An IRAT109 NAM population: Genetic characterization and mapping utility for trait dissection in japonica rice (Oryza...

Complex agronomic traits in rice (Oryza sativa L.) are controlled by many genetic loci; however, dissection is often constrained in biparental mapping populations by limited recombination and narrow genetic diversity, and in diversity sets by spurious associations arising from cryptic relatedness. To overcome these limitations, we developed a nested association mapping (NAM) population of 422 recombinant inbred lines by crossing the upland tropical japonica IRAT109 with three genetically diverse japonica donors (Norin PL8, Langi, and RL11). Genotyping identified 4515 high‑quality polymorphic single nucleotide polymorphisms and revealed clear population stratification of the three subpopulations, with faster linkage disequilibrium decay (∼1.6 Mb) and broad allelic diversity, confirming that the genetic diversity of the NAM was sufficient for dissecting quantitative traits. Phenotyping under aerobic field conditions across two summer seasons for days to heading (DTH) and plant height (PH) recorded high heritabilities (0.96 for DTH; 0.92 for PH) and wide phenotypic ranges, confirming adequate phenotypic diversity for genomic analyses. Using multi-locus genome-wide association study (GWAS) models (Fixed and Random Model Circulating Probability Unification [FarmCPU] and Bayesian-Information and Linkage-Disequilibrium Iteratively Nested Keyway [BLINK]) alongside biparental linkage mapping, NAM identified nine additional loci undetected in biparental populations, improved mapping resolution by up to 6.3 Mb at specific loci, and revealed two quantitative trait loci (QTLs) co-localizing with known genes controlling DTH and PH, while linkage mapping captured family-specific allelic effects complementary to GWAS. Candidate genes were identified for the major‑effect QTLs qDTH6 (LOC_Os06g15370, LOC_Os06g16370, and LOC_Os06g16390) and qDTH7.1/qPH7.1 (LOC_Os07g15770), with sequence polymorphisms co‑segregating with donor alleles identified in GWAS, demonstrating the value of the IRAT109 NAM population for mapping and the discovery of loci underlying quantitative traits in rice.