Development and Evaluation of Intron and Insertion–Deletion Markers for Gossypium barbadense

Abstract

A total of 588 Gossypium barbadense coding sequences (CDSs) from nucleotide databases were selected for marker development. After selection, 125 CDSs were used to design 126 markers, including 39 intron polymorphisms (GbIPs) and 87 insertion–deletion polymorphisms (GbIDPs). These markers were evaluated by analyzing the genetic diversity of 66 tetraploid cotton accessions including 56 G. barbadense accessions and 10 Gossypium hirsutum accessions. The amplification efficiencies of the GbIPs and GbIDPs were 0.560 and 0.489 for polymorphism information content, 0.744 and 0.690 for effective multiplex ratio (E), 0.653 and 0.438 for qualitative of nature of data, and 0.272 and 0.148 for effective marker index. Principal coordinate analysis showed profound differences between G. hirsutum and G. barbadense accessions. In addition, most of the G. barbadense accessions of Xinjiang, China were clearly different from foreign and other Chinese G. barbadense accessions. The 126 markers were also evaluated for their ability to enrich genetic maps, and 16 polymorphic loci were mapped on nine chromosomes with six loci on A subgenome and 10 loci on D subgenome. The mapping efficiencies of GbIPs and GbIDPs primers were 15.38% and 11.49%, respectively. This study well proves that GbIPs and GbIDPs can be successfully applied to the analysis of genetic diversity and construction of genetic maps.