Registration of a recombinant inbred line population from a cross of weedy and cultivated rice

Adaptive traits enable weeds to persist and compete in agroecosystems, undermining crop productivity and complicating management. To provide a permanent resource for dissecting the genetic basis of these traits, 396 recombinant inbred lines (RILs; Reg. no MP‐17, PI NSL 559512 MAP) were developed from a cross between the weedy red rice accession ‘US1’ and the rice ( Oryza sativa L.) breeding line ‘EM93‐1’ by single‐seed descent from the F 2 to F 12 generations at South Dakota State University. The F 12 RILs were evaluated for wild‐like traits (seed dormancy, pigmentations, and appendages) and crop‐mimic traits (flowering time, plant height, seed dimensions, and seed weight). A subpopulation of 250 lines and the parents were genotyped using an array of 7098 single nucleotide polymorphism loci. Based on the genotyping data, the parental polymorphism was 20.2%, and the mean RIL purity was 96.9%. A high‐resolution linkage map of 1259 cM was constructed across the 12 chromosomes. Segregation distortion loci were mapped on chromosomes 6, 7, 8, and 9. The map characterized genome‐wide recombination landscapes and identified 27 recombination hot spots and 13 cold spots. The RIL population is being used to map quantitative trait loci for adaptive traits, to model epistasis and genotype × environment interactions, including seedbank longevity under till and no‐till systems, and to investigate the origins and evolution of weedy rice. The population contains all reported biotypes of weedy rice and can be used for advanced research on the origins and evolution of conspecific and congeneric weeds, as well as for allelic mining to improve crop varieties. The RILs are deposited at the USDA‐ARS Dale Bumpers National Rice Research Center.