Molecular marker-assisted Gene Pyramiding in Rice for Blast Resistance, Early Maturity, Salinity and Submergence Tolerance

Abstract Rice yield is severely affected by many biotic and abiotic stresses; among them, rice blast diseases, submergence, and salinity stress cause significant yield losses. The present study was carried out with the objective of combining the blast resistance genes Pi2, Pi9, and Piz, the salt resistance gene (QTL Saltol), the submergence resistance gene (QTL Sub1), and the early maturing QTL Hd2, into the single genetic background of Malaysian rice through marker-assisted gene pyramiding (MAGP). The blast-resistant Putra-1 rice variety was crossed with the salt-tolerant Binadhan-10 rice variety, and the submergence-resistant Putra-2 rice variety was crossed with the early-maturing MR297 rice variety. "True" F1s were identified and self-selected using target gene-specific markers. F2 plants, which are homozygous for all the target genes, or QTLs, were identified using PCR-based markers and advanced further through the pedigree method of breeding with selection based on phenotypic traits. At the F3 generation, a set of 28 promising homozygous lines carrying the Pi2, Pi9, Piz, Sub1, Saltol, and Hd2 genes was identified through gene-specific markers for phenotypic evaluation. The 24 advanced lines were screened for their agronomic performance, resistance against blast diseases, and tolerance to salinity and submergence stress. Among them, GPL-183, GPL-286, GPL-224, GPL-188, GPL-219, GPL-284, GPL-300, GPL-232, and GPL-195 advanced lines were selected for blast resistance, submergence tolerance, and salinity tolerance with early maturity characteristics and also recommended for large-scale field evaluation and future breeding schemes to generate various stress-resistant rice varieties.