Elucidating the molecular responses to waterlogging stress in onion (Allium cepa L.) leaf by comparative transcriptome profiling.

Introduction: Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown. Methods: This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress. Results: Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666. Discussion: The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.

Genetic diversity of Indian garlic core germplasm using agro-biochemical traits and SRAP markers.

The characterization of garlic germplasm improves its utility, despite the fact that garlic hasn't been used much in the past. Garlic has an untapped genetic pool of immense economic and medicinal value in India. Hence, using heuristic core collection approach, a core set of 46 accessions were selected from 625 Indian garlic accessions based on 13 quantitative and five qualitative traits. The statistical measures (CV per cent, CR per cent, VR per cent) were used to sort the core set using Shannon-Wiener diversity index and the Nei diversity index. In addition, the variation within the core set was tested for 18 agro-morphological and six biochemical characteristics (allicin, phenol content, pyruvic acid, protein, allyl methyl thiosulfinate (AMTHS), and methyl allyl thiosulfinate (MATHS)). Further study of the core set's molecular diversity was performed using sequence related amplified polymorphism (SRAP) markers, which revealed a wide range of diversity among the core set's accessions, with an average polymorphism efficiency (PE) of 80.59 percent, polymorphism information content (PIC) of 0.29, effective multiplex ratio (EMR) of 3.51, and marker index (MI) of 0.99. The findings of this study will be useful in identifying high-yielding, elite garlic germplasm lines with the trait of interest. Since this core set is indicative of total germplasm, these selected breeding lines will be used for genetic improvement of garlic in the future.

Screening of Onion (Allium cepa L.) Genotypes for Waterlogging Tolerance.

Onion production is severely affected by waterlogging conditions, which are created due to heavy rainfall. Hence, the identification of waterlogging-tolerant onion genotypes is crucial for increasing onion production. In the present study, 100 distinct onion genotypes were screened for waterlogging tolerance under artificial conditions by using the phenotypic approach in the monsoon season of 2017. Based on plant survival and recovery and changes in bulb weight, we identified 19 tolerant, 27 intermediate tolerant, and 54 highly sensitive onion genotypes. The tolerant genotypes exhibited higher plant survival and better recovery and bulb size, whereas sensitive genotypes exhibited higher plant mortality, poor recovery, and small bulb size under waterlogging conditions. Furthermore, a subset of 12 contrasting genotypes was selected for field trials during monsoon seasons 2018 and 2019. Results revealed that considerable variation in the morphological, physiological, and yield characteristics were observed across the genotypes under stress conditions. Waterlogging-tolerant genotypes, namely, Acc. 1666, Acc. 1622, W-355, W-208, KH-M-2, and RGP-5, exhibited higher plant height, leaf number, leaf area, leaf length, chlorophyll content, membrane stability index (MSI), pyruvic acid, antioxidant content, and bulb yield than sensitive genotypes under stress conditions. Furthermore, the principal component analysis biplot revealed a strong association of leaf number, leaf area, chlorophyll content, MSI, and bulb yield with tolerant genotypes under stress conditions. The study indicates that the waterlogging-tolerant onion genotypes with promising stress-adaptive traits can be used in plant breeding programs for developing waterlogging-tolerant onion varieties.