QTL Analysis for Heading Date and Yield-Related Traits Using the Recombinant Inbred Lines Derived from a Cross between ‘Koshihikari’ and ‘IS592BB’

‘Koshihikari’ is a high-quality <i>japonica</i> rice cultivar from Japan, exhibiting a medium-early heading type under Korean conditions, with tall plant height and susceptibility to lodging. ‘IS592BB’ is an early-maturing <i>japonica</i> rice cultivar in Korea, characterized by short culm, lodging tolerance, and multiple disease resistance. In this study, a recombinant inbred line population derived from a cross between ‘Koshihikari’ and ‘IS592BB’ (KSIS_RIL) was developed to investigate the genetic basis of heading date (HD) and yield-related traits through QTL analysis. QTLs associated with HD were identified on chromosomes 3, 6, and 8, and the candidate genes were assigned as <i>Hd1</i> (<i>Heading date 1</i>), <i>Hd16, Hd17</i>, and <i>Hd18</i>. Among these, <i>Hd1</i> was identified as the major QTL with the largest effect on HD variation and exhibited pleiotropic effects on multiple yield-related traits, including culm length (CL), panicle length (PL), number of spikelets per panicle (NS), ratio of ripened grain (RRG), brown/rough rice ratio (BRR), and grain yield per plant. <i>Hd17</i> also affected HD, NS, and 1,000-grain weight (TGW), whereas <i>Hd16</i> showed a masking effect because of interactions with other heading date genes. Combinations of alleles at <i>Hd1, Hd16, Hd17</i>, and <i>Hd18</i> resulted in approximately 20 days of variation in HD, and specific allele combinations exhibited 4-5 days earlier heading than ‘IS592BB,’ indicating their potential for developing early-harvest cultivars. QTLs for CL were detected on chromosomes 1 and 11, with <i>SD1</i> (<i>Semi-dwarf 1</i>) and <i>OsCPL3</i> (<i>C-terminal domain phosphatase-like 3</i>) identified as candidate genes. <i>SD1</i> was associated with variations in the CL, PL, NS, and TGW. OsCPL3 was identified within QTL associated with CL and BRR, suggesting its potential involvement in variations in plant architecture and milling-related traits. Notably, the <i>OsCPL3</i> allele from ‘Koshihikari’ was associated with higher BRR compared to that from ‘IS592BB,’ indicating its potential utility as a favorable allele for improving milling quality in rice breeding programs.