Genome- and Transcriptome-Wide Identification of C3Hs in Common Bean (Phaseolus vulgaris L.) and Structural and Expression-Based Analyses of Their Functions During the Sprout Stage Under Salt-Stress Conditions

Genome-wide characterization of aldehyde dehydrogenase gene family members in groundnut (Arachis hypogaea) and the analysis under saline-alkali stress

Groundnut or peanut (Arachis hypogaea) is a legume crop. Its seeds are rich in protein and oil. Aldehyde dehydrogenase (ALDH, EC: 1.2.1.3) is an important enzyme involved in detoxification of aldehyde and cellular reactive oxygen species, as well as in attenuation of lipid peroxidation-meditated cellular toxicity under stress conditions. However, few studies have been identified and analyzed about ALDH members in Arachis hypogaea. In the present study, 71 members of the ALDH superfamily (AhALDH) were identified using the reference genome obtained from the Phytozome database. A systematic analysis of the evolutionary relationship, motif, gene structure, cis-acting elements, collinearity, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and expression patterns was conducted to understand the structure and function of AhALDHs. AhALDHs exhibited tissue-specific expression, and quantitative real-time PCR identified significant differences in the expression levels of AhALDH members under saline-alkali stress. The results revealed that some AhALDHs members could be involved in response to abiotic stress. Our findings on AhALDHs provide insights for further study.

Exogenous melatonin enhances cell wall response to salt stress in common bean (Phaseolus vulgaris) and the development of the associated predictive molecular markers

Common bean (Phaseolus vulgaris) is an important food crop; however, its production is affected by salt stress. Salt stress can inhibit seed germination, promote senescence, and modify cell wall biosynthesis, assembly, and architecture. Melatonin, an indole heterocycle, has been demonstrated to greatly impact cell wall structure, composition, and regulation in plants under stress. However, the molecular basis for such assumptions is still unclear. In this study, a common bean variety, "Naihua" was treated with water (W), 70 mmol/L NaCl solution (S), and 100 μmol/L melatonin supplemented with salt solution (M+S) to determine the response of common bean to exogenous melatonin and explore regulatory mechanism of melatonin against salt stress. The results showed that exogenous melatonin treatment alleviated salt stress-induced growth inhibition of the common bean by increasing the length, surface area, volume, and diameter of common bean sprouts. Moreover, RNA sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) indicated that the cell wall regulation pathway was involved in the salt stress tolerance of the common bean enhanced by melatonin. Screening of 120 germplasm resources revealed that melatonin treatment improved the salt tolerance of more than 65% of the common bean germplasm materials. Melatonin also up-regulated cell wall pathway genes by at least 46%. Furthermore, we analyzed the response of the common bean germplasm materials to melatonin treatment under salt stress using the key genes associated with the synthesis of the common bean cell wall as the molecular markers. The results showed that two pairs of markers were significantly associated with melatonin, and these could be used as candidate markers to predict whether common bean respond to exogenous melatonin and then enhance salt tolerance at the sprouting stage. This study shows that cell wall can respond to exogenous melatonin and enhance the salt tolerance of common bean. The makers identified in this study can be used to select common bean varieties that can respond to melatonin under stress. Overall, the study found that cell wall could response melatonin and enhance the salt tolerance and developed the makers for predicting varieties fit for melatonin under stress in common bean, which may be applied in the selection or development of common bean varieties with abiotic stress tolerance.

Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes

The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.

The bZIP Transcription Factor Family in Adzuki Bean (Vigna Angularis): Genome-Wide Identification, Evolution, and Expression Under Abiotic Stress During the Bud Stage

Adzuki bean (Vigna angularis) is an important dietary legume crop that was first cultivated and domesticated in Asia. Currently, little is known concerning the evolution and expression patterns of the basic leucine zipper (bZIP) family transcription factors in the adzuki bean. Through the PFAM search, 72 bZIP members of adzuki bean (VabZIP) were identified from the reference genome. Most of them were located on 11 chromosomes and seven on an unknown chromosome. A comprehensive analysis, including evolutionary, motifs, gene structure, cis-elements, and collinearity was performed to identify VabZIP members. The subcellular localization results showed VabZIPs might locate on the nuclear. Quantitative real-time PCR (qRT-PCR) analysis of the relative expression of VabZIPs in different tissues at the bud stage revealed that VabZIPs had a tissue-specific expression pattern, and its expression was influenced by abiotic stress. These characteristics of VabZIPs provide insights for future research aimed at developing interventions to improve abiotic stress resistance.

Heat shock transcription factor (Hsf) gene family in common bean (Phaseolus vulgaris): genome-wide identification, phylogeny, evolutionary expansion and expression analyses at the sprout stage under abiotic stress

BACKGROUND

Common bean (Phaseolus vulgaris) is an essential crop with high economic value. The growth of this plant is sensitive to environmental stress. Heat shock factor (Hsf) is a family of antiretroviral transcription factors that regulate plant defense system against biotic and abiotic stress. To date, few studies have identified and bio-analyzed Hsfs in common bean.

RESULTS

In this study, 30 Hsf transcription factors (PvHsf1-30) were identified from the PFAM database. The PvHsf1-30 belonged to 14 subfamilies with similar motifs, gene structure and cis-acting elements. The Hsf members in Arabidopsis, rice (Oryza sativa), maize (Zea mays) and common bean were classified into 14 subfamilies. Collinearity analysis showed that PvHsfs played a role in the regulation of responses to abiotic stress. The expression of PvHsfs varied across different tissues. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PvHsfs were differentially expressed under cold, heat, salt and heavy metal stress, indicating that PvHsfs might play different functions depending on the type of abiotic stress.

CONCLUSIONS

In this study, we identified 30 Hsf transcription factors and determined their location, motifs, gene structure, cis-elements, collinearity and expression patterns. It was found that PvHsfs regulates responses to abiotic stress in common bean. Thus, this study provides a basis for further analysis of the function of PvHsfs in the regulation of abiotic stress in common bean.

The molecular events underpinning cultivar differences in melatonin counteracting salt damage in Phaseolus vulgaris

Melatonin (N -acetyl-5-methoxytryptamine) plays important roles in multiple stress responses, especially under salt stress. However, cultivar differences in melatonin mediated salt stress tolerance are unclear. Phaseolus vulgaris L. (common bean) cultivars Jiyin 1 (JY, salt-tolerant) and Xuliyabai (XL, salt-sensitive) were used in this study. Exogenous melatonin significantly improved root growth under salt stress in JY, but had little effect on XL. Physiology analysis showed significant differences in activities of antioxidant enzymes (superoxide, SOD; and catalase, CAT) and malondialdehyde content between JY and XL. Meanwhile, the change of ABA content in JY and XL root was opposite in salt plus melatonin treatment. Comparative root transcriptomes of JY and XL revealed 3505 and 668 differentially expressed genes (DEGs) regulated by salt stress and melatonin. The most enriched melatonin-responsive genes under salt stress are mainly involved in regulation of transcription, oxidation-reduction process, transcription factor activity, oxidoreductase activity. In addition, melatonin induced more obvious changes of DEGs in JY than that in XL under salt condition. Melatonin also significantly induced 41 DEGs only in JY, including signal transduction genes, transcription factors, ubiquitin protein ligases, ion homeostasis and osmotic adjustment genes etc. This study uncovered the molecular mechanism of cultivar difference of melatonin response under salt stress in common bean.

Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.