Physical mapping of qDTH3 for heading date reveals the evolutionary history of cultivated rice

Abstract

Crop breeding programs can improve traits associated with desirable phenotypic characteristics to different local environmental conditions. In rice, such improvements were achieved depending on genetic diversity among local populations. Here, we examined whether differences in traits of elite varieties are due to genetic differences and from what the genetic differences are derived. Previously, we identified one quantitative trait locus associated with heading date, i.e., the quantitative trait locus for days to heading on chromosome 3 (qDTH3). Using 592 plants of the F2 generation, fine mapping narrowed the qDTH3 locus down to a 158-kb region of the corresponding rice reference genome. Based on the genome sequences of a 656-kb region including the qDTH3 locus among four Oryza species populations, we propose the historic evolutionary process of cultivated rice, considering nucleotide polymorphisms and intrapopulation recombination. Phenotypic differences in qDTH3 in elite varieties may be derived from a different lineage split from the ancestor.