Haplotype analysis of SCM2 loci for identification of donor for lodging resistance in rice

Lodging resistance is one of the vital traits in improving the yield and sustainability of production in rice (Oryza sativa L.). A quantitative trait loci (QTL), SCM2 for enhancing the culm strength and increased spikelet number has been reported. In the present study, a diverse collection of 150 accessions from the rice 3K-RG panel were assembled and evaluated for the STRONG CULM2 locus. All the accessions under study showed a normal phenotypic distribution for culm diameter and the allelic diversity analysis for SCM2 resulted in four INDEL's and 17 SNP's in both coding and non-coding regions of the genome. Haplotype analysis grouped the entire population into three significant haplotype groups with 114 accessions in H1, 19 accessions in H2 and 17 accessions in H3. Haplotypes were formed using two significant SNP sites viz., 27480778 and 27481339. Dunnett's test disclosed a significant variation between H1-H2 and H1-H3 haplotypes. Phenotypic evaluation for culm diameter in all the three haplotype groups revealed that the genotypes BR IRGA and PERUNEL in H1, CICA 9 and MOSHI in H2 and KITRANA in H3 possess a maximum culm diameter. H2 and H3 were found to be superior to H1 hence can be utilized for lodging resistance in further breeding programs.