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The effect of the crosstalk between photoperiod and temperature on the heading-date in rice.

Luan W, Chen H, Fu Y, Si H, Peng W, Song S, Liu W, Hu G, Sun Z, Xie D, Sun C - PLoS ONE (2009)

Bottom Line: Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type.The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime.Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, People's Republic of China.

ABSTRACT
Photoperiod and temperature are two important environmental factors that influence the heading-date of rice. Although the influence of the photoperiod on heading has been extensively reported in rice, the molecular mechanism for the temperature control of heading remains unknown. This study reports an early heading mutant derived from tissue culture lines of rice and investigates the heading-date of wild type and mutant in different photoperiod and temperature treatments. The linkage analysis showed that the mutant phenotype cosegregated with the Hd1 locus. Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type. The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions.

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Related in: MedlinePlus

Sequence analysis of Hd1 in lf1132 and wild type.A: The sequence differences between wild type and lf1132. The black triangle represents insertion; vertical lines represent single-base substitutions; blue vertical lines and numbers are relative positions in hd1-3. SEF and SER shown by arrows are primers to detect the 315 bp insertion. B: PCR detection of the 315 bp insertion on the hd1-3 locus for lf1132. C: The expression of Hd1 in the wild type and mutant. Leaves were harvested from 30 day old seedlings at the indicated times (once every 3 h for 24 h) in natural fields (day-length is about 14 h light and 10 h dark) and RT-PCR was carried out for the analysis of Hd1 expression. Primer pairs HD1F and HD1R were used for the analysis of Hd1 expression in RT-PCR. D: Deduced amino acid sequence of the Hd1 and deduced lf1132 proteins. The black line indicates the zinc-finger domain; asterisks are amino acid substitutions between the Nipponbare Hd1 protein and the deduced lf1132 protein. E: the linkage analysis of the mutant and Hd1 locus. P1 is Zhonghua 11; P2 is lf1132.
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pone-0005891-g003: Sequence analysis of Hd1 in lf1132 and wild type.A: The sequence differences between wild type and lf1132. The black triangle represents insertion; vertical lines represent single-base substitutions; blue vertical lines and numbers are relative positions in hd1-3. SEF and SER shown by arrows are primers to detect the 315 bp insertion. B: PCR detection of the 315 bp insertion on the hd1-3 locus for lf1132. C: The expression of Hd1 in the wild type and mutant. Leaves were harvested from 30 day old seedlings at the indicated times (once every 3 h for 24 h) in natural fields (day-length is about 14 h light and 10 h dark) and RT-PCR was carried out for the analysis of Hd1 expression. Primer pairs HD1F and HD1R were used for the analysis of Hd1 expression in RT-PCR. D: Deduced amino acid sequence of the Hd1 and deduced lf1132 proteins. The black line indicates the zinc-finger domain; asterisks are amino acid substitutions between the Nipponbare Hd1 protein and the deduced lf1132 protein. E: the linkage analysis of the mutant and Hd1 locus. P1 is Zhonghua 11; P2 is lf1132.

Mentions: In previous studies, the se1 mutants HS66 and HS110 both displayed an early heading phenotype with lower photoperiod sensitivity, and Yano et al. [12] later confirmed that Se1 was an allele of Hd1. Sequence analysis found that HS66 and HS110 contained a 43 bp deletion and a 433 bp insertion, respectively [12]. In addition, HS66, HS110 and their progenitor variety Ginbouzu all contained a 36 bp insertion and a nucleotide substitution compared to Nipponbare. As the phenotype of lf1132 was similar to the phenotype of se1 mutants, we investigated whether lf1132 harbored a mutation of the Hd1 locus through sequencing verification of lf1132 and Zhonghua 11. We found that the Hd1 locus contained a 36 bp insertion and a nucleotide substitution compared to Nipponbare in Zhonghua 11 (Fig. 3A). However, the Hd1 locus contained 6 new single-base substitutions and two new insertions, a 129 bp insertion and a 150 bp insertion in lf1132, in addition to a 36 bp insertion and a nucleotide substitution at the same position compared to Zhonghua 11 (Fig. 3A). These two new insertions are located in the first exon and consist of genome duplications with several single-base substitutions. Three insertions (36 bp insertion, 129 bp insertion and 150 bp insertion) are located at the position 327 bp, 475 bp and 498 bp far from ATG site, respectively. The distances between two near insertions are 148 bp and 23 bp respectively. Therefore, these two new insertions resulted in reading-frame shift in mutated region (from the position 327 bp to 498 bp), but no reading-frame shift after the position 499 bp. These insertions and single-base substitutions do not locate in the zinc-finger domain and CCT domain, also do not cause a premature stop codon in lf1132 (Fig. 3A). We speculated that the early heading phenotype was caused by 6 new single-base substitutions and two new insertions, but not by the 36 bp insertion and substitution because Zhonghua 11 also contained these same elements. SEF and SER primers can successfully detect these two new insertions in lf1132, but not in Zhonghua 11 or Nipponbare (Fig. 3B). These results indicate that this gene is an allele of Hd1, and is designated Hd1-3.


The effect of the crosstalk between photoperiod and temperature on the heading-date in rice.

Luan W, Chen H, Fu Y, Si H, Peng W, Song S, Liu W, Hu G, Sun Z, Xie D, Sun C - PLoS ONE (2009)

Sequence analysis of Hd1 in lf1132 and wild type.A: The sequence differences between wild type and lf1132. The black triangle represents insertion; vertical lines represent single-base substitutions; blue vertical lines and numbers are relative positions in hd1-3. SEF and SER shown by arrows are primers to detect the 315 bp insertion. B: PCR detection of the 315 bp insertion on the hd1-3 locus for lf1132. C: The expression of Hd1 in the wild type and mutant. Leaves were harvested from 30 day old seedlings at the indicated times (once every 3 h for 24 h) in natural fields (day-length is about 14 h light and 10 h dark) and RT-PCR was carried out for the analysis of Hd1 expression. Primer pairs HD1F and HD1R were used for the analysis of Hd1 expression in RT-PCR. D: Deduced amino acid sequence of the Hd1 and deduced lf1132 proteins. The black line indicates the zinc-finger domain; asterisks are amino acid substitutions between the Nipponbare Hd1 protein and the deduced lf1132 protein. E: the linkage analysis of the mutant and Hd1 locus. P1 is Zhonghua 11; P2 is lf1132.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2690821&req=5

pone-0005891-g003: Sequence analysis of Hd1 in lf1132 and wild type.A: The sequence differences between wild type and lf1132. The black triangle represents insertion; vertical lines represent single-base substitutions; blue vertical lines and numbers are relative positions in hd1-3. SEF and SER shown by arrows are primers to detect the 315 bp insertion. B: PCR detection of the 315 bp insertion on the hd1-3 locus for lf1132. C: The expression of Hd1 in the wild type and mutant. Leaves were harvested from 30 day old seedlings at the indicated times (once every 3 h for 24 h) in natural fields (day-length is about 14 h light and 10 h dark) and RT-PCR was carried out for the analysis of Hd1 expression. Primer pairs HD1F and HD1R were used for the analysis of Hd1 expression in RT-PCR. D: Deduced amino acid sequence of the Hd1 and deduced lf1132 proteins. The black line indicates the zinc-finger domain; asterisks are amino acid substitutions between the Nipponbare Hd1 protein and the deduced lf1132 protein. E: the linkage analysis of the mutant and Hd1 locus. P1 is Zhonghua 11; P2 is lf1132.
Mentions: In previous studies, the se1 mutants HS66 and HS110 both displayed an early heading phenotype with lower photoperiod sensitivity, and Yano et al. [12] later confirmed that Se1 was an allele of Hd1. Sequence analysis found that HS66 and HS110 contained a 43 bp deletion and a 433 bp insertion, respectively [12]. In addition, HS66, HS110 and their progenitor variety Ginbouzu all contained a 36 bp insertion and a nucleotide substitution compared to Nipponbare. As the phenotype of lf1132 was similar to the phenotype of se1 mutants, we investigated whether lf1132 harbored a mutation of the Hd1 locus through sequencing verification of lf1132 and Zhonghua 11. We found that the Hd1 locus contained a 36 bp insertion and a nucleotide substitution compared to Nipponbare in Zhonghua 11 (Fig. 3A). However, the Hd1 locus contained 6 new single-base substitutions and two new insertions, a 129 bp insertion and a 150 bp insertion in lf1132, in addition to a 36 bp insertion and a nucleotide substitution at the same position compared to Zhonghua 11 (Fig. 3A). These two new insertions are located in the first exon and consist of genome duplications with several single-base substitutions. Three insertions (36 bp insertion, 129 bp insertion and 150 bp insertion) are located at the position 327 bp, 475 bp and 498 bp far from ATG site, respectively. The distances between two near insertions are 148 bp and 23 bp respectively. Therefore, these two new insertions resulted in reading-frame shift in mutated region (from the position 327 bp to 498 bp), but no reading-frame shift after the position 499 bp. These insertions and single-base substitutions do not locate in the zinc-finger domain and CCT domain, also do not cause a premature stop codon in lf1132 (Fig. 3A). We speculated that the early heading phenotype was caused by 6 new single-base substitutions and two new insertions, but not by the 36 bp insertion and substitution because Zhonghua 11 also contained these same elements. SEF and SER primers can successfully detect these two new insertions in lf1132, but not in Zhonghua 11 or Nipponbare (Fig. 3B). These results indicate that this gene is an allele of Hd1, and is designated Hd1-3.

Bottom Line: Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type.The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime.Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, People's Republic of China.

ABSTRACT
Photoperiod and temperature are two important environmental factors that influence the heading-date of rice. Although the influence of the photoperiod on heading has been extensively reported in rice, the molecular mechanism for the temperature control of heading remains unknown. This study reports an early heading mutant derived from tissue culture lines of rice and investigates the heading-date of wild type and mutant in different photoperiod and temperature treatments. The linkage analysis showed that the mutant phenotype cosegregated with the Hd1 locus. Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type. The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions.

Show MeSH
Related in: MedlinePlus