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Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich).

Lu C, Zou C, Zhang Y, Yu D, Cheng H, Jiang P, Yang W, Wang Q, Feng X, Prosper MA, Guo X, Song G - BMC Genomics (2015)

Bottom Line: Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes.Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers.The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China. lucr99@126.com.

ABSTRACT

Background: Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes.

Results: A total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes of Gossypium arboreum L. and Gossypium raimondii Ulbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available.

Conclusion: Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species.

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Distribution of di- and trinucleotide repeats in the genomes ofGossypium arboreumandGossypium raimondii. Frequency values are expressed as the number of repeats per million base pairs of sequence. Detailed information on frequencies of individual di- and trinucleotide repeat motifs is provided in Additional file 2.
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Fig2: Distribution of di- and trinucleotide repeats in the genomes ofGossypium arboreumandGossypium raimondii. Frequency values are expressed as the number of repeats per million base pairs of sequence. Detailed information on frequencies of individual di- and trinucleotide repeat motifs is provided in Additional file 2.

Mentions: Detailed analyses of individual repeat motifs were carried out for each type of SSR found in G. arboreum and G. raimondii (Additional file 4). In general, G. raimondii had a higher density of all repeat types except A motifs, which were similarly and significantly overrepresented in both G. arboreum (94.5% of mononucleotide motifs) and G. raimondii genomes (94.1%; Figure 2 and Additional file 4). Among dinucleotide repeats, the AT motif was dramatically overrepresented in both genomes (Figure 2 and Additional file 4), representing 87.9% of the dinucleotide motifs in G. arboreum and 83.3% in G. raimondii. AT repeats were also the most abundant motif overall in cotton genomes (25.36 and 31.33 SSRs/Mb), accounting for 19.36% and 16.48% of the total SSRs, respectively. CG repeats were the least frequent dinucleotides; only five were found in G. arboreum and 10 in G. raimondii.Figure 2


Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich).

Lu C, Zou C, Zhang Y, Yu D, Cheng H, Jiang P, Yang W, Wang Q, Feng X, Prosper MA, Guo X, Song G - BMC Genomics (2015)

Distribution of di- and trinucleotide repeats in the genomes ofGossypium arboreumandGossypium raimondii. Frequency values are expressed as the number of repeats per million base pairs of sequence. Detailed information on frequencies of individual di- and trinucleotide repeat motifs is provided in Additional file 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4325953&req=5

Fig2: Distribution of di- and trinucleotide repeats in the genomes ofGossypium arboreumandGossypium raimondii. Frequency values are expressed as the number of repeats per million base pairs of sequence. Detailed information on frequencies of individual di- and trinucleotide repeat motifs is provided in Additional file 2.
Mentions: Detailed analyses of individual repeat motifs were carried out for each type of SSR found in G. arboreum and G. raimondii (Additional file 4). In general, G. raimondii had a higher density of all repeat types except A motifs, which were similarly and significantly overrepresented in both G. arboreum (94.5% of mononucleotide motifs) and G. raimondii genomes (94.1%; Figure 2 and Additional file 4). Among dinucleotide repeats, the AT motif was dramatically overrepresented in both genomes (Figure 2 and Additional file 4), representing 87.9% of the dinucleotide motifs in G. arboreum and 83.3% in G. raimondii. AT repeats were also the most abundant motif overall in cotton genomes (25.36 and 31.33 SSRs/Mb), accounting for 19.36% and 16.48% of the total SSRs, respectively. CG repeats were the least frequent dinucleotides; only five were found in G. arboreum and 10 in G. raimondii.Figure 2

Bottom Line: Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes.Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers.The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China. lucr99@126.com.

ABSTRACT

Background: Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes.

Results: A total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes of Gossypium arboreum L. and Gossypium raimondii Ulbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available.

Conclusion: Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species.

Show MeSH