Quantitative Gene Expression Analysis Across Contrasting Linseed Genotypes Identifies New Candidates for Aluminum Toxicity and Low‐Phosphorus Tolerance

In the North East Hill Region (NEHR) of India, acidic soils cause aluminum (Al³⁺) toxicity and phosphorus (Pi) deficiency, severely limiting crop productivity. Linseed offers potential for enhancing cropping intensity and diversification in this region. Contrasting oilseed-type linseed genotypes identified for yield traits under acidic soils were further validated for root and shoot traits through hydroponic screening. Using an orthology-based approach, eight gene families-MATE, ALMT1, MGT1, PT6, PAP15, WD40-38, SPL4, and ACA3-known to confer Al³⁺ toxicity and P deficiency tolerance in other plant species were targeted. Thirty-one genic regions were identified. In roots of four genotypes (Lus 37, Lus 237, Lus 4, and Lus 49) exposed to Al³⁺ toxicity, UGT74, MATE1365, MGT1272, and MGT1577 were upregulated in tolerant genotypes, indicating their probable roles in detoxification, transport, and ion homeostasis. Under low Pi conditions, eleven genes exhibited differential expression in shoots and roots of Lus 37, Lus 29, and Lus 4, with PT6826 and PT6635 upregulated in roots of tolerant Lus 37. Overall, LusMATE1365, LusUGT74, and LusPT6635 were identified as key candidate genes that could potentially confer tolerance to Al³⁺ toxicity and P deficiency. These insights will aid molecular breeding for linseed adaptation to acidic soils of NEHR.