Raman, M. S. | bioRxiv Science

bioRxiv2025

Omics-driven Identification of Candidate Genes and SNP markers in a Major QTL Controlling Early Heading in Rice

Precise control of heading date is essential for optimizing regional adaptability, enhancing climate resilience, and maximizing grain yield in rice, making it a key breeding target. The SM93 rice line exhibits a 7-10-day earlier heading than the elite Indian variety, Samba Mahsuri (SM). F2 populations derived from a cross of SM with SM93 were phenotyped for heading date across three successive kharif (rainy) seasons (2019-2021), revealing consistent early heading and notable transgressive segregation. Initial QTL-seq analysis identified a high-confidence QTL on Chr3, qDTH3, strongly associated with days to heading (DTH). KASP assays and association mapping were subsequently performed to refine the QTL, narrowing it down to a 2.53 Mb region, explaining [~]25% of the trait. SNP markers closely linked to heading were identified. Transcriptomic analysis revealed significant differential regulation of genes within qDTH3 and upregulation of the MADS- box network in SM93 during panicle initiation, suggesting their role in promoting early heading. Our integrative strategy led to the identification of candidate genes within qDTH3, associated with heading date, phytohormone regulation, and protein turnover, include the transcription factors, OsMADS34/PAP2 (Os03g0753100), OsZHD11 (Os03g0718500), HSFA2A (Os03g0745000), OsH3 (Os03g0727200), OSH1/Oskn1 (Os03g0727000), a histidine kinase, HK4 (Os03g0717700), and a Serine carboxypeptidase, OsSCP19 (Os03g0730400). Our findings provide SNP markers in and around these genes, as potentially valuable tools for breeding early-maturing rice varieties with improved adaptability. HIGHLIGHTThis study on the SM93 rice line identifies a major QTL for early heading and describes genes and SNP markers that are closely linked to this trait, which can be used in trait advancement. By fine-tuning heading date, we can help rice varieties better withstand temperature extremes, drought, and other climate-related stresses, making it a key target for genetic improvement and breeding strategies.

plant biology↗

bioRxiv2023

Multiomics-assisted characterization of rice-Yellow Stem Borer interaction provides genomic and mechanistic insights into stem borer tolerance in rice

Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice in India, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate source of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB tolerance at vegetative phase in a highly tolerant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB tolerance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and tolerant lines revealed multiple genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB tolerance. Taken together, our study provides insights on rice-YSB interaction at genomic, transcriptomic and metabolomic level, thereby facilitating the understanding of tolerance mechanism. Importantly, a promising breeding line and markers for YSB tolerance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars. SIGNIFICANCE STATEMENTGlobal rice production is threatened by various pests, among which stem borers pose serious challenges. Hence, understanding the molecular intricacies of rice-stem borer interaction is necessary for effective pest management. Here, we used a multi-omics approach to unravel the mechanisms that might help rice combat yellow stem borer infestation, thus providing insights and scope for developing YSB tolerant rice varieties. To facilitate the latter, we developed markers that co-segregate with tolerance.

plant biology↗