ABSTRACT
North-East (NE) India, the probable origin of rice has diverse genetic resources. Many rice landraces of NE India were not yet characterized for blast resistance. A set of 232 landraces of NE India, were screened for field resistance at two different hotspots of rice blast, viz., IIRR-UBN, Hyderabad and ICAR-NEH, Manipur in two consecutive seasons. The phenotypic evaluation as well as gene profiling for 12 major blast resistance genes (Pitp, Pi33, Pi54, Pib, Pi20, Pi38, Pita2, Pi1, Piz, Pi9, Pizt, and Pi40) with linked as well as gene-specific markers, identified 84 resistant landraces possessing different gene(s) either in singly or in combinations and also identified seven resistant landraces which do not have the tested genes, indicating the valuable genetic resources for blast resistance. To understand the molecular diversity existing in the population, distance and model based analysis were performed using 120 SSR markers. Results of both analyses are highly correlated by forming two distinct subgroups and the existence of high diversity (24.9% among the subgroups; 75.1% among individuals of each subgroup) was observed. To practically utilize the diversity in the breeding program, a robust core set having an efficiency index of 0.82 which consists of 33 landraces were identified through data of molecular, blast phenotyping, and important agro-morphological traits. The association of eight novel SSR markers for important agronomic traits which includes leaf and neck blast resistance was determined using genome-wide association analysis. The current study focuses on identifying novel resources having field resistance to blast as well as markers which can be explored in rice improvement programs. It also entails the development of a core set which can aid in representing the entire diversity for efficiently harnessing its properties to broaden the gene pool of rice.
ABSTRACT
Improvement of host plant resistance is one of the best methods to protect the yield from biotic stresses. Incorporation of major resistance genes or their variants into elite rice varieties will enhance the host plant resistance and its durability. Allele mining is a preferred choice to discover the novel allelic variants of major genes from wide range of germplasm. 'True' allele mining includes coding and noncoding regions, which are known to affect the plant phenotype, eventually. In this study, major blast resistance gene, Pita was analyzed by allele and promoter mining strategy and its different allelic variants were discovered from landraces and wild Oryza species. Polymorphisms at allelic sequences as well as transcription factor binding motif (TFBM) level were examined. At motif level, MYB1AT is present in Pita(Tadukan) and other resistance alleles, but was absent in the susceptible allele. Core promoter was demarked with 449 bp, employing serial promoter deletion strategy. Promoter with 1592 bp upstream region could express the gfp two fold higher than the core promoter. The identified Pita resistance allele (Pita(Konibora)) can be directly used in rice blast resistance breeding programs. Moreover, characterization of Pita core promoter led to deeper understanding of resistance gene's regulation and the identified core promoter can be utilized to express similar genes in rice.
