Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
Identifieur interne : 000556 ( Main/Exploration ); précédent : 000555; suivant : 000557Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
Auteurs : Amir Sherman [Israël] ; Mor Rubinstein [Israël] ; Ravit Eshed [Israël] ; Miri Benita [Israël] ; Mazal Ish-Shalom [Israël] ; Michal Sharabi-Schwager [Israël] ; Ada Rozen [Israël] ; David Saada [Israël] ; Yuval Cohen [Israël] ; Ron Ophir [Israël]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2015.
Abstract
Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers.
We describe a
Whole-transcriptome reconstruction was used to significantly broaden the mango’s genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.
The online version of this article (doi:10.1186/s12870-015-0663-6) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-015-0663-6
PubMed: 26573148
PubMed Central: 4647706
Affiliations:
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Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Cohen, Yuval" sort="Cohen, Yuval" uniqKey="Cohen Y" first="Yuval" last="Cohen">Yuval Cohen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Ophir, Ron" sort="Ophir, Ron" uniqKey="Ophir R" first="Ron" last="Ophir">Ron Ophir</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26573148</idno><idno type="pmc">4647706</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647706</idno><idno type="RBID">PMC:4647706</idno><idno type="doi">10.1186/s12870-015-0663-6</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000637</idno><idno 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xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Rubinstein, Mor" sort="Rubinstein, Mor" uniqKey="Rubinstein M" first="Mor" last="Rubinstein">Mor Rubinstein</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Eshed, Ravit" sort="Eshed, Ravit" uniqKey="Eshed R" first="Ravit" last="Eshed">Ravit Eshed</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Benita, Miri" sort="Benita, Miri" uniqKey="Benita M" first="Miri" last="Benita">Miri Benita</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Ish Shalom, Mazal" sort="Ish Shalom, Mazal" uniqKey="Ish Shalom M" first="Mazal" last="Ish-Shalom">Mazal Ish-Shalom</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Sharabi Schwager, Michal" sort="Sharabi Schwager, Michal" uniqKey="Sharabi Schwager M" first="Michal" last="Sharabi-Schwager">Michal Sharabi-Schwager</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot</wicri:regionArea><wicri:noRegion>Rehovot</wicri:noRegion></affiliation></author><author><name sortKey="Rozen, Ada" sort="Rozen, Ada" uniqKey="Rozen A" first="Ada" last="Rozen">Ada Rozen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Saada, David" sort="Saada, David" uniqKey="Saada D" first="David" last="Saada">David Saada</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Cohen, Yuval" sort="Cohen, Yuval" uniqKey="Cohen Y" first="Yuval" last="Cohen">Yuval Cohen</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author><author><name sortKey="Ophir, Ron" sort="Ophir, Ron" uniqKey="Ophir R" first="Ron" last="Ophir">Ron Ophir</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion</wicri:regionArea><wicri:noRegion>Rishon Lezion</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers.</p></sec><sec><title>Results</title><p>We describe a <italic>de novo</italic> transcriptome assembly from mango cultivar ‘Keitt’. Variation discovery was performed using Illumina resequencing of ‘Keitt’ and ‘Tommy Atkins’ cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1 %) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5 % were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (F<sub>S</sub> = −0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (F<sub>ST</sub> = 0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background.</p></sec><sec><title>Conclusions</title><p>Whole-transcriptome reconstruction was used to significantly broaden the mango’s genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-015-0663-6) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bompard, J" uniqKey="Bompard J">J Bompard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mukherjee, S" uniqKey="Mukherjee S">S Mukherjee</name></author><author><name sortKey="Litz, R" uniqKey="Litz R">R Litz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olano, Ct" uniqKey="Olano C">CT Olano</name></author><author><name sortKey="Schnell, Rj" uniqKey="Schnell R">RJ Schnell</name></author><author><name sortKey="Quintanilla, We" uniqKey="Quintanilla W">WE 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sortKey="Robles, M" uniqKey="Robles M">M Robles</name></author><author><name sortKey="Talon, M" uniqKey="Talon M">M Talon</name></author><author><name sortKey="Dopazo, J" uniqKey="Dopazo J">J Dopazo</name></author><author><name sortKey="Conesa, A" uniqKey="Conesa A">A Conesa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kofler, R" uniqKey="Kofler R">R Kofler</name></author><author><name sortKey="Schlotterer, C" uniqKey="Schlotterer C">C Schlotterer</name></author><author><name sortKey="Lelley, T" uniqKey="Lelley T">T Lelley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weir, Bs" uniqKey="Weir B">BS Weir</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bowcock, Am" uniqKey="Bowcock A">AM Bowcock</name></author><author><name sortKey="Ruiz Linares, A" uniqKey="Ruiz Linares A">A Ruiz-Linares</name></author><author><name sortKey="Tomfohrde, J" uniqKey="Tomfohrde J">J Tomfohrde</name></author><author><name sortKey="Minch, E" uniqKey="Minch E">E Minch</name></author><author><name sortKey="Kidd, Jr" uniqKey="Kidd J">JR Kidd</name></author><author><name sortKey="Cavalli Sforza, Ll" uniqKey="Cavalli Sforza L">LL Cavalli-Sforza</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Odong, Tl" uniqKey="Odong T">TL Odong</name></author><author><name sortKey="Van Heerwaarden, J" uniqKey="Van Heerwaarden J">J van Heerwaarden</name></author><author><name sortKey="Jansen, J" uniqKey="Jansen J">J Jansen</name></author><author><name sortKey="Van Hintum, Tj" uniqKey="Van Hintum T">TJ van Hintum</name></author><author><name sortKey="Van Eeuwijk, Fa" uniqKey="Van Eeuwijk F">FA van Eeuwijk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paradis, E" uniqKey="Paradis E">E Paradis</name></author><author><name sortKey="Claude, J" uniqKey="Claude J">J Claude</name></author><author><name sortKey="Strimmer, K" uniqKey="Strimmer K">K Strimmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pritchard, Jk" uniqKey="Pritchard J">JK Pritchard</name></author><author><name sortKey="Stephens, M" uniqKey="Stephens M">M Stephens</name></author><author><name sortKey="Donnelly, P" uniqKey="Donnelly P">P Donnelly</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wright, S" uniqKey="Wright S">S Wright</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Israël</li></country></list><tree><country name="Israël"><noRegion><name sortKey="Sherman, Amir" sort="Sherman, Amir" uniqKey="Sherman A" first="Amir" last="Sherman">Amir Sherman</name></noRegion><name sortKey="Benita, Miri" sort="Benita, Miri" uniqKey="Benita M" first="Miri" last="Benita">Miri Benita</name><name sortKey="Cohen, Yuval" sort="Cohen, Yuval" uniqKey="Cohen Y" first="Yuval" last="Cohen">Yuval Cohen</name><name sortKey="Eshed, Ravit" sort="Eshed, Ravit" uniqKey="Eshed R" first="Ravit" last="Eshed">Ravit Eshed</name><name sortKey="Ish Shalom, Mazal" sort="Ish Shalom, Mazal" uniqKey="Ish Shalom M" first="Mazal" last="Ish-Shalom">Mazal Ish-Shalom</name><name sortKey="Ophir, Ron" sort="Ophir, Ron" uniqKey="Ophir R" first="Ron" last="Ophir">Ron Ophir</name><name sortKey="Rozen, Ada" sort="Rozen, Ada" uniqKey="Rozen A" first="Ada" last="Rozen">Ada Rozen</name><name sortKey="Rubinstein, Mor" sort="Rubinstein, Mor" uniqKey="Rubinstein M" first="Mor" last="Rubinstein">Mor Rubinstein</name><name sortKey="Saada, David" sort="Saada, David" uniqKey="Saada D" first="David" last="Saada">David Saada</name><name sortKey="Sharabi Schwager, Michal" sort="Sharabi Schwager, Michal" uniqKey="Sharabi Schwager M" first="Michal" last="Sharabi-Schwager">Michal Sharabi-Schwager</name><name sortKey="Sharabi Schwager, Michal" sort="Sharabi Schwager, Michal" uniqKey="Sharabi Schwager M" first="Michal" last="Sharabi-Schwager">Michal Sharabi-Schwager</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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