DNA Extraction from Rice Endosperm (Including a Protocol for Extraction of DNA from Ancient Seed Samples) View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2014

AUTHORS

Chiaki Mutou , Katsunori Tanaka , Ryuji Ishikawa

ABSTRACT

Deoxyribonucleic acid (DNA) extracted from endosperm can be effectively used for rapid genotyping using seed tissue, to evaluate seed quality from packaged grains and to determine the purity of milled grains. Methods outlined here are optimal procedures to isolate DNA from endosperm tissue of modern rice grains and of aged rice remains preserved between 50 and 100 years. The extracted DNA can be used to amplify regions of chloroplast genomic DNA (ctDNA), mitochondrial genomic DNA (mtDNA), and nuclear genomic DNA using standard PCR protocols. In addition, we describe an optimal procedure to process archaeological grain specimens, aged for a couple of thousand years, to isolate DNA from these ancient samples, referred to here as ancient DNA (aDNA). The aDNA can be successfully amplified by PCR using appropriate primer pairs designed specifically for aDNA amplification. More... »

PAGES

7-15

Book

TITLE

Cereal Genomics

ISBN

978-1-62703-714-3
978-1-62703-715-0

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-62703-715-0_2

DOI

http://dx.doi.org/10.1007/978-1-62703-715-0_2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1005497048

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24243191


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chemical Fractionation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Plant", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Endosperm", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oryza", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Seeds", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "National Institute of Aerobiological Sciences, Tsukuba, Ibaraki, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mutou", 
        "givenName": "Chiaki", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Hirosaki University", 
          "id": "https://www.grid.ac/institutes/grid.257016.7", 
          "name": [
            "Faculty of Humanities, Hirosaki University, Hirosaki, Aomori, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tanaka", 
        "givenName": "Katsunori", 
        "id": "sg:person.014463774551.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014463774551.84"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Hirosaki University", 
          "id": "https://www.grid.ac/institutes/grid.257016.7", 
          "name": [
            "Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ishikawa", 
        "givenName": "Ryuji", 
        "id": "sg:person.016367075465.51", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016367075465.51"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1002/(sici)1096-8644(199804)105:4<539::aid-ajpa10>3.0.co;2-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005062030"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.genet.37.110801.143214", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014567048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1079179462", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2014", 
    "datePublishedReg": "2014-01-01", 
    "description": "Deoxyribonucleic acid (DNA) extracted from endosperm can be effectively used for rapid genotyping using seed tissue, to evaluate seed quality from packaged grains and to determine the purity of milled grains. Methods outlined here are optimal procedures to isolate DNA from endosperm tissue of modern rice grains and of aged rice remains preserved between 50 and 100 years. The extracted DNA can be used to amplify regions of chloroplast genomic DNA (ctDNA), mitochondrial genomic DNA (mtDNA), and nuclear genomic DNA using standard PCR protocols. In addition, we describe an optimal procedure to process archaeological grain specimens, aged for a couple of thousand years, to isolate DNA from these ancient samples, referred to here as ancient DNA (aDNA). The aDNA can be successfully amplified by PCR using appropriate primer pairs designed specifically for aDNA amplification. ", 
    "editor": [
      {
        "familyName": "Henry", 
        "givenName": "Robert J.", 
        "type": "Person"
      }, 
      {
        "familyName": "Furtado", 
        "givenName": "Agnelo", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-62703-715-0_2", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-62703-714-3", 
        "978-1-62703-715-0"
      ], 
      "name": "Cereal Genomics", 
      "type": "Book"
    }, 
    "name": "DNA Extraction from Rice Endosperm (Including a Protocol for Extraction of DNA from Ancient Seed Samples)", 
    "pagination": "7-15", 
    "productId": [
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-62703-715-0_2"
        ]
      }, 
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "1a31407d8dd9023d3f86cd60b85a6dd62690dadae95a8e70fcb2a451514f736b"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1005497048"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "24243191"
        ]
      }
    ], 
    "publisher": {
      "location": "Totowa, NJ", 
      "name": "Humana Press", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-62703-715-0_2", 
      "https://app.dimensions.ai/details/publication/pub.1005497048"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-15T20:59", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8690_00000246.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/978-1-62703-715-0_2"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-715-0_2'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-715-0_2'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-715-0_2'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-715-0_2'


 

This table displays all metadata directly associated to this object as RDF triples.

118 TRIPLES      23 PREDICATES      36 URIs      26 LITERALS      14 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-62703-715-0_2 schema:about N03beefbac5794325916a7790a3242aed
2 N29a8c9e3ec614ef3bede8aac63898f70
3 N6a130a928f054265a0f01a9373a7b4c6
4 N7af3b30bfbec4af1afc0798ec43a88a9
5 Nb93197620f5544d8aa97def1028ee995
6 anzsrc-for:06
7 anzsrc-for:0604
8 schema:author N54f254b0ae194cddb5ad091a107bb58b
9 schema:citation https://app.dimensions.ai/details/publication/pub.1079179462
10 https://doi.org/10.1002/(sici)1096-8644(199804)105:4<539::aid-ajpa10>3.0.co;2-1
11 https://doi.org/10.1146/annurev.genet.37.110801.143214
12 schema:datePublished 2014
13 schema:datePublishedReg 2014-01-01
14 schema:description Deoxyribonucleic acid (DNA) extracted from endosperm can be effectively used for rapid genotyping using seed tissue, to evaluate seed quality from packaged grains and to determine the purity of milled grains. Methods outlined here are optimal procedures to isolate DNA from endosperm tissue of modern rice grains and of aged rice remains preserved between 50 and 100 years. The extracted DNA can be used to amplify regions of chloroplast genomic DNA (ctDNA), mitochondrial genomic DNA (mtDNA), and nuclear genomic DNA using standard PCR protocols. In addition, we describe an optimal procedure to process archaeological grain specimens, aged for a couple of thousand years, to isolate DNA from these ancient samples, referred to here as ancient DNA (aDNA). The aDNA can be successfully amplified by PCR using appropriate primer pairs designed specifically for aDNA amplification.
15 schema:editor Ne26818cd68e34473bd77eadd6294461b
16 schema:genre chapter
17 schema:inLanguage en
18 schema:isAccessibleForFree false
19 schema:isPartOf N078aacf1cf084d24b61a7d552f63d813
20 schema:name DNA Extraction from Rice Endosperm (Including a Protocol for Extraction of DNA from Ancient Seed Samples)
21 schema:pagination 7-15
22 schema:productId N07e9b4ab5dd644318f5de753a0fba93d
23 N1fb1f96b9fef4670aa3f1159374295c2
24 Nacb94a6d0f1a4259909d130c194ded14
25 Nafd0643722f54b7b82f3386d02e6a6ec
26 schema:publisher N60e61959d9c9416ab8bdf50aec56ad1f
27 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005497048
28 https://doi.org/10.1007/978-1-62703-715-0_2
29 schema:sdDatePublished 2019-04-15T20:59
30 schema:sdLicense https://scigraph.springernature.com/explorer/license/
31 schema:sdPublisher Nb8e245dd35fe4776a39b6e9cb75abac8
32 schema:url http://link.springer.com/10.1007/978-1-62703-715-0_2
33 sgo:license sg:explorer/license/
34 sgo:sdDataset chapters
35 rdf:type schema:Chapter
36 N03beefbac5794325916a7790a3242aed schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
37 schema:name Oryza
38 rdf:type schema:DefinedTerm
39 N06777714fc604d3b9ffe09d522c90538 schema:familyName Furtado
40 schema:givenName Agnelo
41 rdf:type schema:Person
42 N078aacf1cf084d24b61a7d552f63d813 schema:isbn 978-1-62703-714-3
43 978-1-62703-715-0
44 schema:name Cereal Genomics
45 rdf:type schema:Book
46 N07e9b4ab5dd644318f5de753a0fba93d schema:name readcube_id
47 schema:value 1a31407d8dd9023d3f86cd60b85a6dd62690dadae95a8e70fcb2a451514f736b
48 rdf:type schema:PropertyValue
49 N0dad7d8847554de585d8124068fb8759 rdf:first sg:person.014463774551.84
50 rdf:rest N93eeb06aa66b4e2c940d91fdd4f9a8df
51 N1fb1f96b9fef4670aa3f1159374295c2 schema:name dimensions_id
52 schema:value pub.1005497048
53 rdf:type schema:PropertyValue
54 N29a8c9e3ec614ef3bede8aac63898f70 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
55 schema:name DNA, Plant
56 rdf:type schema:DefinedTerm
57 N54f254b0ae194cddb5ad091a107bb58b rdf:first Ne4dd0f91240e44269e06546defccd790
58 rdf:rest N0dad7d8847554de585d8124068fb8759
59 N60e61959d9c9416ab8bdf50aec56ad1f schema:location Totowa, NJ
60 schema:name Humana Press
61 rdf:type schema:Organisation
62 N6a130a928f054265a0f01a9373a7b4c6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
63 schema:name Seeds
64 rdf:type schema:DefinedTerm
65 N79c6245a8ea14ddf9baa7f407b6c3bdc schema:familyName Henry
66 schema:givenName Robert J.
67 rdf:type schema:Person
68 N7af3b30bfbec4af1afc0798ec43a88a9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
69 schema:name Endosperm
70 rdf:type schema:DefinedTerm
71 N93eeb06aa66b4e2c940d91fdd4f9a8df rdf:first sg:person.016367075465.51
72 rdf:rest rdf:nil
73 Nacb94a6d0f1a4259909d130c194ded14 schema:name pubmed_id
74 schema:value 24243191
75 rdf:type schema:PropertyValue
76 Nafd0643722f54b7b82f3386d02e6a6ec schema:name doi
77 schema:value 10.1007/978-1-62703-715-0_2
78 rdf:type schema:PropertyValue
79 Nb8e245dd35fe4776a39b6e9cb75abac8 schema:name Springer Nature - SN SciGraph project
80 rdf:type schema:Organization
81 Nb93197620f5544d8aa97def1028ee995 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
82 schema:name Chemical Fractionation
83 rdf:type schema:DefinedTerm
84 Nc3be6997c2764843bc6933c741071ece rdf:first N06777714fc604d3b9ffe09d522c90538
85 rdf:rest rdf:nil
86 Nd30a8b79dff94384a3e11a003a389219 schema:name National Institute of Aerobiological Sciences, Tsukuba, Ibaraki, Japan
87 rdf:type schema:Organization
88 Ne26818cd68e34473bd77eadd6294461b rdf:first N79c6245a8ea14ddf9baa7f407b6c3bdc
89 rdf:rest Nc3be6997c2764843bc6933c741071ece
90 Ne4dd0f91240e44269e06546defccd790 schema:affiliation Nd30a8b79dff94384a3e11a003a389219
91 schema:familyName Mutou
92 schema:givenName Chiaki
93 rdf:type schema:Person
94 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
95 schema:name Biological Sciences
96 rdf:type schema:DefinedTerm
97 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
98 schema:name Genetics
99 rdf:type schema:DefinedTerm
100 sg:person.014463774551.84 schema:affiliation https://www.grid.ac/institutes/grid.257016.7
101 schema:familyName Tanaka
102 schema:givenName Katsunori
103 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014463774551.84
104 rdf:type schema:Person
105 sg:person.016367075465.51 schema:affiliation https://www.grid.ac/institutes/grid.257016.7
106 schema:familyName Ishikawa
107 schema:givenName Ryuji
108 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016367075465.51
109 rdf:type schema:Person
110 https://app.dimensions.ai/details/publication/pub.1079179462 schema:CreativeWork
111 https://doi.org/10.1002/(sici)1096-8644(199804)105:4<539::aid-ajpa10>3.0.co;2-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005062030
112 rdf:type schema:CreativeWork
113 https://doi.org/10.1146/annurev.genet.37.110801.143214 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014567048
114 rdf:type schema:CreativeWork
115 https://www.grid.ac/institutes/grid.257016.7 schema:alternateName Hirosaki University
116 schema:name Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
117 Faculty of Humanities, Hirosaki University, Hirosaki, Aomori, Japan
118 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...