Limits...
Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).

Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: College of Bio-engineering, Shanxi University, Taiyuan, China.

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.

No MeSH data available.


Distribution of monomorphic markers in the Chinese spring wheat genome.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4633229&req=5

pone.0141540.g003: Distribution of monomorphic markers in the Chinese spring wheat genome.

Mentions: All SSRs were selected for SSR marker development, and a total of 295,267 SSR markers were successfully designed from the 21 chromosomes of CSW, covering the whole genome at a density of 29.73 per Mb. The densities of SSR markers on each chromosome were similar, ranging from 25.58 to 31.34 per Mb (Table 4). Among the chromosomes that contained SSR markers, the highest density of SSR markers was found on chromosome 5D, followed by 2D and 7D. Furthermore, all SSR markers were validated and subjected to polymorphism analysis via re-PCR. Markers that amplified prominent PCR products were classified as either polymorphic or monomorphic based on the number of corresponding loci. Of the markers amplified, 70,564 were monomorphic and 224,703 were polymorphic. The monomorphic markers included 2,387 (3.38%) present in compound formation and 8,177 (99.96%) present in perfect formation, whose dinucleotide motifs (34.46%) were the most common, followed by hexanucleotide (28.29%), trinucleotide (23.72%), tetranucleotide (7.88%) and pentanucleotide motifs (5.65%), respectively (Fig 3). Moreover, we also examined the distribution of monomorphic markers on the Chinese spring chromosomes. Chromosome 3B had 5,387 monomorphic markers, which was considerably higher than that of the other chromosomes, followed by chromosome 2B and 5B, containing 5,112 and 4,346 monomorphic markers, respectively. Chromosome 1D contained the fewest monomorphic markers (2,082), while 3B contained the largest number of di-, tetra-, penta- and hexanucleotide motifs and 2B contained the largest number of trinucleotide motifs. Chromosome 1D had the fewest di- and hexanucleotide motifs, 3D had the fewest tri- and pentanucleotide motifs and 4D had the fewest tetranucleotide motifs (Table 5).


Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).

Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X - PLoS ONE (2015)

Distribution of monomorphic markers in the Chinese spring wheat genome.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4633229&req=5

pone.0141540.g003: Distribution of monomorphic markers in the Chinese spring wheat genome.
Mentions: All SSRs were selected for SSR marker development, and a total of 295,267 SSR markers were successfully designed from the 21 chromosomes of CSW, covering the whole genome at a density of 29.73 per Mb. The densities of SSR markers on each chromosome were similar, ranging from 25.58 to 31.34 per Mb (Table 4). Among the chromosomes that contained SSR markers, the highest density of SSR markers was found on chromosome 5D, followed by 2D and 7D. Furthermore, all SSR markers were validated and subjected to polymorphism analysis via re-PCR. Markers that amplified prominent PCR products were classified as either polymorphic or monomorphic based on the number of corresponding loci. Of the markers amplified, 70,564 were monomorphic and 224,703 were polymorphic. The monomorphic markers included 2,387 (3.38%) present in compound formation and 8,177 (99.96%) present in perfect formation, whose dinucleotide motifs (34.46%) were the most common, followed by hexanucleotide (28.29%), trinucleotide (23.72%), tetranucleotide (7.88%) and pentanucleotide motifs (5.65%), respectively (Fig 3). Moreover, we also examined the distribution of monomorphic markers on the Chinese spring chromosomes. Chromosome 3B had 5,387 monomorphic markers, which was considerably higher than that of the other chromosomes, followed by chromosome 2B and 5B, containing 5,112 and 4,346 monomorphic markers, respectively. Chromosome 1D contained the fewest monomorphic markers (2,082), while 3B contained the largest number of di-, tetra-, penta- and hexanucleotide motifs and 2B contained the largest number of trinucleotide motifs. Chromosome 1D had the fewest di- and hexanucleotide motifs, 3D had the fewest tri- and pentanucleotide motifs and 4D had the fewest tetranucleotide motifs (Table 5).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: College of Bio-engineering, Shanxi University, Taiyuan, China.

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.

No MeSH data available.