In Silico Evaluation of the Structural Dynamics Beta-Amylase from Sweet Potato (Ipomoea batatas)

Knowledge of genetic variations can provide clues into the molecular mechanisms regulating key crop traits. Sweet potato (Ipomoea batatas (L.) Lam.) is an important starch-producing crop, but little is known about the genetic variations in starch biosynthesis and sucrose metabolism genes. Here, we used high-throughput sequencing of pooled amplicons of target genes to identify sequence variations in 20 genes encoding key enzymes involved in starch biosynthesis and sucrose metabolism in 507 sweet potato germplasms. After filtering potential variations between gene copies within the genome, we identified 622 potential allelic single nucleotide polymorphisms (SNPs) and 85 insertions/deletions (InDels), including 50 non-synonymous SNPs (nsSNPs) and 12 frameshift InDels. Three nsSNPs were confirmed to be present in eight sweet potato varieties with various starch properties using cleaved amplified polymorphic sequence (CAPS) markers. Gene copy with loss of the fifth intron was detected in IbAGPb3 genes, and loss of multiple introns were observed in IbGBSS1-1 genes and various among germplasms based on intron length polymorphism (ILP) markers. Thus, we identified sequence variations between germplasms in 20 genes involved in starch biosynthesis and sucrose metabolism, and demonstrated the diversity in intron-loss alleles among sweet potato germplasms. These findings provide critical genetic information and useful molecular markers for revealing regulatory mechanism of starch properties.

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Transcriptome Analysis of Sweet Potato Responses To Potassium Deficiency

10.21203/rs.3.rs-1089066/v1 ◽

2021 ◽

Author(s):

Fang Wang ◽

Wen-Fang Tan ◽

Wei Song ◽

Song-Tao Yang ◽

Shuai Qiao

Keyword(s):

Sweet Potato ◽

Calcium Binding ◽

Ipomoea Batatas ◽

Molecular Mechanisms ◽

Valuable Insight ◽

New Genes ◽

Transcriptional Changes ◽

Nutrient Signaling ◽

High Level ◽

Low K

Abstract Background: Potassium is one of the three essential nutrients and is regarded as a main limited factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of the seven major food crops grown worldwide, and it is both a nutrient-rich food and a bioenergy crop. Sweet potato is a typical “K-favoring” crop, and the level of potassium ion (K+) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K+ condition. To uncover the effect of low-K+ stress, we analyzed the transcriptomic profiles of sweet potato roots in response to K+ deficiency.Result: The roots of sweet potato seedlings with or without K+ treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K+ groups. Among the DEGs, 336 were upregulated and 223 downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. In the result, some new genes were founded that involved in low-K+ stress, which can be further investigated to improve low K+ tolerance in plant. Confirmation of RNA-seq results using qRT-PCR displayed a high level of consistency between the two experiments. Our analysis showed that many auxin-related genes, ethylene-related genes and jasmonic acid-related genes responsed to K+ deficiency, indicated that these hormones may play more important roles in K+ nutrient signaling in sweetpotato. Conclusions: According to the transcriptome data, fewer sweetpotato genes showed transcriptional changes in response to low-K+ stress. However, the expression level of some kinases, transporters, transcription factors, hormone-related genes, and plant defense related genes were markedly changed, suggesting that they play important roles during K+ deficiency. This study identifes potential genes for genetic improvement of low-K+ stress and provides valuable insight into the molecular mechanisms regulating low K+ tolerance in sweet potato. Further research is required to clarify the founction of these significant changed genes under low-K+ stress.

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Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid biosynthesis in leafy sweet potato

PLoS ONE ◽

10.1371/journal.pone.0245266 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0245266

Author(s):

Yi Liu ◽

Wenjin Su ◽

Lianjun Wang ◽

Jian Lei ◽

Shasha Chai ◽

...

Keyword(s):

Chlorogenic Acid ◽

Sweet Potato ◽

Small Rna ◽

In Silico ◽

Molecular Mechanisms ◽

Target Genes ◽

Ethylene Response Factor ◽

Sequencing Data ◽

Degradome Sequencing ◽

Phenylpropanoid Biosynthesis

Leafy sweet potato is rich in total phenolics (TP) which play key roles in health protection, the chlorogenic acid (CGA) constitutes the major components of phenolic compounds in leafy sweet potato. Unfortunately, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. To dissect the mechanisms of CGA biosynthesis, we performed transcriptome, small RNA (sRNA) and degradome sequencing of one low-CGA content and one high-CGA content genotype at two stages. A total of 2,333 common differentially expressed genes (DEGs) were identified, and the enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. The functional genes, such as CCR, CCoAOMT and HCT in the CGA biosynthetic pathway were down-regulated, indicating that the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. A total of 38 DE miRNAs were identified, and 1,799 targets were predicated for 38 DE miRNAs by using in silico approaches. The target genes were enriched in lignin and phenylpropanoid catabolic processes. Transcription factors (TFs) such as apetala2/ethylene response factor (AP2/ERF) and Squamosa promoter binding protein-like (SPL) predicated in silico were validated by degradome sequencing. Association analysis of the DE miRNAs and transcriptome datasets identified that miR156 family negatively targeted AP2/ERF and SPL. Six mRNAs and six miRNAs were validated by qRT-PCR, and the results showed that the expression levels of the mRNAs and miRNAs were consistent with the sequencing data. This study established comprehensive functional genomic resources for the CGA biosynthesis, and provided insights into the molecular mechanisms involving in this process. The results also enabled the first perceptions of the regulatory roles of mRNAs and miRNAs, and offered candidate genes for leafy sweet potato improvements.

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Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid (CGA) biosynthesis in leafy sweet potato

10.21203/rs.2.14343/v3 ◽

2020 ◽

Author(s):

Yi Liu ◽

Wenjin Su ◽

Lianjun Wang ◽

Jian Lei ◽

Shasha Chai ◽

...

Keyword(s):

Phenolic Compounds ◽

Chlorogenic Acid ◽

Sweet Potato ◽

Small Rna ◽

In Silico ◽

Molecular Mechanisms ◽

Target Genes ◽

Ethylene Response Factor ◽

Degradome Sequencing ◽

Dicaffeoylquinic Acid

Abstract Background: Phenolic compounds play key roles in health protection and leafy sweet potato is an excellent source of total phenolics (TP). The chlorogenic acid (CGA) family, which includes caffeoylquinic acid (CQA), 3,4-O-dicaffeoylquinic acid (3,4-diCQA), 3,5-O-dicaffeoylquinic acid (3,5-diCQA) and 4,5-O-dicaffeoylquinic acid (4,5-diCQA) , constitutes the major components of phenolic compounds in leafy sweet potato. However, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. The objective of present study is to dissect the mechanisms of CGA biosynthesis by using transcriptome, small RNA (sRNA) and degradome sequencing. Results: Transcriptome sequencing of twelve samples (triple replicates) from one low-CGA content genotype and one high-CGA content genotype at two stages (65 and 85 days after planting) identified a total of 2333 common differentially expressed genes (DEGs). The enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. In this study, functional genes CCR , CCoAOMT and HCT in the CGA biosynthetic pathway were uniformly downregulated, indicating the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. The sRNA sequencing identified a total of 38 DE miRNAs. Using in silico approaches, 1799 targets were predicated for 38 DE miRNAs. The target genes were enriched in lignin and phenylpropanoid catabolic processes. Transcription factors (TFs) such as apetala2 /ethylene response factor ( AP2/ERF ) and Squamosa promoter binding protein-like ( SPL ) predicated in silico were validated by degradome sequencing. Association analysis of the DE miRNAs and transcriptome datasets identified that miR156 family targeted DHQ / SDH (3-dehydroquinate dehydratase/shikimate dehydrogenase), the key gene in the phenylpropanoid pathway. Conclusions: This study established comprehensive functional genomic resources for the CGA biosynthesis and provided insights into the molecular mechanisms involving in this process. The results also enabled the first perceptions of the regulatory roles of mRNAs and miRNAs and offered candidate genes for leafy sweet potato improvement s.

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Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid (CGA) biosynthesis in leafy sweet potato

10.21203/rs.2.14343/v2 ◽

2019 ◽

Author(s):

Yi Liu ◽

Wenjin Su ◽

Lianjun Wang ◽

Jian Lei ◽

Shasha Chai ◽

...

Keyword(s):

Phenolic Compounds ◽

Chlorogenic Acid ◽

Sweet Potato ◽

Small Rna ◽

In Silico ◽

Molecular Mechanisms ◽

Target Genes ◽

Ethylene Response Factor ◽

Degradome Sequencing ◽

Dicaffeoylquinic Acid

Abstract Background: Phenolic compounds play key roles in health protection and leafy sweet potato is an excellent source of total phenolics (TP). The chlorogenic acid (CGA) family, which includes caffeoylquinic acid (CQA), 3,4-O-dicaffeoylquinic acid (3,4-diCQA), 3,5-O-dicaffeoylquinic acid (3,5-diCQA) and 4,5-O-dicaffeoylquinic acid (4,5-diCQA) , constitutes the major components of phenolic compounds in leafy sweet potato. However, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. The objective of present study is to dissect the mechanisms of CGA biosynthesis by using transcriptome, small RNA (sRNA) and degradome sequencing. Results: Transcriptome sequencing of twelve samples (triple replicates) from one low-CGA content genotype and one high-CGA content genotype at two stages (65 and 85 days after planting) identified a total of 2333 common differentially expressed genes (DEGs). The enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. In this study, functional genes CCR , CCoAOMT and HCT in the CGA biosynthetic pathway were uniformly downregulated, indicating the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. The sRNA sequencing identified a total of 38 DE miRNAs. Using in silico approaches, 1799 targets were predicated for 38 DE miRNAs. The target genes were enriched in lignin and phenylpropanoid catabolic processes. Transcription factors (TFs) such as apetala2 /ethylene response factor ( AP2/ERF ) and Squamosa promoter binding protein-like ( SPL ) predicated in silico were validated by degradome sequencing. Association analysis of the DE miRNAs and transcriptome datasets identified that miR156 family targeted DHQ / SDH (3-dehydroquinate dehydratase/shikimate dehydrogenase), the key gene in the phenylpropanoid pathway. Conclusions: This study established comprehensive functional genomic resources for the CGA biosynthesis and provided insights into the molecular mechanisms involving in this process. The results also enabled the first perceptions of the regulatory roles of mRNAs and miRNAs and offered candidate genes for leafy sweet potato improvement s.

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Batatins VII-X, glycolipid ester-type dimers from sweet potato (Ipomoea batatas)

Planta Medica ◽

10.1055/s-0032-1321291 ◽

2012 ◽

Vol 78 (11) ◽

Author(s):

D Rosas-Ramírez ◽

R Pereda-Miranda

Keyword(s):

Sweet Potato ◽

Ipomoea Batatas

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Pengaruh Profilaksis Ekstrak Ubi Jalar Ungu (Ipomoea batatas L.) terhadap Kadar Malondialdehida Hepar Tikus Putih (Rattus norvegicus) Jantan Galur Wistar yang Diinduksi Karagenan

Hang Tuah Medical journal ◽

10.30649/htmj.v15i2.66 ◽

2018 ◽

Vol 15 (2) ◽

pp. 146

Author(s):

BRILIAN DINANTI ◽

FITRI HANDAJANI

Keyword(s):

Sweet Potato ◽

Ipomoea Batatas ◽

Wistar Rats ◽

Group Method ◽

Control Group ◽

Intraplantar Injection ◽

Significant Difference ◽

Male Wistar Rats ◽

Potato Extract ◽

Purple Sweet Potato

Liver is an organ with complex metabolism. When the liver is inflamed, cellular immunity will defend against inflammatory agents by stimulating immune cells to produce reactive oxygen species (ROS). Excessive ROS accumulation cause oxydative stress with increased liver malondialdehyde (MDA) level. Some researches showed that purple sweet potato contain flavonoids (anthocyanins) that functioned as antioxydants. This study aimed to show the prophylactic effect of purple sweet potato extract to the liver MDA level of male Wistar rats induced by carrageenan.This study used post-only control group method using 18 male Wistar rats divided into 3 groups: group of rats without treatment, group of rats induced by 0,1 ml of 1% carrageenan by intraplantar injection on day-8, and group of rats given with 872 mg/kgBW of purple sweet potato extract for 7 days and induced by 0,1 ml of 1% carrageenan. In the end of the study, the liver MDA levels were measured by Thio-Barbituric Acid method on each groups.The results of One-Way ANOVA test showed there was no significant difference (p = 0,290) between group of rats without treatment (x̅= 207,50) and group of rats induced by carrageenan (x̅=233,17). Then, there is no significant difference (p = 0.978) between group of rats induced by carrageenan and group of rats given with prophylactic purple sweet potato extract and induced by carrageenan (x̅= 232,50).The conclusion of this study is giving intraplantar injection of carrageenan can increase liver MDA level insignificantly and giving prophylactic purple sweet potato extract has an effect to decrease the liver MDA level of rats induced by carragenan insignificantly because it contains anthocyanins as antioxidants. Keywords: Liver, Ipomoea batatas L., Malondialdehyde, Anthocyanins

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Analisis Nutrisi Umbi Ubi Jalar (Ipomoea batatas (L.) Lam.) untuk Konsumsi Bayo dan Anak-anak Suku Dani di Distrik Kurulu Kabupaten Jayawijaya

Agrotek ◽

10.30862/agt.v3i2.563 ◽

2018 ◽

Vol 3 (2) ◽

Author(s):

Andrew B. Pattikawa ◽

Antonius Suparno ◽

Saraswati Prabawardani

Keyword(s):

Sweet Potato ◽

Ipomoea Batatas ◽

Nutritional Value ◽

Animal Feed ◽

Ash Content ◽

Infants And Children ◽

Chemical Analyses ◽

Food Crop ◽

Sweet Potatoes ◽

Development Center

Sweet potato is an important staple food crop especially for the local people of Central Highlands Jayawijaya. There are many accessions that have always been maintained its existence to enrich their various uses. Traditionally, sweet potato accessions were grouped based on the utilization, such as for animal feed, cultural ceremonies, consumption for adults, as well as for infants and children. This study was aimed to analyze the nutritional value of sweet potatoes consumed by infants and children of the Dani tribe. Chemical analyses were conducted at the Laboratory of Post-Harvest Research and Development Center, Cimanggu, Bogor. The results showed that each of 4 (four) sweet potato accessions which were consumed by infants and children had good nutrient levels. Accession Sabe showed the highest water content (72.56%), vitamin C (72.71 mg/100 g), Fe (11.85 mg/100 g), and K levels (130.41 mg / 100 grams). The highest levels of protein (1.44%), fat (1.00%), energy (154.43 kkal/100 gram), carbohydrate (35.47%), starch (30.26%), reducing sugar (3.44%), riboflavin (0.18 mg/100 g), and vitamin A (574.40 grams IU/100 were produced by accession Manis. On the other hand, accession Saborok produced the highest value for ash content (1.32%), vitamin E (28.30 mg/100 g), and ?-carotene (64.69 ppm). The highest level of crude fiber (1.81 %) and thiamin (0.36 mg/100 g) was produced by accession Yuaiken.

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