Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.)
Identifieur interne : 000633 ( Main/Merge ); précédent : 000632; suivant : 000634Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.)
Auteurs : Bin Han [République populaire de Chine] ; Changbiao Wang [République populaire de Chine] ; Zhaohui Tang [République populaire de Chine] ; Yongkang Ren [République populaire de Chine] ; Yali Li [République populaire de Chine] ; Dayong Zhang [République populaire de Chine] ; Yanhui Dong [République populaire de Chine] ; Xinghua Zhao [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
Url:
DOI: 10.1371/journal.pone.0141540
PubMed: 26536014
PubMed Central: 4633229
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sortKey="Zhao, Xinghua" sort="Zhao, Xinghua" uniqKey="Zhao X" first="Xinghua" last="Zhao">Xinghua Zhao</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan</wicri:regionArea><wicri:noRegion>Taiyuan</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26536014</idno><idno type="pmc">4633229</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4633229</idno><idno type="RBID">PMC:4633229</idno><idno type="doi">10.1371/journal.pone.0141540</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000195</idno><idno type="wicri:Area/Pmc/Curation">000195</idno><idno type="wicri:Area/Pmc/Checkpoint">000497</idno><idno 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last="Wang">Changbiao Wang</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan</wicri:regionArea><wicri:noRegion>Taiyuan</wicri:noRegion></affiliation></author><author><name sortKey="Tang, Zhaohui" sort="Tang, Zhaohui" uniqKey="Tang Z" first="Zhaohui" last="Tang">Zhaohui Tang</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan</wicri:regionArea><wicri:noRegion>Taiyuan</wicri:noRegion></affiliation></author><author><name sortKey="Ren, Yongkang" sort="Ren, Yongkang" uniqKey="Ren Y" first="Yongkang" last="Ren">Yongkang Ren</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan</wicri:regionArea><wicri:noRegion>Taiyuan</wicri:noRegion></affiliation></author><author><name sortKey="Li, Yali" sort="Li, Yali" uniqKey="Li Y" first="Yali" last="Li">Yali Li</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan</wicri:regionArea><wicri:noRegion>Taiyuan</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Dayong" sort="Zhang, Dayong" uniqKey="Zhang D" first="Dayong" last="Zhang">Dayong Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Dong, Yanhui" sort="Dong, Yanhui" uniqKey="Dong Y" first="Yanhui" last="Dong">Yanhui Dong</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan</wicri:regionArea><wicri:noRegion>Taiyuan</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Xinghua" sort="Zhao, Xinghua" uniqKey="Zhao X" first="Xinghua" last="Zhao">Xinghua Zhao</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan</wicri:regionArea><wicri:noRegion>Taiyuan</wicri:noRegion></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>Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Makharia, Gk" uniqKey="Makharia G">GK Makharia</name></author><author><name sortKey="Mulder, Cj" uniqKey="Mulder C">CJ Mulder</name></author><author><name sortKey="Goh, Kl" uniqKey="Goh K">KL Goh</name></author><author><name sortKey="Ahuja, V" uniqKey="Ahuja V">V Ahuja</name></author><author><name sortKey="Bai, Jc" uniqKey="Bai J">JC Bai</name></author><author><name sortKey="Catassi, C" uniqKey="Catassi C">C Catassi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paux, E" uniqKey="Paux E">E Paux</name></author><author><name sortKey="Sourdille, P" uniqKey="Sourdille P">P Sourdille</name></author><author><name sortKey="Mackay, I" uniqKey="Mackay I">I Mackay</name></author><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C 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