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)

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.

Figure 1

Relative frequency (%) of SSR types in the genomes of Gossypium arboreum and Gossypium raimondii . SSRs are organized by the number of repeats. The graph was based on a total of 200,744 and 142,409 SSRs detected in the genomes of G. arboreum and G. raimondii, respectively.

Figure 2

Distribution of di- and trinucleotide repeats in the genomes of Gossypium arboreum and Gossypium 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.

Figure 3

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.