Dataset Information

Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

ABSTRACT: Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.

SUBMITTER: Awasthi P

PROVIDER: S-EPMC5671454 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

Awasthi Praveen P Singh Ashish A Sheikh Gulfam G Mahajan Vidushi V Gupta Ajai Prakash AP Gupta Suphla S Bedi Yashbir S YS Gandhi Sumit G SG

Physiology and molecular biology of plants : an international journal of functional plant biology 20171011 4

Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled ...[more]

PMID: 29158639

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Project description:BackgroundBiocompatible Pickering emulsions (PE) stabilized by tailor-made antioxidant-loaded particles have been known for some time now, but antioxidant-rich natural plant particle-based emulsions are much less well known. This study aimed to investigate the physico-chemical properties of commercial Zingiber officinale powders obtained from biological and conventional agricultural practice and ginger powder-based PE.ResultsThe physico-chemical and biological properties of Zingiber officinale powders (GDPs) obtained from conventional (GDPC1 and GDPC2) and biological agricultural (GDPBIO) practices, and the properties of derived PE (PE_GDPs) were examined. All GDPs showed weak aggregation in aqueous media and a sufficiently hydrophobic surface to stabilize oil-in-water (O/W) PE against coalescence for at least 1 month. Zingiber officinale powders (2% w/w) derived from biological agricultural practices (GDPBIO) demonstrated the best emulsifying properties. The Zingiber officinale powders and PE_GDPs were also characterized by their phytochemical profiles. All the investigated samples exhibited ferric reducing ability power greater than the positive control, butylated hydroxytoluene (BHT), with values ranging from 91.21 to 102.63 μmol L-1 Fe (II) g-1 for GDPC2 and 05PE_GDPC1 (O/W=1:1), respectively. In β-carotene bleaching test the following trend GDPC1 > GDPBIO > GDPC2 was observed. A 05PE_GDPBIO sample with the oil volume fraction equal to 50% was stable to oxidation and exhibited a promising α-amylase inhibitory activity.ConclusionThe results suggest that ginger powder should be used as a starting point to design biocompatible PEs for different applications in the functional food, nutraceutical, and pharmaceutical industries. In fact, powder and based PE are characterized by a promising antioxidant activity, carbohydrate hydrolyzing enzyme and lipase inhibitory properties. Further in vivo studies are necessary to confirm these findings. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Project description:BackgroundThe Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus.ResultsIn this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility.ConclusionsThis study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.

Dataset Information

Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

Publications

Mining and characterization of EST-SSR markers for <i>Zingiber officinale</i> Roscoe with transferability to other species of Zingiberaceae.

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