Genetic dissection

Rice is the major cereal food crop that feeds more than half of the world’s population. In the current scenario, rice false smut (RFS) is a serious disease affecting both floral and grain parts, caused by Ustilaginoidea virens, resulting in a reduction in grain yield ranging from 2.8 to 81%, depending on the varietal type and disease severity (Yang et al., 2012). RFS fungus produces mycotoxins, which cause serious health issues in humans and animals (Koiso et al., 1994). A study of false smut reported that the initial infection has three stages: i) initial colonisation on the pistil, ii) multiplication on the anthers, and iii) sporulation in the chambers of the anthers (Chao et al. 2014). In another study conducted by Fan et al. (2020), in floral defective mutants reported that false smut balls matured in defective floral pistil mutants and did not mature in mutants that lack stamen. Most research work focuses on screening accessions and identifying resistance sources; however, there is a lack of understanding of the site of disease development and the molecular mechanism of RFS in tissue-specific disease development. This research provides basic knowledge and understanding of RFS at the genome as well as at the transcriptome and metabolome levels. In this study, the traditional rice varieties, maintained at the Department of Genetics and Plant Breeding, School of Agriculture, Kaveri University (250 to 300 accessions) collected from different geographical locations of India will be artificially inoculated with a virulent strain of false smut pathogen and screened under glasshouse condition maintaining proper temperature and relative humidity (In-vitro) as well as in protected field condition (In-vivo) or hotspot regions. The various stages of false smut pathogen development will be critically studied in the stamens of susceptible genotypes and resistant genotypes. The disease variables will be scored in the rice panel both in-vitro and in-vivo conditions. The resistant donor identified from the panel will be crossed with a susceptible, high-yielding popular variety to develop an F2 biparental mapping population. The F2 population will also be screened artificially in both in-vitro and in-vivo to identify the extreme individuals for RFS. The stamens from the RFS-resistant and susceptible genotypes will be collected, and RNA extraction will be done individually. An equal quantity of RNA from both extreme phenotypes of individuals (10 genotypes) will be pooled to form the resistant RNA and susceptible RNA bulks. Differential transcriptomic profiling of stamens collected from resistant and susceptible bulks will be aligned, which leads to SNP calling and associations. These associations lead to the identification of candidate genes and gene-specific SNP markers associated with RFS. Likewise, comparative metabolomic profiling will also be done to identify the key metabolic pathways associated with RFS resistance and related to transcriptome profiling. The identified candidate genes from this study will be functionally characterised, annotated, and validated in the backcross population (BC1F2) developed in parallel, which led to the development of a new high-yielding improved version of the cultivar with enhanced resistance to RFS. Haplotype analysis will be conducted to study haplotype diversity in the mapping panel to identify desirable superior haplotypes for RFS, and these haplotypes will be used in haplotype-based breeding programs to develop resistant genotypes with improved yield.