Generation and characterization of novel genetic variation in rice for the enhancement of grain quality and agronomic performance

A quantitative trait loci (QTL) analysis of seedling vigor traits was conducted under dry-seeded conditions using recombinant inbred lines derived from a cross of the California varieties M-203 and M-206. Height at early seedling (HES) and height at late seedling (HLS) stage, growth rate (GR), and fresh weight (FW) were evaluated under controlled environmental conditions. HES, HLS, and GR were also evaluated in outdoor basins over two years. M-203 was significantly better for all traits in the growth chamber, however, no significant differences were observed between the parents in the outdoor basins with the exception of HES in 2015. A map consisting of >6,000 single nucleotide polymorphisms derived from genotyping by sequencing was constructed to facilitate QTL analysis. Six QTL were identified in the controlled environment, one each on chromosomes 2, 9, 10, and 12 and two at the same position on 1. qFW1 and qHES1 explained 34.6% and 8.7% of the variation observed for their traits and this locus corresponds to previously reported shoot length QTL. All positive effects were contributed by the M-203 parent with the exception of qHLS12. For the outdoor basin environment, the QTL qHES8 (12.3%; M-206 allele) and qHES9 (9.4%; M-203 allele) were detected in 2016, but no QTL were identified in 2015. RIL-187 was consistently among the highest vigor lines in all environments examined. The molecular and genetic resources developed here will allow further investigation of seedling vigor and breeding of improved temperate japonica varieties. Identification of useful grain quality characteristics in rice mutants using TILLING and