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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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Genetic linkage groups of chr07 and chr16 in tetraploid cotton. Linkage groups were developed from 184 individuals of a BC1 population derived from TM-1 and T586 using chromosome-specific SSRs. AC01 represents chromosome-specific SSRs designed from chr01 of Gossypium arboreum (corresponding to chr07 of tetraploid cotton). DC01 represents chromosome-specific SSRs designed from chr01 of Gossypium raimondii (corresponding to chr16 of tetraploid cotton). Markers MUSS004 and NAU1048 mapped only to chr07, and NAU2626 mapped only to chr16 in the published genetic maps. The other published markers, including MGHES58, BNL3319, BNL2441, BNL2733, JESPR297, mapped to one or more other chromosomes, in addition to chr07 or chr16 in the published genetic maps.
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Fig3: Genetic linkage groups of chr07 and chr16 in tetraploid cotton. Linkage groups were developed from 184 individuals of a BC1 population derived from TM-1 and T586 using chromosome-specific SSRs. AC01 represents chromosome-specific SSRs designed from chr01 of Gossypium arboreum (corresponding to chr07 of tetraploid cotton). DC01 represents chromosome-specific SSRs designed from chr01 of Gossypium raimondii (corresponding to chr16 of tetraploid cotton). Markers MUSS004 and NAU1048 mapped only to chr07, and NAU2626 mapped only to chr16 in the published genetic maps. The other published markers, including MGHES58, BNL3319, BNL2441, BNL2733, JESPR297, mapped to one or more other chromosomes, in addition to chr07 or chr16 in the published genetic maps.

Mentions: A BC1 population of 184 individuals was constructed by crossing TM-1 and T586 (both are G. hirsutum). 22, 23, and 9 polymorphic markers between the parents were obtained from the 459 SSRs designed from chr01 of G. arboreum, 448 from chr01 of G. raimondii, and 211 from published genetic maps, respectively. All 54 SSRs were included in the linkage analysis. Two linkage groups, containing 44 markers, were constructed: 20 markers in linkage group (LG) I, and 24 in LG II (FigureĀ 3). The other 10 loci were not part of any linkage group. 17 of the 22 polymorphic SSRs from G. arboreum mapped to LG I, and 19 of the 23 SSRs designed from G. raimondii mapped to LG II. No SSR designed from G. arboreum mapped to LG II, and no SSR designed from G. raimondii mapped to LG I.Figure 3


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)

Genetic linkage groups of chr07 and chr16 in tetraploid cotton. Linkage groups were developed from 184 individuals of a BC1 population derived from TM-1 and T586 using chromosome-specific SSRs. AC01 represents chromosome-specific SSRs designed from chr01 of Gossypium arboreum (corresponding to chr07 of tetraploid cotton). DC01 represents chromosome-specific SSRs designed from chr01 of Gossypium raimondii (corresponding to chr16 of tetraploid cotton). Markers MUSS004 and NAU1048 mapped only to chr07, and NAU2626 mapped only to chr16 in the published genetic maps. The other published markers, including MGHES58, BNL3319, BNL2441, BNL2733, JESPR297, mapped to one or more other chromosomes, in addition to chr07 or chr16 in the published genetic maps.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Genetic linkage groups of chr07 and chr16 in tetraploid cotton. Linkage groups were developed from 184 individuals of a BC1 population derived from TM-1 and T586 using chromosome-specific SSRs. AC01 represents chromosome-specific SSRs designed from chr01 of Gossypium arboreum (corresponding to chr07 of tetraploid cotton). DC01 represents chromosome-specific SSRs designed from chr01 of Gossypium raimondii (corresponding to chr16 of tetraploid cotton). Markers MUSS004 and NAU1048 mapped only to chr07, and NAU2626 mapped only to chr16 in the published genetic maps. The other published markers, including MGHES58, BNL3319, BNL2441, BNL2733, JESPR297, mapped to one or more other chromosomes, in addition to chr07 or chr16 in the published genetic maps.
Mentions: A BC1 population of 184 individuals was constructed by crossing TM-1 and T586 (both are G. hirsutum). 22, 23, and 9 polymorphic markers between the parents were obtained from the 459 SSRs designed from chr01 of G. arboreum, 448 from chr01 of G. raimondii, and 211 from published genetic maps, respectively. All 54 SSRs were included in the linkage analysis. Two linkage groups, containing 44 markers, were constructed: 20 markers in linkage group (LG) I, and 24 in LG II (FigureĀ 3). The other 10 loci were not part of any linkage group. 17 of the 22 polymorphic SSRs from G. arboreum mapped to LG I, and 19 of the 23 SSRs designed from G. raimondii mapped to LG II. No SSR designed from G. arboreum mapped to LG II, and no SSR designed from G. raimondii mapped to LG I.Figure 3

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