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Updated: Jul 12, 2026
A Method to Preserve Wetland Roots and Rhizospheres for Elemental Imaging
Published on: February 15, 2021
Multi-layered meta-analytical insights into arsenic and cadmium tolerance in rice: high confidence genomic landscape
Anurag Mishra1,2, Praful Mukund Damdar1, Md Shamim2,3
1Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad, Central Agricultural University, Pusa, Samastipur, Bihar 848125 India.
Abstract:
Heavy metals and metalloids (HMs), particularly arsenic (As) and cadmium (Cd), are hazardous contaminants with strong carcinogenic properties that adversely affect rice production in major growing regions worldwide. In the present study, meta-quantitative trait loci (MQTL) analysis identified 35 MQTLs associated with As and Cd tolerance, achieving a 4.46-fold reduction in confidence intervals (CIs) and thereby enhancing the precision of the identified genomic regions. A total of 9432 candidate genes were detected within these MQTL regions. Transcriptomic analysis under As and Cd stress conditions revealed 170 meta-differentially expressed genes (mDEGs), and their integration with MQTL-associated genes led to the identification of 48 key candidate genes. Functional annotation classified these genes into five major biological processes associated with stress tolerance: redox regulation, glutathione metabolism, cell wall biogenesis, root development, and membrane transport. Among these, 14 highly expressed genes were selected for validation, and quantitative real-time PCR analysis in contrasting rice genotypes demonstrated that 12 genes were significantly upregulated in the resistant genotype (CSR30) under both individual and combined As and Cd stress conditions. Furthermore, haplotype analysis of these validated genes revealed considerable variation in SNP number (3-188) and haplotype frequency (0.353-0.641), along with moderate haplotype diversity (Hd: 0.4698-0.7551) and nucleotide diversity (π: 0.2834-0.4825). Predominantly negative Tajima's D values indicate purifying selection or population expansion, while positive values in some genes suggest balancing selection, highlighting their potential utility in haplotype-based genomic selection and marker-assisted breeding for developing rice cultivars with enhanced tolerance to As and Cd stress.
Supplementary Information:
The online version contains supplementary material available at 10.1007/s12298-026-01774-8.
