DNA polymorphisms of genes involved in fiber development in a selected set of cultivated tetraploid cotton
The lack of genetic diversity within cultivated upland cotton (Gossypium hirsutum L.) has hindered the construction of genomewide linkage maps and their applications in genetics and breeding. The objective of this investigation was to develop candidate gene markers for fiber quality and yield on the basis of approximately 90 genes implicated in fiber development. Polymorphisms using sequence-tagged site (STS) and single nucleotide polymorphism (SNP) markers based on single strand conformation polymorphism (SSCP) and cleaved amplified polymorphism (CAP) were evaluated among three upland and five Pima cotton (G. barbadense L.) genotypes. Of the 90 primer pairs, 75 resulted in polymerase chain reaction amplifications, including 11 that yielded polymorphic STS markers. Of the 48 primer pairs that produced polymorphic SSCP markers, 27 yielded interspecific polymorphism, while 15 yielded both inter- and intraspecific polymorphisms. Six pairs yielded only intraspecific polymorphisms. A total of 18 SNPs, including four indels, were identified in seven of the 15 fiber gene fragments on the basis of direct DNA sequencing, and the average length was 350 bp, with a mean of 1.3 SNPs per fragment. The average rate of SNPs per nucleotide was 0.34%, and 0.31% and 0.41% in coding and noncoding regions, respectively. Eight of the 15 SNPs were interspecific and 78% were nucleotide substitutions, with the four indels contributing to interspecific polymorphism. Six selected SNPs were confirmed by restriction enzyme digestion. The high level of SSCP polymorphism observed within a selected set of agronomically improved lines of upland cotton suggests that the use of SSCP will greatly facilitate genomewide mapping in upland cotton.