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Fine mapping and candidate gene analysis of LM3, a novel lesion mimic gene in rice

Zeng, Yuxiang, Ma, Liangyong, Ji, Zhijuan, Wen, Zhihua, Li, Ximing, Shi, Chunhai, Yang, Changdeng
Biologia 2012 v.68 no.1 pp. 82-90
cultivars, exons, gamma radiation, heading, leaves, loci, microsatellite repeats, mutagenesis, mutants, open reading frames, phenotype, proline, recessive genes, rice, ripening, seedlings, sequence analysis, serine, single nucleotide polymorphism
A rice lesion mimic mutant, lm3, was obtained by the mutagenesis of an indica cultivar, 93-11, using γ-ray radiation. Brownish lesions appeared on the leaves of lm3 at the young seedling stage and persisted until the ripening stage. The lm3 mutant was characterised by a shorter plant height and delayed heading compared with the wild-type 93-11. A genetic analysis indicated that the lesion mimic phenotype was controlled by a single recessive gene. Using simple sequence repeat (SSR) markers, the target gene LM3 was first located between marker RM5748 and RM14906 on chromosome 3. We then developed Insertion-Deletion (InDel) markers to fine-map LM3, and the locus was localised to a 29 kb region defined by two InDel markers, In12571 and In12600. Five ORFs were predicted in the candidate region, and DNA sequencing detected a single-nucleotide polymorphism (SNP) in the coding region of LOC Os03g21900. The SNP in the fourth exon (C in 93-11; T in lm3) of LOC_Os03g21900 results in the substitution of a proline (P) with a serine (S) at the 140th amino acid of the deduced uroporphyrinogen decarboxylase protein. We did not detect polymorphisms in the other predicted ORF regions between lm3 and 93-11. These results suggest that LOC_Os03g21900 is the most likely candidate gene for LM3.