Converging QTL mapping with MutMap identifies novel genomic regions associated with strong culm in rice (Oryza sativa...

This study characterizes wild-type and mutants of rice for culm strength at morphological, histological, and molecular levels, identifying key genes and genomic regions that govern the strong culm trait. Strong culm trait in rice has gained importance for sustainability in the realm of climate change. The mutants having economic important traits have become a potential source for the identification of genomic regions. The present study aimed to characterize rice mutants having strong culms and to identify genomic regions through conventional as well as NGS-based mapping approaches. Morphological characterization of Samba Mahsuri mutants with strong culms showed that they had a greater culm diameter and physical strength than the wild type. Histological analysis confirmed the morphological parameters, which included increased thickness in culm tissue, wider intervascular bundle spacing, and thicker lignified epi- and sub-epidermal layers, as well as parenchymal layers. Exploring one of the chemically mutagenized Samba Mahsuri mutants, SB170-B having strong culm, a genetic linkage map was constructed and identified four novel QTLs: qSC-5 (chromosome 5), qSC-6a (chromosome 6), qSC-6b (chromosome 6), and qSC-10 (chromosome 10), explaining 23.76%, 21.60%, 15.40%, and 40.50% of the phenotypic variance for strong culm, respectively. MutMap, an NGS-based analysis of the weak and strong culm pools from the F₂ population derived from SB170-B×BPT 5204, also identified a genomic region (27.0-29.6 Mb) which was corresponding to the qSC-5. This genomic region comprised of 17 genic SNPs, which converted into kompetitive allele-specific PCR (KASP) assays. Among those, one KASP marker, KASP 5-2 (chr5:27972606; C/T), located in the gene LOC_Os05g48810, which encodes a DNA/J-binding protein was shown strong co-segregation with the strong culm trait, indicating its potential to use in improvement of strong culm trait through molecular breeding.