Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.)
Identifieur interne : 001307 ( Main/Merge ); précédent : 001306; suivant : 001308Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.)
Auteurs : Yongli Zhao [États-Unis] ; Roxanne Williams [États-Unis] ; C S Prakash [États-Unis] ; Guohao He [États-Unis]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2012.
Abstract
Date palm (
In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs) and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs). We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7%) were the most common, followed by tetranucleotide (10.4%) and dinucleotide motifs (9.6%). The motif AG (85.7%) was most abundant in dinucleotides, while motifs AGG (26.8%), AAG (19.3%), and AGC (16.1%) were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4%) of such ESTs had homology with known proteins.
Date palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.
Url:
DOI: 10.1186/1471-2229-12-237
PubMed: 23241238
PubMed Central: 3568718
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification and characterization of gene-based SSR markers in date palm (<italic>Phoenix dactylifera</italic> L.)</title><author><name sortKey="Zhao, Yongli" sort="Zhao, Yongli" uniqKey="Zhao Y" first="Yongli" last="Zhao">Yongli Zhao</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author><author><name sortKey="Williams, Roxanne" sort="Williams, Roxanne" uniqKey="Williams R" first="Roxanne" last="Williams">Roxanne Williams</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author><author><name sortKey="Prakash, C S" sort="Prakash, C S" uniqKey="Prakash C" first="C S" last="Prakash">C S Prakash</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author><author><name sortKey="He, Guohao" sort="He, Guohao" uniqKey="He G" first="Guohao" last="He">Guohao He</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23241238</idno><idno type="pmc">3568718</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568718</idno><idno type="RBID">PMC:3568718</idno><idno type="doi">10.1186/1471-2229-12-237</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000B38</idno><idno type="wicri:Area/Pmc/Curation">000B37</idno><idno type="wicri:Area/Pmc/Checkpoint">000C88</idno><idno type="wicri:Area/Ncbi/Merge">001177</idno><idno type="wicri:Area/Ncbi/Curation">001177</idno><idno type="wicri:Area/Ncbi/Checkpoint">001177</idno><idno type="wicri:Area/Main/Merge">001307</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification and characterization of gene-based SSR markers in date palm (<italic>Phoenix dactylifera</italic> L.)</title><author><name sortKey="Zhao, Yongli" sort="Zhao, Yongli" uniqKey="Zhao Y" first="Yongli" last="Zhao">Yongli Zhao</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author><author><name sortKey="Williams, Roxanne" sort="Williams, Roxanne" uniqKey="Williams R" first="Roxanne" last="Williams">Roxanne Williams</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author><author><name sortKey="Prakash, C S" sort="Prakash, C S" uniqKey="Prakash C" first="C S" last="Prakash">C S Prakash</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author><author><name sortKey="He, Guohao" sort="He, Guohao" uniqKey="He G" first="Guohao" last="He">Guohao He</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088</wicri:regionArea><wicri:noRegion>36088</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Date palm (<italic>Phoenix dactylifera</italic> L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding.</p></sec><sec><title>Results</title><p>In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs) and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs). We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7%) were the most common, followed by tetranucleotide (10.4%) and dinucleotide motifs (9.6%). The motif AG (85.7%) was most abundant in dinucleotides, while motifs AGG (26.8%), AAG (19.3%), and AGC (16.1%) were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4%) of such ESTs had homology with known proteins.</p></sec><sec><title>Conclusion</title><p>Date palm EST sequences exhibits a good resource for developing gene-based markers. 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Götz</name></author><author><name sortKey="Garcia Gomez, Jm" uniqKey="Garcia Gomez J">JM Garcia-Gomez</name></author><author><name sortKey="Terol, J" uniqKey="Terol J">J Terol</name></author><author><name sortKey="Talon, M" uniqKey="Talon M">M Talon</name></author><author><name sortKey="Robles, M" uniqKey="Robles M">M Robles</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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