Regulation of hormone-related genes involved in adventitious root formation in sweetpotato

Hualin Nie,김수정,이용재,박형준,이종은,김지성,김도연,김선형 한국식물생명공학회 2020 JOURNAL OF PLANT BIOTECHNOLOGY Vol.47 No.3

The sweetpotatoes (Ipomoea batatas) generate adventitious roots (ARs) from cut stems that develop into storage roots and make for an important means of propagation. However, few studies have investigated the hormones involved in AR development in sweetpotato. In this study, the expression patterns of hormone-related genes involved in AR formation were identified using the transcriptome data. RNA-seq data from stems grown for 0 and 3 days after cutting were analyzed. In addition, hormone-related genes were identified among differentially expressed genes (DEGs) and filtered genes, and cluster analysis was used to characterize expression patterns by function. Most hormone-related regulated genes expressed 3 days after growing the cut stems were abscisic acid (ABA)- related genes, followed by ethylene- and auxin-related genes. For ABA, the biosynthesis genes (including genes annotated to NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3)) and signal transduction and perception genes (including genes annotated to PROTEIN PHOSPHATASE 2Cs (PP2Cs)) tended to decrease. Expression patterns of auxin- and ethylene-related genes differed by function. These results suggest that ABA, auxin, and ethylene genes are involved in AR formation and that they may be regulated in a hormone function-dependent manner. These results contribute to the identification of hormone functions during AR formation and may contribute to understanding the mechanism of AR formation in the sweetpotato.

Comparative analysis of AGPase proteins and conserved domains in sweetpotato (Ipomoea batatas (L.) Lam.) and its two wild relatives

Hualin Nie,Sujung Kim,김종보,권석윤,김선형 한국식물생명공학회 2022 JOURNAL OF PLANT BIOTECHNOLOGY Vol.49 No.1

Conserved domains are defined as recurring units in molecular evolution and are commonly used to interpret the molecular function and biochemical structure of proteins. Herein, the ADP-glucose pyrophosphorylase (AGPase) amino acid sequences of three species of the Ipomoea genus [Ipomoea trifida, I. triloba, and I. batatas (L.) Lam. (sweetpotato)] were identified to investigate their physicochemical and biochemical characteristics. The molecular weight, isoelectric point, instability index, and grand average of hyropathy markedly differed among the three species. The aliphatic index values of sweetpotato AGPase proteins were higher in the small subunit than in the large subunit. The AGPase proteins from sweetpotato were found to contain an LbH_G1P_AT_C domain in the C-terminal region and various domains (NTP_transferase, ADP_Glucose_PP, or Glyco_tranf_GTA) in the N-terminal region. Conversely, most of its two relatives (I. trifida and I. triloba) were found to only contain the NTP_transferase domain in the N-terminal region. These findings suggested that these conserved domains were species-specific and related to the subunit types of AGPase proteins. The study may enable research on the AGPase-related specific characteristics of sweetpotatoes that do not exist in the other two species, such as starch metabolism and tuberization mechanism.

Physiological and proteomic analysis of plant growth enhancement by the rhizobacteria Bacillus sp. JS

김지성,이정은,Hualin Nie,이용재,김선태,김선형 한국유전학회 2018 Genes & Genomics Vol.40 No.2

In this study, the effects of the plant growthpromoting rhizobacterium (PGPR), Bacillus sp. JS on the growth of tobacco (Nicotiana tabacum ‘Xanthi’) and lettuce (Lactuca sativa ‘Crispa’), were evaluated by comparing various growth parameters between plants treated with the bacterium and those exposed to water or nutrient broth as control. In both tobacco and lettuce, fresh weight and length of shoots were increased upon exposure to Bacillus sp. JS. To explain the overall de novo expression of plant proteins by bacterial volatiles, two-dimensional gel electrophoresis was performed on samples from PGPR-treated tobacco plants. Our results showed that chlorophyll a/b binding proteins were significantly up-regulated, and total chlorophyll content was also increased. Our findings indicate the potential benefits of using Bacillus sp. JS as a growth-promoting factor in agricultural practice, and highlight the need for further research to explore these benefits.

Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation

Sujung Kim,Hualin Nie,Byungki Jun,Jiseong Kim,Jeongeun Lee,Seungill Kim,Ekyune Kim,Sunhyung Kim 한국유전학회 2020 Genes & Genomics Vol.42 No.5

Background Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear. Objective To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato. Methods RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression. Results 42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation. Conclusions The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

Hyungjun Park,Sujung Kim,Hualin Nie,Jiseong Kim,Jeongeun Lee,Sunhyung Kim 한국식물생명공학회 2020 JOURNAL OF PLANT BIOTECHNOLOGY Vol.47 No.2

The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties (‘Beniharuka’, ‘Annobeni’, ‘Pungwonmi’, ‘Hogammi’) and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the ‘Beniharuka’, ‘Pungwonmi’, and ‘Annobeni’ sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.

식물 생장 촉진 진균에 의한 담배의 생장 촉진과 뿌리 발달

홍은혜,이진옥,김수정,김영남,김지성,김선형,Hong, Eunhye,Lee, Jinok,Kim, Sujung,Nie, Hualin,Kim, Young-Nam,Kim, Jiseong,Kim, Sunhyung 한국식물생명공학회 2020 JOURNAL OF PLANT BIOTECHNOLOGY Vol.47 No.4

식물생장촉진 미생물은 식물 뿌리에 영양을 원활하게 공급하거나 휘발성 유기화합물(Volatile Organic Compound, VOC)를 이용하여 식물의 내재 인자와 상호작용을 통해 생장을 촉진한다. 본 연구에서는 식물 생장 촉진 진균 UOS의 담배에서의 생장 촉진 효과를 평가하고, 계통발생학적 분석을 통해 동정하였다. 또한, UOS의 식물 생장 촉진 인자를 탐색하고자 Gas Chromatography-Mass Spectrometry (GC-MS) 분석을 통해 UOS의 VOCs를 확인하였다. UOS를 처리한 담배는 무처리구에 비해서 3.8배의 생중량이 증가하였고, I-plate를 이용한 분리된 공간에서는 UOS처리구가 무처리에 비해 생중량이 4.2배 증가하였다. 또한, UOS 처리구의 식물은 주근의 길이가 약2배 짧아지고 측근의 수가 약2배 증가하였다. UOS은 포자 및 균사 형태와 Internal transcribed spacer (ITS) 유전자 염기서열을 통하여 Phoma sp.으로 동정되었으며, 이들은 GC-MS분석을 통해 UOS는 hexamethylcyclotrisiloxane (D3)라는 VOC를 갖고 있는 것이 밝혀졌다. 이 결과들은 Phoma sp.의 진균 UOS가 VOC물질인 D3을 통해서 간접적으로 식물 생장 촉진 및 뿌리 발달에 영향을 미치는 것을 나타낸다. UOS와 그의 VOC인 D3의 활용은 농업에서 생장량 증대에 기여할 것으로 판단된다. Plant growth-promoting microorganisms promote plant growth by supplying nutrients to roots and interacting with the intrinsic factors in plants through volatile organic compounds (VOCs). In this study, we evaluated the effect of UOS, plant growth-promoting fungi (PGPF) isolated from previous study, on the growth of Nicotiana tabacum L. var Xanthi nc. Phylogenetic analysis and GC-MS were used to identify the fungal species and the VOCs emitted by the UOS, respectively. The fresh weight of UOS-treated Nicotiana tabacum L. was 3.8 and 4.2-fold higher than that of the control groups grown in vertical and I-plates, respectively. Moreover, in the UOS-treated plants, the length of the primary root was half and the number of lateral roots were twice compared to those in control plants. The UOS was identified as Phoma sp. by studying spore and mycelial morphology and using phylogenetic analysis. GC-MS revealed that the VOC emitted by the UOS was hexamethylcyclotrisiloxane (D3). These results suggest that the UOS of Phoma sp. influences plant growth and root development through D3. We expect this UOS and its VOC, D3 to be utilized in the future to increase growth and enhance yield for other plants.