Genome-wide mining, characterization, and development of microsatellite markers in gossypium species

Abstract

Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite markers in genomic studies and marker-assisted selection is limited. To identify microsatellites for cotton research, we mined 100,290, 83,160, and 56,937 microsatellites with frequencies of 41.2, 49.1, and 74.8 microsatellites per Mb in the recently sequenced Gossypium species: G. hirsutum, G. arboreum, and G. raimondii, respectively. The distributions of microsatellites in their genomes were non-random and were positively and negatively correlated with genes and transposable elements, respectively. Of the 77,996 developed microsatellite markers, 65,498 were physically anchored to the 26 chromosomes of G. hirsutum with an average marker density of 34 markers per Mb. We confirmed 67,880 (87%) universal and 7,705 (9.9%) new genic microsatellite markers. The polymorphism was estimated in above three species by in silico PCR and validated with 505 markers in G. hirsutum. We further predicted 8,825 polymorphic microsatellite markers within G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. In our study, genome-wide mining and characterization of microsatellites, and marker development were very useful for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome mapping.

Figure 1

Distribution of microsatellites identified in the assembled genomic sequences of G. hirsutum (TM-1), G. arboreum and G. raimondii. (A) Frequency distribution of microsatellites with different motif lengths in Gossypium species. (B) Distribution of microsatellites in genic and intergenic regions in G. hirsutum (TM-1).

Figure 2

Distribution of SSR motif repeat numbers from mono- to hexanucleotide.The vertical axis shows the abundance of microsatellites that have different motif repeat numbers (from 3 to >20), which are discriminated by legends of different colors.

Figure 3

The genomic distributions of microsatellites, genes, and TEs in the assembled genome of G. hirsutum. (A) Genome-wide distributions of microsatellites, genes, and TEs in the A_t. (B) Genome-wide distributions of microsatellites, genes, and TEs in the D_t. The horizontal axis indicates the chromosomes A01-A13 and D01-D13, and each chromosome was divided into 1-Mb for statistical analysis of microsatellites, genes, and TEs. The left vertical axis indicates the frequencies of the microsatellites and genes, and the right vertical axis indicates the frequencies of TE. The curves represent practical frequencies and the lines show average frequencies.