Precision marker-based breeding (PMBB) for precise transfer of pre-harvest sprouting resistance from indica donor to the elite Korean temperate japonica rice varieties

Pre-harvest sprouting (PHS) on rice panicles before harvesting severely affects yield and grain quality. Due to climate change, PHS has become a prevalent problem in Korea where temperate japonica varieties are grown. Genetic improvement through marker-assisted backcross (MAB) breeding has been significantly contributing to fast trait improvement in the elite varieties. However, final breeding products of MAB occasionally exhibit improved target traits together with undesirable traits due to linkage drag and/or presence of geneunlinked donor introgressions, especially with crosses between genetically distant parents. Precision marker-based breeding (PMBB) is an improved MAB methodology developed to bridge this gap. This involves foreground, recombinant, and background selections (FS, RS, and BS) to develop 'single small introgression lines' to eliminate linkage drag and geneunlinked donor introgressions. In this study, an indica cultivar, Kasalath possessing the major PHS resistance gene (Sdr4) was crossed with the elite Korean japonica varieties Ilpum and Gopum. For FS, Sdr4-allele specific markers were developed and used to select the donor target allele. For RS, a set of polymorphic flanking markers near Sdr4 (-350 Kb and +420 Kb) were developed and used to select the smallest Sdr4-Kasalath introgression. Through two rounds of RS (one for upstream and another for downstream of Sdr4), we obtained ~125Kb and ~120Kb sizes of Sdr4-Kasalath introgression in Ilpum (BC4F1) and in Gopum (BC2F2) background respectively. After RS, the selected lines were subjected to genotyping with genome-wide SNP markers to detect other existing donor introgressions. Based on the background genotyping results, PCR-gel based markers which can detect the other donor introgressions were selected for BS in each line. Through backcrossing with BS, the lines possessing Sdr4-Kasalath introgression (~125 Kb) with minimum other introgressions (0-4) were selected in Ilpum background and were phenotyped at the IRRI field, Philippines. The PMBB lines in Ilpum background showed significant improvement of PHS resistance while other agronomic traits such as heading date, plant height, tiller number and panicle length were highly similar to those of recurrent. The PMBB method might be one of ideal breeding techniques to improve target trait only without any other unexpected phenotypes in the local popular varieties.