Integrated QTL-seq and transcriptome analyses identify a DUF1677 candidate gene with a Predicted Kelch β-propeller-like fold associated with iron deficiency response in rice

Abstract

Iron deficiency is a major abiotic constraint in rice production, especially in direct-seeded and aerobic cultivation systems, yet the genes controlling tolerance, especially at the seedling stage, remain poorly understood. In this study, we screened 116 rice genotypes under iron deficiency hydroponics system, selecting RA23 (tolerant) and Lalat MAS (susceptible) as parents for an F 2 mapping population. QTL-seq of the extreme F 2 bulks identified two QTLs, qFe2.1 and qFe9.1 , supported by both ΔSNP-index and G′ statistic analysis. RNA-seq of the parental lines under iron deficiency further narrowed down these intervals to 14 candidate genes. Among these, an uncharacterised gene OsFe2200 (Os02g0152200 / LOC_Os02g05810) , a DUF1677-family gene, showed the strongest signal, i.e., ~ 80-fold higher expression in the susceptible parent, confirmed by qRT-PCR. Structural analyses indicated that OsFe2200 adopts a putative Kelch β-propeller-like fold, while additional structural comparisons identified β-propeller- and Kelch-like proteins as moderate confidence homologs, suggesting that OsFe2200 is a structurally conserved but sequence divergent protein. The OsFe2200 promoter contains iron-responsive motifs and a 21 bp insertion specific to RA23, which may contribute to its lower expression in the tolerant line, though this remains to be tested directly. Haplotype analysis in the Bengal and Assam Aus Panel showed greater phenotypic variability associated with OsFe2200, the haplotype harbouring a shared mutation with RA23 (D90V) was superior and significantly different for the number of crown roots but was non-significant for SPAD values. Together, these results identify OsFe2200 as a strong putative candidate gene for iron deficiency tolerance in rice, providing a starting point for future functional studies and breeding programmes.