Genetic and molecular analyses of natural variation facilitate
understanding of genetic control of flowering time in rice
Masahiro Yano1, Atsushi Yoshimura2 and Takuji Sasaki1
1
National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan 2Plant
Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
Recent progress in rice genome analysis has made it possible to analyze the naturally
occurring allelic variation underlying complex traits, such as heading date (flowering time) of
rice. We detected and characterized quantitative trait loci (QTLs) and identified genes at
QTLs at the molecular level. QTLs for heading date were mapped by using several types of
progeny derived from a cross between Nipponbare and Kasalath. Nine QTLs were mapped
precisely as single Mendelian factors by the use of advanced backcross progeny. Nearly
isogenic lines (NILs) of QTLs were also developed by marker-assisted selection and were
used to identify the function of each detected QTL. Substituting Kasalath alleles of 2 QTLs
into the genetic background of Nipponbare allowed us to investigate epistatic gene
interactions among QTLs. We used a map-based strategy to narrow down candidate genomic
regions for target QTLs. These analyses revealed 10- to 50-kb regions as candidates for the
target genes. Sequencing and expression analyses were used to identify the most probable
candidate genes. The function of these candidate genes was verified by a genetic
complementation test. As a result, 3 QTLs—Hd1, Hd3a, and Hd6—were found to encode
homologues of Arabidopsis CO, FT, and the CK2 alpha subunit, respectively. Molecular
identification of other QTLs is progressing. The use of wild relatives as donor parental lines
enabled us to detect additional QTLs for heading date. The analysis of natural variation has
contributed greatly to our understanding of the genetic control of heading date in rice.