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

Abstract

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 140 th 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.

Development of 1047 insertion-deletion markers for rice genetic studies and breeding

“…SNP and InDel polymorphisms, the first and the second largest polymorphic mutations in the rice genome, provide suitable resources for designing primers with higher density than SSR markers. The higher frequencies of InDel and SNP markers in the rice genome make them preferable for fine mapping rice genes (Pan et al, 2008;Wu et al, 2011;Xu et al, 2011;Kwon et al, 2012;Zeng et al, 2013). It is worth noting that special equipment or hardware is indispensable for SNP genotyping, which has restricted the application of SNP markers.…”

Combination of Eight Alleles at Four Quantitative Trait Loci Determines Grain Length in Rice

“…DNA extraction and PCR were performed as described by Zhang et al [ 33 ] and Zeng et al [ 34 ], respectively. Briefly, a total of 179 polymorphic markers were used in QTL analysis.…”

“…Briefly, a total of 179 polymorphic markers were used in QTL analysis. All the 179 markers are co-dominant markers, including simple sequence repeat and insertion-deletion markers [ 34 ]. Composite interval mapping (CIM) was used to identify QTLs for grain length using Windows QTL Cartographer 2.5 ( http://statgen.ncsu.edu/qtlcart/WQTLCart.htm ).…”

Mapping quantitative trait loci for sheath blight disease resistance in Yangdao 4 rice

“…The 41 markers covered the regions of the QTL detected in E1 and E2. DNA extraction and the polymerase chain reaction protocol were described previously (Zeng et al, 2013a).…”