Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential
Identifieur interne : 000628 ( Main/Exploration ); précédent : 000627; suivant : 000629Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential
Auteurs : Manosh Kumar Biswas [République populaire de Chine] ; Yuxuan Liu [République populaire de Chine] ; Chunyu Li [République populaire de Chine] ; Ou Sheng [République populaire de Chine] ; Christoph Mayer [Allemagne] ; Ganjun Yi [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.
Url:
DOI: 10.1371/journal.pone.0131312
PubMed: 26121637
PubMed Central: 4488140
Affiliations:
- Allemagne, République populaire de Chine
- District de Cologne, Guangdong, Rhénanie-du-Nord-Westphalie
- Bonn, Jiangmen
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type="city">Bonn</settlement></placeName></affiliation></author><author><name sortKey="Yi, Ganjun" sort="Yi, Ganjun" uniqKey="Yi G" first="Ganjun" last="Yi">Ganjun Yi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province</wicri:regionArea><wicri:noRegion>Guangdong Province</wicri:noRegion></affiliation><affiliation wicri:level="3"><nlm:aff id="aff002"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pillay, M" uniqKey="Pillay M">M Pillay</name></author><author><name sortKey="Ude, G" uniqKey="Ude G">G Ude</name></author><author><name sortKey="Kole, C" uniqKey="Kole C">C Kole</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Backiyarani, S" uniqKey="Backiyarani S">S Backiyarani</name></author><author><name sortKey="Uma, S" uniqKey="Uma S">S Uma</name></author><author><name sortKey="Varatharj, P" uniqKey="Varatharj P">P Varatharj</name></author><author><name sortKey="Saraswathi, Ms" uniqKey="Saraswathi M">MS Saraswathi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Passos, Ma" uniqKey="Passos M">MA Passos</name></author><author><name sortKey="De Oliveira Cruz, V" 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uniqKey="Bakry F">F Bakry</name></author><author><name sortKey="Seguin, M" uniqKey="Seguin M">M Seguin</name></author><author><name sortKey="Gardes, L" uniqKey="Gardes L">L Gardes</name></author><author><name sortKey="Rivallan, R" uniqKey="Rivallan R">R Rivallan</name></author><author><name sortKey="Risterucci, Am" uniqKey="Risterucci A">AM Risterucci</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>République populaire de Chine</li></country><region><li>District de Cologne</li><li>Guangdong</li><li>Rhénanie-du-Nord-Westphalie</li></region><settlement><li>Bonn</li><li>Jiangmen</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name></noRegion><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name><name sortKey="Li, Chunyu" sort="Li, Chunyu" uniqKey="Li C" first="Chunyu" last="Li">Chunyu Li</name><name sortKey="Li, Chunyu" sort="Li, Chunyu" uniqKey="Li C" first="Chunyu" last="Li">Chunyu Li</name><name sortKey="Liu, Yuxuan" sort="Liu, Yuxuan" uniqKey="Liu Y" first="Yuxuan" last="Liu">Yuxuan Liu</name><name sortKey="Sheng, Ou" sort="Sheng, Ou" uniqKey="Sheng O" first="Ou" last="Sheng">Ou Sheng</name><name sortKey="Sheng, Ou" sort="Sheng, Ou" uniqKey="Sheng O" first="Ou" last="Sheng">Ou Sheng</name><name sortKey="Yi, Ganjun" sort="Yi, Ganjun" uniqKey="Yi G" first="Ganjun" last="Yi">Ganjun Yi</name><name sortKey="Yi, Ganjun" sort="Yi, Ganjun" uniqKey="Yi G" first="Ganjun" last="Yi">Ganjun Yi</name></country><country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Mayer, Christoph" sort="Mayer, Christoph" uniqKey="Mayer C" first="Christoph" last="Mayer">Christoph Mayer</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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