Genotyping single nucleotide polymorphisms for selection of barley β-amylase alleles View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2002-06

AUTHORS

Maxime Paris, Michael G. K. Jones, Jason K. Eglinton

ABSTRACT

A high-throughput single nucleotide polymorphism (SNP) genotyping system was developed and used to select barley seedlings carrying superior alleles of β-amylase. In the malting process, β-amylase is a key enzyme involved in the degradation of starch. Four allelic forms of the enzyme are found in barley, each exhibiting a different rate of thermal inactivation, or thermostability. The level of thermostability influences starch degradation, which determines the yield of fermentable sugars for alcohol production during brewing. Control of the fermentability level is important for barley breeding programs to allow targeting quality profiles of new varieties to suit end-user requirements. Alignment of the cDNA sequences encoding the 4 enzyme forms revealed 6 SNPs (cSNPs). The 4 alleles could be identified unambiguously by codominantly genotyping 2 of the cSNPs using a duplex single nucleotide primer extension (SNuPE) assay. Two genotyping primers with their 3′ ends directly flanking the selected SNPs were annealed to the amplified target sequences and extended by single dideoxynucleotides complementary to the polymorphic nucleotides. Extended primers were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). Making use of the inherent molecular weight difference between DNA bases, incorporated nucleotides were identified by the increase in mass of the extended primers. A cleaved amplified polymorphic sequence (CAPS) assay enabling broader classification of the alleles was also developed to facilitate the transfer of this marker to other laboratories. Plants carrying alternative β-amylase alleles were selected at the seedling stage for barley breeding. More... »

PAGES

149-159

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/bf02799430

DOI

http://dx.doi.org/10.1007/bf02799430

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1007889450


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"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Western Australian State Agricultural Biotechnology Centre, Murdoch University, 6150, WA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Paris", 
        "givenName": "Maxime", 
        "id": "sg:person.015605117161.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015605117161.62"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Western Australian State Agricultural Biotechnology Centre, Murdoch University, 6150, WA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jones", 
        "givenName": "Michael G. K.", 
        "id": "sg:person.016427007024.24", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016427007024.24"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Department of Plant Science, Waite Campus, The University of Adelaide, 5064, Glen Osmond, South Australia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Eglinton", 
        "givenName": "Jason K.", 
        "id": "sg:person.01255065336.06", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01255065336.06"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1006/jcrs.1997.0119", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004311219"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1439-0523.1998.tb01967.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009071891"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.117.2.679", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026922074"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jcrs.2000.0364", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037180754"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1026535407570", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039706887", 
          "https://doi.org/10.1023/a:1026535407570"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0031-9422(75)85281-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042726994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0733-5210(98)90010-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043440730"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/star.19920440906", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046635413"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1439-0523.2000.00496.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051810195"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2002-06", 
    "datePublishedReg": "2002-06-01", 
    "description": "A high-throughput single nucleotide polymorphism (SNP) genotyping system was developed and used to select barley seedlings carrying superior alleles of \u03b2-amylase. In the malting process, \u03b2-amylase is a key enzyme involved in the degradation of starch. Four allelic forms of the enzyme are found in barley, each exhibiting a different rate of thermal inactivation, or thermostability. The level of thermostability influences starch degradation, which determines the yield of fermentable sugars for alcohol production during brewing. Control of the fermentability level is important for barley breeding programs to allow targeting quality profiles of new varieties to suit end-user requirements. Alignment of the cDNA sequences encoding the 4 enzyme forms revealed 6 SNPs (cSNPs). The 4 alleles could be identified unambiguously by codominantly genotyping 2 of the cSNPs using a duplex single nucleotide primer extension (SNuPE) assay. Two genotyping primers with their 3\u2032 ends directly flanking the selected SNPs were annealed to the amplified target sequences and extended by single dideoxynucleotides complementary to the polymorphic nucleotides. Extended primers were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). Making use of the inherent molecular weight difference between DNA bases, incorporated nucleotides were identified by the increase in mass of the extended primers. A cleaved amplified polymorphic sequence (CAPS) assay enabling broader classification of the alleles was also developed to facilitate the transfer of this marker to other laboratories. Plants carrying alternative \u03b2-amylase alleles were selected at the seedling stage for barley breeding.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/bf02799430", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1124107", 
        "issn": [
          "0735-9640", 
          "1556-469X"
        ], 
        "name": "Plant Molecular Biology Reporter", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "2", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "20"
      }
    ], 
    "name": "Genotyping single nucleotide polymorphisms for selection of barley \u03b2-amylase alleles", 
    "pagination": "149-159", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "25951254ed6e88e2121386110f52b9e6196dd13684e66bd093d668ed8219b40e"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/bf02799430"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1007889450"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/bf02799430", 
      "https://app.dimensions.ai/details/publication/pub.1007889450"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T20:45", 
    "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_8684_00000503.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007%2FBF02799430"
  }
]
 

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/bf02799430'

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/bf02799430'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/bf02799430'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/bf02799430'


 

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

106 TRIPLES      21 PREDICATES      36 URIs      19 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/bf02799430 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N314b9c82fd344884827b3aab1c1bf8a6
4 schema:citation sg:pub.10.1023/a:1026535407570
5 https://doi.org/10.1002/star.19920440906
6 https://doi.org/10.1006/jcrs.1997.0119
7 https://doi.org/10.1006/jcrs.2000.0364
8 https://doi.org/10.1016/0031-9422(75)85281-2
9 https://doi.org/10.1016/s0733-5210(98)90010-8
10 https://doi.org/10.1046/j.1439-0523.2000.00496.x
11 https://doi.org/10.1104/pp.117.2.679
12 https://doi.org/10.1111/j.1439-0523.1998.tb01967.x
13 schema:datePublished 2002-06
14 schema:datePublishedReg 2002-06-01
15 schema:description A high-throughput single nucleotide polymorphism (SNP) genotyping system was developed and used to select barley seedlings carrying superior alleles of β-amylase. In the malting process, β-amylase is a key enzyme involved in the degradation of starch. Four allelic forms of the enzyme are found in barley, each exhibiting a different rate of thermal inactivation, or thermostability. The level of thermostability influences starch degradation, which determines the yield of fermentable sugars for alcohol production during brewing. Control of the fermentability level is important for barley breeding programs to allow targeting quality profiles of new varieties to suit end-user requirements. Alignment of the cDNA sequences encoding the 4 enzyme forms revealed 6 SNPs (cSNPs). The 4 alleles could be identified unambiguously by codominantly genotyping 2 of the cSNPs using a duplex single nucleotide primer extension (SNuPE) assay. Two genotyping primers with their 3′ ends directly flanking the selected SNPs were annealed to the amplified target sequences and extended by single dideoxynucleotides complementary to the polymorphic nucleotides. Extended primers were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). Making use of the inherent molecular weight difference between DNA bases, incorporated nucleotides were identified by the increase in mass of the extended primers. A cleaved amplified polymorphic sequence (CAPS) assay enabling broader classification of the alleles was also developed to facilitate the transfer of this marker to other laboratories. Plants carrying alternative β-amylase alleles were selected at the seedling stage for barley breeding.
16 schema:genre research_article
17 schema:inLanguage en
18 schema:isAccessibleForFree false
19 schema:isPartOf Naaabfaecb46d4ef9ae87670af0a48370
20 Nf6e1e8d7dead4af1a6b7e355b4b25d1b
21 sg:journal.1124107
22 schema:name Genotyping single nucleotide polymorphisms for selection of barley β-amylase alleles
23 schema:pagination 149-159
24 schema:productId N25f6bbc4d72e4a0e834817fa658153f6
25 N6fc5cf9e3eb342bea8cc813ce2291238
26 Ne4e9699646c24eefb75ba103ba76520c
27 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007889450
28 https://doi.org/10.1007/bf02799430
29 schema:sdDatePublished 2019-04-10T20:45
30 schema:sdLicense https://scigraph.springernature.com/explorer/license/
31 schema:sdPublisher N61b89caffaeb456983747fe9da30e4f4
32 schema:url http://link.springer.com/10.1007%2FBF02799430
33 sgo:license sg:explorer/license/
34 sgo:sdDataset articles
35 rdf:type schema:ScholarlyArticle
36 N25f6bbc4d72e4a0e834817fa658153f6 schema:name readcube_id
37 schema:value 25951254ed6e88e2121386110f52b9e6196dd13684e66bd093d668ed8219b40e
38 rdf:type schema:PropertyValue
39 N314b9c82fd344884827b3aab1c1bf8a6 rdf:first sg:person.015605117161.62
40 rdf:rest Nd4b1e042792d48e58e35bc0dfd1aa73a
41 N5c47195163374ee4ac87abd731627dca rdf:first sg:person.01255065336.06
42 rdf:rest rdf:nil
43 N61b89caffaeb456983747fe9da30e4f4 schema:name Springer Nature - SN SciGraph project
44 rdf:type schema:Organization
45 N6fc5cf9e3eb342bea8cc813ce2291238 schema:name doi
46 schema:value 10.1007/bf02799430
47 rdf:type schema:PropertyValue
48 Naaabfaecb46d4ef9ae87670af0a48370 schema:volumeNumber 20
49 rdf:type schema:PublicationVolume
50 Nc1d6391150bd4dfa92180a6b7abe8c3a schema:name Western Australian State Agricultural Biotechnology Centre, Murdoch University, 6150, WA
51 rdf:type schema:Organization
52 Nd3dc35dd1eea4549b01ccb3950e441b9 schema:name Western Australian State Agricultural Biotechnology Centre, Murdoch University, 6150, WA
53 rdf:type schema:Organization
54 Nd4b1e042792d48e58e35bc0dfd1aa73a rdf:first sg:person.016427007024.24
55 rdf:rest N5c47195163374ee4ac87abd731627dca
56 Nda04c23f02914eda90ec86ded39a2300 schema:name Department of Plant Science, Waite Campus, The University of Adelaide, 5064, Glen Osmond, South Australia
57 rdf:type schema:Organization
58 Ne4e9699646c24eefb75ba103ba76520c schema:name dimensions_id
59 schema:value pub.1007889450
60 rdf:type schema:PropertyValue
61 Nf6e1e8d7dead4af1a6b7e355b4b25d1b schema:issueNumber 2
62 rdf:type schema:PublicationIssue
63 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
64 schema:name Biological Sciences
65 rdf:type schema:DefinedTerm
66 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
67 schema:name Genetics
68 rdf:type schema:DefinedTerm
69 sg:journal.1124107 schema:issn 0735-9640
70 1556-469X
71 schema:name Plant Molecular Biology Reporter
72 rdf:type schema:Periodical
73 sg:person.01255065336.06 schema:affiliation Nda04c23f02914eda90ec86ded39a2300
74 schema:familyName Eglinton
75 schema:givenName Jason K.
76 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01255065336.06
77 rdf:type schema:Person
78 sg:person.015605117161.62 schema:affiliation Nd3dc35dd1eea4549b01ccb3950e441b9
79 schema:familyName Paris
80 schema:givenName Maxime
81 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015605117161.62
82 rdf:type schema:Person
83 sg:person.016427007024.24 schema:affiliation Nc1d6391150bd4dfa92180a6b7abe8c3a
84 schema:familyName Jones
85 schema:givenName Michael G. K.
86 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016427007024.24
87 rdf:type schema:Person
88 sg:pub.10.1023/a:1026535407570 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039706887
89 https://doi.org/10.1023/a:1026535407570
90 rdf:type schema:CreativeWork
91 https://doi.org/10.1002/star.19920440906 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046635413
92 rdf:type schema:CreativeWork
93 https://doi.org/10.1006/jcrs.1997.0119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004311219
94 rdf:type schema:CreativeWork
95 https://doi.org/10.1006/jcrs.2000.0364 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037180754
96 rdf:type schema:CreativeWork
97 https://doi.org/10.1016/0031-9422(75)85281-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042726994
98 rdf:type schema:CreativeWork
99 https://doi.org/10.1016/s0733-5210(98)90010-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043440730
100 rdf:type schema:CreativeWork
101 https://doi.org/10.1046/j.1439-0523.2000.00496.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1051810195
102 rdf:type schema:CreativeWork
103 https://doi.org/10.1104/pp.117.2.679 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026922074
104 rdf:type schema:CreativeWork
105 https://doi.org/10.1111/j.1439-0523.1998.tb01967.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1009071891
106 rdf:type schema:CreativeWork
 




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


...