Changing allele frequencies associated with specific resistance genes to leaf blast in backcross introgression lines of Khao Dawk Mali 105 developed from a conventional selection program

Key genomic regions associated with blast resistance against a broad spectrum of isolates could be identified in backcross introgression lines developed by conventional breeding program. In this article, eighty three BC3F2 backcross introgression lines (BILs) derived from a cross between IR68835-98-2-B-2-1-1 (a broad spectrum blast resistance variety) and KDML105 (a susceptible variety) were developed by phenotypic selection against a mixture of six virulent blast isolates (MXL) that are widely spread out in the rainfed lowland of the North and Northeast of Thailand. The resistance spectrum of the BILs was assessed by inoculating with 12 different Magnaporthe oryzae isolates that showed differential responses on the parental cultivars and the MXL that was used for phenotypic selection. All BILs showed highly resistant reactions (low disease score) to the MXL and to two blast isolates THL48 and THL149. Four markers, i.e., RM246, RM241, RM303 and RM164 completely favoring the IR68835 allele (shifting of allele frequencies from KDML105 to IR68835) were identified on chromosomes 1, 4 and 5, respectively. Therefore, these markers could be linked to the resistance genes functioning against the MXL, THL48 and THL149. Furthermore, significant shifting of alleles was identified at six markers located on chromosomes 2, 4, 8, 9 and 12. Seven DNA markers linked to specific resistance genes were identified, in which allele from IR68835 at 6 markers, i.e., RM6, RM205, RM211, RM252, RM273 and RM342 reduced disease score (DS), against blast isolates THL16, THL329, THL458, THL831, THL868 and THL96036 while allele from KDML105 at RM208 (Pi-kd on chromosomes 2) reduce DS against THL84, THL191, THL557 and THL1108. In this study, the use of DNA markers enabled the identification of specific resistance genes in the backcross breeding materials developed from routine rice breeding program through the conventional phenotypic selection. In this experiment, the usefulness of breeding materials from conventional breeding program in identifying genes corresponding to the selection was illustrated. Linked markers and their genomic location provide necessary information for further use of marker-assisted selection to improve blast resistance in rice breeding program.

Research highlights
► Introgression of broad-spectrum resistance through conventional breeding using mixed isolates in screening introgression lines.
► Molecular markers aid in identifying genomic regions associated with blast resistance.
► Allele shift allows the identification of specific resistance genes against blast disease in rice.
► Linked markers that are tightly linked to blast resistance may be useful in marker-assisted breeding programs.