Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar

Abstract

As an extremely early flowering cultivar, rice cultivar Kitaake is a suitable model system for molecular studies. Expression analyses revealed that transcript levels of the flowering repressor Ghd7 were decreased while those of its downstream genes, Ehd1, Hd3a, and RFT1, were increased. Sequencing the known flowering-regulator genes revealed mutations in Ghd7 and OsPRR37 that cause early translation termination and amino acid substitutions, respectively. Genetic analysis of F2 progeny from a cross between cv. Kitaake and cv. Dongjin indicated that those mutations additively contribute to the early-flowering phenotype in cv. Kitaake. Because the short life cycle facilitates genetics research, this study generated 10 000 T-DNA tagging lines and deduced 6758 flanking sequence tags (FSTs), in which 3122 were genic and 3636 were intergenic. Among the genic lines, 367 (11.8%) were inserted into new genes that were not previously tagged. Because the lines were generated by T-DNA that contained the promoterless GUS reporter gene, which had an intron with triple splicing donors/acceptors in the right border region, a high efficiency of GUS expression was shown in various organs. Sequencing of the GUS-positive lines demonstrated that the third splicing donor and the first splicing acceptor of the vector were extensively used. The FST data have now been released into the public domain for seed distribution and facilitation of rice research.

Effects ofHd2in the presence of the photoperiod-insensitive functional allele ofHd1in rice

“…Interactions between Hd2 and other flowering genes were firstly reported by Yamamoto et al (2000) and Lin et al (2000), showing that this gene was interacted with Hd1 , Hd3 and Hd6 but the interaction changed under different day-length conditions. Later, Hd2 was also found to interact with other genes such as Ghd7 and Ghd8 (Fujino and Sekiguchi, 2005; Gu and Foley, 2007; Shibaya et al, 2011; Kim et al, 2013). Consequently, the response of Hd2 to photoperiod varies depending on genetic backgrounds and environmental conditions.…”

“…First, only RM248 located in the Hd2 region was used for selecting NILs used by Yan et al (2013) and genotype information on other heading date genes were not clarified, it is possible that functional alleles at Ghd7 or other loci that required for the PS activity of Hd2 were preserved in the genetic background of the NILs they used. Second, Hd2 has been found to interact with multiple genes (Lin et al, 2000; Yamamoto et al, 2000; Fujino and Sekiguchi, 2005; Gu and Foley, 2007; Shibaya et al, 2011; Kim et al, 2013), thus, its effects under LDs and SDs are highly diversified.…”

“…Loss-of-function variants for genes controlling PS has been known to be the most important resource for japonica rice in northern cultivation regions to successfully reproduce under NLD conditions in a short summer period (Takahashi and Shimamoto, 2011; Wei et al, 2012; Fujino et al, 2013; Kim et al, 2013; Koo et al, 2013; Gómez-Ariza et al, 2015). At the same time, little knowledge has been accumulated for the genetic basis underlying the photoperiod-insensitive character of early-season indica rice cultivars in Southern China which also require successful reproduction under NLD conditions in summer thus sufficient time could be provided for late-season cropping.…”

Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes

“…Artificial selection of rice varieties adapted to grow in Europe or Asia has taken advantage of loss-of-function alleles at such loci, because de-repression of Ehd1 expression results in up-regulation of the florigens and subsequent flowering also under non-inductive day lengths [14–16,21,22]. Sensitivity to day length can be compromised to the extent that pyramiding of specific mutations completely abolishes it [23,24]. …”

Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world

“…Group II were the pedigree of group I established between 1919and 1953. Group V were established after 1983 KITAAKE, one of the rice varieties from Hokkaido, is known to possess unique features such as an extremely short life cycle and high transformation efficiency (Kim et al 2013). Group IIIb established between 1962and 1989.…”