Research Projects

1. Scientific Rationale Blast disease, caused by Magnaporthe oryzae, is an emerging threat to foxtail millet (Setaria italica) production, causing ~60% yield losses under favourable conditions (Ref 14;2;3;4). Foxtail millet has gained attention as a C₄ model due to its small genome (~515 Mb), inbreeding tendency, and short life cycle (10). Its blast resistance mechanisms remain poorly characterized compared to rice (32). Increasing frequency of virulent strains in diverse agroecologies of India underscores the urgent need to identify and deploy broad-spectrum resistance alleles (16). Landraces shaped under local agro-climatic pressures, represent a genetically rich underutilized reservoir of novel alleles.However, systematic efforts to exploit this diversity through integrative genomics approaches are currently lacking Research Background Over the past 15 years, our group has working on collecting landraces and developing pure lines of foxtail millet. So far, we have created 20 pure lines. a) In-depth phenotypic and molecular studies found new alleles for yield, drought tolerance, and seed nutritional quality. This shows that these lines could be used as parents (Ref 25; 20; 9; 15) b) RIL mapping population was developed with a combination of Landrace × Landrace or Landrace × Cultivar (DST-SERB-CRG/2018/003280). Parents sequenced and SNPs linked to yield related traits were identified (Unpublished) c) Under natural infection (Rabi 2023), distinct responses to Blast were seen, and confirmed in 2024. These were found to have broad spectrum resistance alleles in response to various isolates in controlled conditions and AMMI/GGE analysis (Dr. Rajan Sharma's Lab, ICRISAT). These resources uniquely position us to propose the present project, “To Dissect the Genetic Architecture of Blast Resistance in S. italica.” Genesis of the Hypothesis: Glasshouse screening with various pathogen isolates of parental lines revealed the contrasting nature of blast responses. The preliminary ddRAD seq indicated novel SNP haplotypes co segregating with resistance. Therefore, we hypothesize a systematic evaluation of RIL mapping population along with parents using diverse isolates could lead to the identification of landrace-derived alleles (loci) that are currently uncharacterized, confer durable, broad-spectrum blast resistance, and that integrating high-resolution genotyping with transcriptomic profiling will pinpoint the underlying genes and regulatory networks in foxtail millet. Objectives: 1. Genotyping of Parental Lines using SSR and EST-SSR markers to identify Polymorphic backbone markers for linkage map construction 2. High-resolution Phenotyping of RIL Mapping Population and parental lines against diverse M. oryzae isolates under controlled glasshouse/Field Conditions 3. Construction of Genetic Linkage Map using backbone markers and ddRAD-based polymorphic SNP’s 4. QTL identification for blast resistance using composite interval mapping and validating key loci in an independent association panel 5. Transcriptomic analysis of the post-infection extreme bulks and parents to identify QTL-linked DEGs and to develop functional Markers Novelty This study leverages untapped landrace genomic diversity through integrative genomics and phenomics to analyze blast resistance and develop breeder-ready markers that enable the pyramiding of validated resistance alleles into elite foxtail millet cultivars through marker-assisted breeding. Anticipated impact Fundamental blast resistance mechanisms in foxtail millet will be identified and developed, breeder-ready markers will directly benefit foxtail millet improvement programs as well the knowledge can apply in other millets by comparative genomics Together, these aims address an urgent production constraint with a cutting edge, multidisciplinary strategy, positioning foxtail millet as a model for translating landrace diversity into climate smart varietal development.