Deciphering genetic mechanisms of Al toxicity tolerance through meta-QTL analysis in rice (Oryza sativa L.)

Rice is known for its tolerance to high aluminum (Al) concentrations in soil. However, the precise genetic and physiological mechanisms are yet to be fully understood. Recent research has identified several candidate genes (CGs) and quantitative trait loci (QTLs) associated with Al toxicity tolerance in rice. Nevertheless, many more QTLs/genes are yet to be precisely mapped. We employed meta-QTL (M-QTL) analysis, integrating 12 independent mapping studies and 5 Genome-Wide Association Studies (GWAS). The meta-analysis identified 53 M-QTLs from 157 projected QTLs, which were further narrowed down to 28 M-QTLs based on the number of overlapping QTLs on a consensus map. Gene identification through batch retrieval from the RAP database yielded 2765 non-redundant genes within the 28 M-QTL regions. Comparison of M-QTL CGs with six expression datasets associated with Al toxicity tolerance in rice resulted in the identification of 219 CGs with significant differential expression. Notably, 34 CGs were identified to be common across at least 2 studies. Further downstream analyses of CGs revealed the presence of cis-regulatory elements, transcription factors, and transporter proteins related to the Al toxicity tolerance response. Additionally, we analyzed the expression patterns of the four CGs, namely NRT2.3, ALMT4, MT1, and MTP11, which showed significant upregulation in the Al toxicity-tolerant rice genotype, Anjali. Conversely, in the sensitive genotype Swarna, only NRT2.3 exhibited upregulation, while ALMT4, MT1, and MTP11 were downregulated. Our study highlights significant meta-regions that hold the potential for improving rice genotypes for enhanced tolerance to Al toxicity in acidic soils.