Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae
Identifieur interne : 000623 ( Main/Exploration ); précédent : 000622; suivant : 000624Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae
Auteurs : Yi Wang [République populaire de Chine] ; Chao Yang [République populaire de Chine] ; Qiaojun Jin [République populaire de Chine] ; Dongjie Zhou [République populaire de Chine] ; Shuangshuang Wang [République populaire de Chine] ; Yuanjie Yu [République populaire de Chine] ; Long Yang [République populaire de Chine]Source :
- BMC Genetics [ 1471-2156 ] ; 2015.
Abstract
The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability.
In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database,
Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.
Url:
DOI: 10.1186/s12863-015-0178-z
PubMed: 25886726
PubMed Central: 4333251
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae</title><author><name sortKey="Wang, Yi" sort="Wang, Yi" uniqKey="Wang Y" first="Yi" last="Wang">Yi Wang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Chao" sort="Yang, Chao" uniqKey="Yang C" first="Chao" last="Yang">Chao Yang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Jin, Qiaojun" sort="Jin, Qiaojun" uniqKey="Jin Q" first="Qiaojun" last="Jin">Qiaojun Jin</name><affiliation wicri:level="1"><nlm:aff id="Aff3">College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, 712100 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Plant Protection, Northwest Agriculture and Forestry University, Yangling</wicri:regionArea><wicri:noRegion>Yangling</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Dongjie" sort="Zhou, Dongjie" uniqKey="Zhou D" first="Dongjie" last="Zhou">Dongjie Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Big-Data Research Center, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Shuangshuang" sort="Wang, Shuangshuang" uniqKey="Wang S" first="Shuangshuang" last="Wang">Shuangshuang Wang</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Big-Data Research Center, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Yuanjie" sort="Yu, Yuanjie" uniqKey="Yu Y" first="Yuanjie" last="Yu">Yuanjie Yu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Long" sort="Yang, Long" uniqKey="Yang L" first="Long" last="Yang">Long Yang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Big-Data Research Center, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25886726</idno><idno type="pmc">4333251</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333251</idno><idno type="RBID">PMC:4333251</idno><idno type="doi">10.1186/s12863-015-0178-z</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000565</idno><idno type="wicri:Area/Pmc/Curation">000564</idno><idno type="wicri:Area/Pmc/Checkpoint">000487</idno><idno type="wicri:Area/Ncbi/Merge">001A91</idno><idno type="wicri:Area/Ncbi/Curation">001A91</idno><idno type="wicri:Area/Ncbi/Checkpoint">001A91</idno><idno type="wicri:Area/Main/Merge">000623</idno><idno type="wicri:Area/Main/Curation">000623</idno><idno type="wicri:Area/Main/Exploration">000623</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae</title><author><name sortKey="Wang, Yi" sort="Wang, Yi" uniqKey="Wang Y" first="Yi" last="Wang">Yi Wang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Chao" sort="Yang, Chao" uniqKey="Yang C" first="Chao" last="Yang">Chao Yang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Jin, Qiaojun" sort="Jin, Qiaojun" uniqKey="Jin Q" first="Qiaojun" last="Jin">Qiaojun Jin</name><affiliation wicri:level="1"><nlm:aff id="Aff3">College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, 712100 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Plant Protection, Northwest Agriculture and Forestry University, Yangling</wicri:regionArea><wicri:noRegion>Yangling</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Dongjie" sort="Zhou, Dongjie" uniqKey="Zhou D" first="Dongjie" last="Zhou">Dongjie Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Big-Data Research Center, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Shuangshuang" sort="Wang, Shuangshuang" uniqKey="Wang S" first="Shuangshuang" last="Wang">Shuangshuang Wang</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Big-Data Research Center, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Yuanjie" sort="Yu, Yuanjie" uniqKey="Yu Y" first="Yuanjie" last="Yu">Yuanjie Yu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Long" sort="Yang, Long" uniqKey="Yang L" first="Long" last="Yang">Long Yang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Big-Data Research Center, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genetics</title><idno type="eISSN">1471-2156</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>The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability.</p></sec><sec><title>Results</title><p>In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, <ext-link ext-link-type="uri" xlink:href="http://biodb.sdau.edu.cn/pssrd/">http://biodb.sdau.edu.cn/pssrd/</ext-link>).</p></sec><sec><title>Conclusions</title><p>Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Clayton, Wd" uniqKey="Clayton W">WD Clayton</name></author><author><name sortKey="Renvoize, Sa" uniqKey="Renvoize S">SA Renvoize</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sonah, H" uniqKey="Sonah H">H Sonah</name></author><author><name sortKey="Deshmukh, Rk" uniqKey="Deshmukh R">RK Deshmukh</name></author><author><name sortKey="Sharma, A" uniqKey="Sharma 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Horová</name></author><author><name sortKey="Leitch, Ij" uniqKey="Leitch I">IJ Leitch</name></author><author><name sortKey="Mucina, L" uniqKey="Mucina L">L Mucina</name></author><author><name sortKey="Pacini, E" uniqKey="Pacini E">E Pacini</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tortereau, F" uniqKey="Tortereau F">F Tortereau</name></author><author><name sortKey="Servin, B" uniqKey="Servin B">B Servin</name></author><author><name sortKey="Frantz, L" uniqKey="Frantz L">L Frantz</name></author><author><name sortKey="Megens, Hj" uniqKey="Megens H">HJ Megens</name></author><author><name sortKey="Milan, D" uniqKey="Milan D">D Milan</name></author><author><name sortKey="Rohrer, G" uniqKey="Rohrer G">G Rohrer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Clement, Y" uniqKey="Clement Y">Y Clément</name></author><author><name sortKey="Arndt, Pf" uniqKey="Arndt P">PF Arndt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Assis, R" uniqKey="Assis R">R Assis</name></author><author><name sortKey="Kondrashov, As" uniqKey="Kondrashov A">AS Kondrashov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schaeffer, Ml" uniqKey="Schaeffer M">ML Schaeffer</name></author><author><name sortKey="Harper, Lc" uniqKey="Harper L">LC Harper</name></author><author><name sortKey="Gardiner, Jm" uniqKey="Gardiner J">JM Gardiner</name></author><author><name sortKey="Andorf, Cm" uniqKey="Andorf C">CM Andorf</name></author><author><name sortKey="Campbell, Da" uniqKey="Campbell D">DA Campbell</name></author><author><name sortKey="Cannon, Ek" uniqKey="Cannon E">EK Cannon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Untergasser, A" uniqKey="Untergasser A">A Untergasser</name></author><author><name sortKey="Cutcutache, I" uniqKey="Cutcutache I">I Cutcutache</name></author><author><name sortKey="Koressaar, T" uniqKey="Koressaar T">T Koressaar</name></author><author><name sortKey="Ye, J" uniqKey="Ye J">J Ye</name></author><author><name sortKey="Faircloth, Bc" uniqKey="Faircloth B">BC Faircloth</name></author><author><name sortKey="Remm, M" uniqKey="Remm M">M Remm</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lanar, De" uniqKey="Lanar D">DE Lanar</name></author><author><name sortKey="Kain, Kc" uniqKey="Kain K">KC Kain</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Rh" uniqKey="Liu R">RH Liu</name></author><author><name sortKey="Meng, Jl" uniqKey="Meng J">JL Meng</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Yi" sort="Wang, Yi" uniqKey="Wang Y" first="Yi" last="Wang">Yi Wang</name></noRegion><name sortKey="Jin, Qiaojun" sort="Jin, Qiaojun" uniqKey="Jin Q" first="Qiaojun" last="Jin">Qiaojun Jin</name><name sortKey="Wang, Shuangshuang" sort="Wang, Shuangshuang" uniqKey="Wang S" first="Shuangshuang" last="Wang">Shuangshuang Wang</name><name sortKey="Yang, Chao" sort="Yang, Chao" uniqKey="Yang C" first="Chao" last="Yang">Chao Yang</name><name sortKey="Yang, Long" sort="Yang, Long" uniqKey="Yang L" first="Long" last="Yang">Long Yang</name><name sortKey="Yang, Long" sort="Yang, Long" uniqKey="Yang L" first="Long" last="Yang">Long Yang</name><name sortKey="Yu, Yuanjie" sort="Yu, Yuanjie" uniqKey="Yu Y" first="Yuanjie" last="Yu">Yuanjie Yu</name><name sortKey="Zhou, Dongjie" sort="Zhou, Dongjie" uniqKey="Zhou D" first="Dongjie" last="Zhou">Dongjie Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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