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Summary: The diversification of flowering time in response to natural environments is critical for the spread of crops to diverse geographic regions. In contrast with recent advances in understanding the molecular basis of photoperiodic flowering in rice (Oryza sativa), little is known about how flowering‐time diversification is structured within rice subspecies. By analyzing genome sequencing data and a set of 429 chromosome segment substitution lines (CSSLs) originating from 10 diverse rice accessions with wide distributions, we revealed diverse effects of allelic variations for common flowering‐time quantitative trait loci in the recipient's background. Although functional variations associated with a few loci corresponded to standing variations among subspecies, the identified functional nucleotide polymorphisms occurred recently after rice subgroup differentiation, indicating that the functional diversity of flowering‐time gene sequences was not particularly associated with phylogenetic relationship between rice subspecies. Intensive analysis of the Hd1 genomic region identified the signature of an early introgression of the Hd1 with key mutation(s) in aus and temperate japonica accessions. Our data suggested that, after such key introgressions, new mutations were selected and accelerated the flowering‐time diversity within subspecies during the expansion of rice cultivation area. This finding may imply that new genome‐wide changes for flowering‐time adaptation are one of the critical determinants for establishing genomic architecture of local rice subgroups. In‐depth analyses of various rice genomes coupling with the genetically confirmed phenotypic changes in a large set of CSSLs enabled us to demonstrate how rice genome dynamics has coordinated with the adaptation of cultivated rice during the expansion of cultivation area. [ABSTRACT FROM AUTHOR]

Genetic dissection of a wide range of naturally occurring variations in rice has significantly progressed by means of quantitative trait locus analysis. This genetic dissection has resulted in molecular cloning of genes and loci with biological and agronomic interest. The success of these analyses depends strongly on the plant materials used. In the last decade, many kinds of plant materials, and particularly advanced backcross populations, have been developed for the genetic analysis of traits of interest. Some of those materials have been deposited in the public domain in order to facilitate further analyses of rice genetics and molecular biology. In this review, we describe how such plant materials, including chromosome segment substitution lines (CSSLs) and introgression lines, could be used in genetic analysis, as well as the kinds of plant materials that could be developed and that are now available to the rice research community. Furthermore, we introduce our current activities related to large-scale development of CSSLs using diverse Asian rice accessions as donors. [ABSTRACT FROM AUTHOR]