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Transcriptomic analysis of American ginseng seeds during the dormancy release process by RNA-Seq.

Qi J, Sun P, Liao D, Sun T, Zhu J, Li X - PLoS ONE (2015)

Bottom Line: Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release.There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared.This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medicinal Plants Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.

ABSTRACT
American ginseng (Panax quinquefolius L.) is an important herb that is cultivated in China, North American, and South Korea. It is propagated from seed, but the seed has deep dormancy characteristics described as morphophysiological dormancy. Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release. However, little is known about the molecular mechanisms of seed dormancy release in the stratification process. In this study, seed development after pollination and seed development in the dormancy release process were investigated in American ginseng. The transcriptome during seed dormancy release was analyzed using RNA-Seq technology and 78,207 unigenes (mean length 531 bp) were generated. Based on similarity searches of public databases, 54,292 of the unigenes (69.4%) were functionally annotated. Further, three digital gene expression (DGE) libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined. The greatest number of differentially expressed genes occurred in the 90DCS versus 180DCS libraries, while the lowest number of differentially expressed genes occurred in the 135DCS verus 180DCS libraries. GO enrichment analysis revealed that 59, 29, and 39 GO terms were significantly enriched in the biological process, molecular function, and cell component GO categories, respectively. There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared. The gene expressions of 30 selected unigenes were validated using quantitative PCR. This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release. These data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in non-model plants.

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Relative expression level analysis of 8 selected genes.0d, 45d, 90d, 135d, and 180d: cold seed stratification period;0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.
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pone.0118558.g007: Relative expression level analysis of 8 selected genes.0d, 45d, 90d, 135d, and 180d: cold seed stratification period;0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.

Mentions: Eight genes were successfully performed in real-time PCR. Fig. 7 showed that GA3ox4, GA20ox3, CYP707A4 and KAO2 genes presented increased expression with dormancy release indicating these genes might be positively associated with seed dormancy release. GA2ox participated in the catabolism of biological active GA and ZEP involved in ABA biosynthesis indicating that these two genes might be negatively related with dormancy release[39,40]. In this study, the GA2ox3 expression level Day 0 was almost the same as Day90 and Day180 The ZEP expression level also had no significantly difference among the samples. In this work three unigenes were annotated to the dormancy-associated protein gene (DRM) and the mRNA level of the DRM1 gene Day90 and 180(Em) were significantly increased compared with the Day0 (P<0.05). This indicates that DRM activity may be correlated with morphological and physiological dormancy release in American ginseng seeds. GIGANTEA is one of the clock-associated protein that plays an important role in circadian oscillation and flowering-time regulation [41,42]. The expression level of GAGANTEA2 was significantly higher in 180th days’ endosperm than other samples (P<0.05). We also found that relative expression levels of GA3ox4, GA20ox3, DRM1, ZEP and KAO2 were basically consistent with the semi-quantitative PCR showing lower levels in Day0 compared with other seed treatment samples.


Transcriptomic analysis of American ginseng seeds during the dormancy release process by RNA-Seq.

Qi J, Sun P, Liao D, Sun T, Zhu J, Li X - PLoS ONE (2015)

Relative expression level analysis of 8 selected genes.0d, 45d, 90d, 135d, and 180d: cold seed stratification period;0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4366157&req=5

pone.0118558.g007: Relative expression level analysis of 8 selected genes.0d, 45d, 90d, 135d, and 180d: cold seed stratification period;0d, 45d, 90d, 135d, and 180d: seed stratification period; Em: embryo; En: endosperm; root, stem, and leaf as control tissues.
Mentions: Eight genes were successfully performed in real-time PCR. Fig. 7 showed that GA3ox4, GA20ox3, CYP707A4 and KAO2 genes presented increased expression with dormancy release indicating these genes might be positively associated with seed dormancy release. GA2ox participated in the catabolism of biological active GA and ZEP involved in ABA biosynthesis indicating that these two genes might be negatively related with dormancy release[39,40]. In this study, the GA2ox3 expression level Day 0 was almost the same as Day90 and Day180 The ZEP expression level also had no significantly difference among the samples. In this work three unigenes were annotated to the dormancy-associated protein gene (DRM) and the mRNA level of the DRM1 gene Day90 and 180(Em) were significantly increased compared with the Day0 (P<0.05). This indicates that DRM activity may be correlated with morphological and physiological dormancy release in American ginseng seeds. GIGANTEA is one of the clock-associated protein that plays an important role in circadian oscillation and flowering-time regulation [41,42]. The expression level of GAGANTEA2 was significantly higher in 180th days’ endosperm than other samples (P<0.05). We also found that relative expression levels of GA3ox4, GA20ox3, DRM1, ZEP and KAO2 were basically consistent with the semi-quantitative PCR showing lower levels in Day0 compared with other seed treatment samples.

Bottom Line: Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release.There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared.This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medicinal Plants Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.

ABSTRACT
American ginseng (Panax quinquefolius L.) is an important herb that is cultivated in China, North American, and South Korea. It is propagated from seed, but the seed has deep dormancy characteristics described as morphophysiological dormancy. Two-stage temperature stratification, a warm (15-20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release. However, little is known about the molecular mechanisms of seed dormancy release in the stratification process. In this study, seed development after pollination and seed development in the dormancy release process were investigated in American ginseng. The transcriptome during seed dormancy release was analyzed using RNA-Seq technology and 78,207 unigenes (mean length 531 bp) were generated. Based on similarity searches of public databases, 54,292 of the unigenes (69.4%) were functionally annotated. Further, three digital gene expression (DGE) libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined. The greatest number of differentially expressed genes occurred in the 90DCS versus 180DCS libraries, while the lowest number of differentially expressed genes occurred in the 135DCS verus 180DCS libraries. GO enrichment analysis revealed that 59, 29, and 39 GO terms were significantly enriched in the biological process, molecular function, and cell component GO categories, respectively. There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared. The gene expressions of 30 selected unigenes were validated using quantitative PCR. This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release. These data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in non-model plants.

Show MeSH
Related in: MedlinePlus