Genetic architecture of variation in heading date among Asian rice accessions

Hori, Kiyosumi; Nonoue, Yasunori; Ono, Nozomi; Shibaya, Taeko; Ebana, Kaworu; Matsubara, Kazuki; Ogiso‐Tanaka, Eri; Tanabata, Takanari; Sugimoto, Kazuhiko; Taguchi-Shiobara, Fumio; Yonemaru, Jun‐ichi; Mizobuchi, Ritsuko; Uga, Yusaku; Fukuda, Atsunori; Ueda, Taro; Yamamoto, Shin Ichi; Yamanouchi, Utako; Takai, Toshiyuki; Ikka, Takashi; Kondo, Katsuhiko; Hoshino, Tomoki; Yamamoto, Eiji; Adachi, Shunsuke; Nagasaki, Hideki; Shomura, Ayahiko; Shimizu, Takehiko; Kono, Izumi; Ito, Sachie; Mizubayashi, Tatsumi; Kitazawa, Noriyuki; Nagata, Kazufumi; Ando, Tsuyu; Fukuoka, Shuichi; Yamamoto, Tetsuro; Yano, Masahiro

doi:10.1186/s12870-015-0501-x

Cited by 46 publications

(44 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…CSSLs represent genetic resources that introgress a single (or a few) chromosomal segment(s) that collectively span the entire genome. Because the recent quantitative trait locus (QTL) analyses for flowering time derived from diverse Asian rice accessions have mapped the various QTLs influencing the genetic architecture of rice flowering time (Hori et al ., ), this compelled us to elucidate a wide range of naturally occurring variations of rice flowering‐time genes originated from diverse rice accessions in a common genetic background, and to simultaneously compare functional differences among various flowering‐time gene alleles using a large set of CSSL populations (Figure S1).…”

Section: Introductionmentioning

confidence: 99%

Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area

et al. 2018

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…To identify Tos17 insertion mutations of Hd1 , we selected mutant lines showing an early‐flowering phenotype in a paddy field of NIAS (Tsukuba, Japan; 36°03′N, 140°11′E) and then extracted genomic DNA from leaves of the mutant lines by the methods of Hori et al. (). We performed Southern blot analysis according to the method reported by Miyao et al.…”

Section: Methodsmentioning

confidence: 99%

“…, Hori et al. ). Sequence analysis of the known flowering‐time genes has indicated that allelic differences have contributed greatly to this phenotypic variation (Takahashi et al.…”

mentioning

confidence: 99%

A novel Tos17 insertion upstream of Hd1 alters flowering time in rice

et al. 2016

Self Cite

View full text Add to dashboard Cite

Heading date 1 (Hd1) is one of the major determinants of flowering time and regional adaptability in rice (Oryza sativa L.), because there is a significant correlation between Hd1 allelic diversity and phenotypic differences in rice cultivars. In this study, we isolated a novel rice mutant with a Tos17 retrotransposon insertion upstream of Hd1. The Tos17 insertion mutant of Hd1 [designated as Tos17(Hd1)] had decreased photoperiod sensitivity and mRNA expression of Hd1, as compared with wild‐type Nipponbare. Between Tos17(Hd1) and Nipponbare, expression levels of OsPRR1 and OsGI were similar, whereas those of two florigen genes Hd3a and RFT1, were significantly different under both short and long‐day conditions. Tos17(Hd1) showed photoperiod sensitivity intermediate between that of Nipponbare and a near‐isogenic line having a non‐functional allele of Hd1, indicating that Tos17(Hd1) has an attenuated but functional Hd1 allele. Our results revealed that allele mining of Hd1 may provide good opportunities to develop novel rice cultivars showing different levels of photoperiod sensitivity.

show abstract

“…Over-expression of Hd1 causes a delay in flowering under SD conditions and a single extension of day-length decreases Hd3a expression consistently with the duration of daylight [44,59]. The repression of flowering by Hd1 under LD conditions is enhanced by the kinase activity of Heading date 6 (Hd6), a gene encoding the α subunit of protein kinase CK2 (CK2α) [58]. Hd6 is a QTL involved in photoperiod response in rice.…”

Section: Circadian Clock and Photoperiod Responsementioning

confidence: 99%

“…The plant circadian system consists of biochemical timing mechanisms that temporarily modulate the function of several signalling pathways to measures changes in day-length and promote suitable timing of flowering to maximize reproductive success [2,3,6,7,9,10,[13][14][15]21,24,26,28,29,31,36,38,41,42,46,48,49,[56][57][58][59][60][61][62][63][64][65][66]. The photoperiod response on flowering time varies among grasses.…”

Section: Circadian Clock and Photoperiod Responsementioning

confidence: 99%

Molecular Regulation of Flowering Time in Grasses

Nuñez

Yamada

2017

Agronomy

View full text Add to dashboard Cite

Flowering time is a key target trait for extending the vegetative phase to increase biomass in bioenergy crops such as perennial C 4 grasses. Molecular genetic studies allow the identification of genes involved in the control of flowering in different species. Some regulatory factors of the Arabidopsis pathway are conserved in other plant species such as grasses. However, differences in the function of particular genes confer specific responses to flowering. One of the major pathways is photoperiod regulation, based on the interaction of the circadian clock and environmental light signals.Depending on their requirements for day-length plants can be classified as long-day (LD), short-day (SD), and day-neutral. The CONSTANS (CO) and Heading Date 1 (Hd1), orthologos genes, are central regulators in the flowering of Arabidopsis and rice, LD and SD plants, respectively. Additionally, Early heading date 1 (Ehd1) induces the expression of Heading date 3a (Hd3a), conferring SD promotion and controls Rice Flowering Locus T 1 (RFT1) in LD conditions, independently of Hd1. Nevertheless, the mechanisms promoting flowering in perennial bioenergy crops are poorly understood. Recent progress on the regulatory network of important gramineous crops and components involved in flowering control will be discussed.

show abstract

Genetic architecture of variation in heading date among Asian rice accessions

Cited by 46 publications

References 69 publications

Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area

Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area

A novel Tos17 insertion upstream of Hd1 alters flowering time in rice

Molecular Regulation of Flowering Time in Grasses

Contact Info

Product

Resources

About