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Construction of an integrated map through comparative studies allows the identification of candidate regions for resistance to ferrous iron toxicity in rice

Dufey, Inès, Mathieu, Anne-Sophie, Draye, Xavier, Lutts, Stanley, Bertin, Pierre
Euphytica 2015 v.203 no.1 pp. 59-69
Oryza sativa, chromosome mapping, chromosomes, crossing, genes, genetic markers, iron, marker-assisted selection, phytotoxicity, plant breeding, quantitative trait loci, rice, stress tolerance
Breeding for resistance to Fe toxicity in rice remains challenging because of the complex nature of this trait. In the past 15 years, several QTL studies have been conducted using different combinations of crosses and environments. The aim of this study was to compile these data in a unique QTL map to identify candidate regions (CR) and, subsequently, candidate genes involved in rice resistance to Fe toxicity. The integrated QTL map was constructed by aligning the flanking markers on the annotated physical map of the rice reference variety Nipponbare. The heat map of QTL density was developed, highlighting four candidate regions (i.e. genomic regions of high QTL density): CR1 on chromosome 1 between markers RM246 and RM443; CR2 on chromosome 2 between markers RM526 and R758; CR3 on chromosome 3 between markers C515 and C25; and CR4 on chromosome 7 between markers R1245 and RM429. The mining of the two genomic regions harbouring the highest QTL density (CR1 and CR3) allowed the identification of 31 and 23 candidate genes in the first and second regions, respectively, based on their known function and/or on the differences in their expression between control and high Fe²⁺conditions. The integrated map is a useful tool for breeders, highlighting the positions of reliable QTLs and helping to narrow the target candidate regions for marker-assisted selection. This map also provides a strong starting point for the identification of genes underlying the reported QTLs through the candidate gene approach.