues towards utilization of these QTLs and superior landraces in rice breeding for developing nutrition-rich high yielding varieties.

Rice yield formation under high day and night temperatures-A prerequisite to ensure future food security

Increasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular-physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.

Eco-Physiological Screening of Different Tomato Genotypes in Response to High Temperatures: A Combined Field-to-Laboratory Approach

High temperatures represent a limitation for growth and development of many crop species. Several studies have demonstrated that the yield reduction of tomato under high temperatures and drought is mainly due to a photosynthetic decline. In this paper, a set of 15 tomato genotypes were screened for tolerance to elevated temperatures by cultivating plants under plastic walk-in tunnels. To assess the potential tolerance of tomato genotypes to high temperatures, measurements of chlorophyll fluorescence, pigments content and leaf functional traits have been carried out together with the evaluation of the final yields. Based on the greenhouse trials, a group of eight putative heat-sensitive and heat-tolerant tomato genotypes was selected for laboratory experiments aimed at investigating the effects of short-term high temperatures treatments in controlled conditions. The chlorophyll fluorescence induction kinetics were recorded on detached leaves treated for 60 min at 35 °C or at 45 °C. The last treatment significantly affected the photosystem II (PSII) photochemical efficiency (namely maximum PSII quantum efficiency, F_v/F_m, and quantum yield of PSII electron transport, Φ_PSII) and the non-photochemical quenching (NPQ) in the majority of genotypes. The short-term heat shock treatments also led to significant differences in the shape of the slow Kautsky kinetics and its significant time points (chlorophyll fluorescence levels minimum O, peak P, semi-steady state S, maximum M, terminal steady state T) compared to the control, demonstrating heat shock-induced changes in PSII functionality. Genotypes potentially tolerant to high temperatures have been identified. Our findings support the idea that chlorophyll fluorescence parameters (i.e., Φ_PSII or NPQ) and some leaf functional traits may be used as a tool to detect high temperatures-tolerant tomato cultivars.

QTL-seq reveals genomic regions associated with spikelet fertility in response to a high temperature in rice (Oryza sativa L.)

The QTL-seq approach was used to identify QTLs for spikelet fertility under heat stress in rice. QTLs were detected on chromosomes 1, 2 and 3. Rice is a staple food of more than half of the global population. Rice production is increasingly affected by extreme environmental fluctuations caused by climate change. Increasing temperatures that exceed the optimum temperature adversely affect rice growth and development, especially during reproductive stages. Heat stress during the reproductive stages has a large effect on spikelet fertility; hence, the yield decreases. To sustain rice yields under increasing temperatures, the development of rice varieties for heat tolerance is necessary. In this study, we applied the QTL-seq approach to rapidly identify QTLs for spikelet fertility under heat stress (air temperature of 40-45 °C) based on two DNA pools, each consisting of 25 individual plants that exhibited a heat-tolerant or heat-sensitive phenotype from an F₂ population of a cross between M9962 (heat tolerant) and Sinlek (heat sensitive). Three QTLs, qSF1, qSF2 and qSF3, were detected on chromosomes 1, 2 and 3, respectively, according to the highest contrasting SNP index between the two bulks. The QTLs identified in this study were found to overlap or were linked to QTLs previously identified in other crosses using conventional QTL mapping. A few highly abundant and anther-specific genes that contain nonsynonymous variants were identified within the QTLs and were proposed to be potential candidate genes. These genes could be targets in rice breeding programs for heat tolerance.