Nitrogen Nutrition Promotes Rhizome Bud Outgrowth via Regulation of Cytokinin Biosynthesis Genes and an Oryza longistaminata Ortholog of FINE CULM 1

Oryza longistaminata, a wild rice, can propagate vegetatively via rhizome formation and, thereby, expand its territory through horizontal growth of branched rhizomes. The structural features of rhizomes are similar to those of aerial stems; however, the physiological roles of the two organs are different. Nitrogen nutrition is presumed to be linked to the vegetative propagation activity of rhizomes, but the regulation of rhizome growth in response to nitrogen nutrition and the underlying biological processes have not been well characterized. In this study, we analyzed rhizome axillary bud growth in response to nitrogen nutrition and examined the involvement of cytokinin-mediated regulation in the promotion of bud outgrowth in O. longistaminata. Our results showed that nitrogen nutrition sufficiency promoted rhizome bud outgrowth to form secondary rhizomes. In early stages of the response to nitrogen application, glutamine accumulated rapidly, two cytokinin biosynthesis genes, isopentenyltransferase, and CYP735A, were up-regulated with accompanying cytokinin accumulation, and expression of an ortholog of FINE CULM1, a negative regulator of axillary bud outgrowth, was severely repressed in rhizomes. These results suggest that, despite differences in physiological roles of these organs, the nitrogen-dependent outgrowth of rhizome axillary buds in O. longistaminata is regulated by a mechanism similar to that of shoot axillary buds in O. sativa. Our findings provide a clue for understanding how branched rhizome growth is regulated to enhance nutrient acquisition strategies.

Temporal-spatial changes in the belowground bud bank in interdune lowlands of an active sand dune ecosystem in northeastern China

Aims The belowground bud bank plays an important role in vegetation restoration of sand dune ecosystems in semi-arid regions. However, few studies have focused on the temporal-spatial changes of belowground bud banks in interdune lowlands. Methods The size and composition of belowground bud bank in five interdune lowlands with different sizes were investigated for one growing season to determine the temporal and spatial changes in belowground bud bank. Important Findings Total bud bank density was the highest in the medium-sized interdune lowland as was tiller bud density. The density of stem-base buds exhibited an opposite trend while rhizome bud density did not change with interdune lowland size. There was a significant seasonal change in the bud bank size. The total bud density peaked in August and was the lowest in October. A similar trend was found for rhizome bud density, whereas the density of stem-base buds showed an opposite trend, and tiller bud density did not change significantly during the growing season. We conclude that the belowground bud bank density is changed with interdune lowland size and season. These results contribute to the understanding of adaptive strategies of plants growing in active dune ecosystems and provide pointers for adopting effective measures to restore and conserve dune vegetation in semi-arid regions.

Effect of Explants and Low Cost Medium on Morphogenic Response of Aerial Stem and Rhizome Bud Explants of Turmeric (Curcuma longa L.) for Plant Regeneration

This study was done to select suitable explants and low cost medium for plant regeneration of turmeric. Therefore, the different explants were excised from the aerial stems and rhizome buds and surface sterilized. The sterilized explants were cultured on MS medium fortified with 2.0 mg/l BAP. From the survived aerial stem explants, 0.5 cm long vertical half of the aerial stem explants exhibited somatic embryogenic response (69.7%). The highest morphogenic response (74%) of shoot bud initiation was observed from the top slice of the surviving rhizome bud explants. Further, Yara Mila complex fertilizer, which is an ideal granular fertilizer mixture, was used as an alternative to MS medium. Three different concentrations of Yara Mila complex fertilizer (1.0, 3.0, and 5.0 g/l ) supplemented with 2.0 mg/l BAP each were tested with the MS medium fortified with 2.0 mg/l BAP (control treatment) for in vitro establishment from aerial stem explants and top slice of the rhizome bud explants. Both explants were surface sterilized and cultured on MS medium and different concentrations of Yara Mila complex fertilizer fortified with 2.0 mg/l BAP. From the survived explants, aerial stem explants exhibited somatic embryogenic response (69.7%) and shoot bud initiation (74%) on normal MS media. The higher performances were observed in 1.0 g/l concentration of complex fertilizer incorporated medium with 51% embryogenic response from the aerial stem explants and 52.3% shoot bud formation response from the top slice of the rhizome bud. The cost of 1 kg complex fertilizer was Rs. 182. It could be concluded that complex fertilizer is a cost effective alternative medium for MS medium for in vitro propagation reducing the cost of the substituted ingredients by 99.87% in the tissue culture of turmeric.

Revealing the full-length transcriptome of caucasian clover rhizome development

Background Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. Conclusions This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

Revealing the full-length transcriptome of caucasian clover rhizome development

Background: Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant up-regulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

Revealing the full-length transcriptome of caucasian clover rhizome development

Background: Caucasian clover (Trifolium ambiguum M.Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analyzed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs)from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene specific to T5. WGCNA cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analyzed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant upregulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.