Marker-assisted selection (MAS) has been an important way for practical plant breeding, and more available markers are required, especially those linked to the genes of some agronomical important traits. Many kinds of molecular markers are being used in cotton genetic mapping, but there is little report on SNP markers development of cotton genes. FIF1 is predominantly expressed early in developing cotton fibers and identified to be a key regulator of cotton fiber development. In this paper, FIF1 genes from G. hirsutum cv. TM-1 and G. barbadense cv. Hai7124 were cloned on the basis of its published sequence in G. arboreum L. Based on the SNPs between FIF1 genes from two tetraploid cotton, SNP and CAPs markers were developed, and the gene was mapped on our allotetraploid cotton genetic map. This result indicates that SNP marker development is feasible and effective in Gossypium.
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