A cotton fiber cDNA and its genomic sequences encoding an A-type cyclin-dependent kinase (GhCDKA) were cloned and characterized. The encoded GhCDKA protein contains the conserved cyclin-binding, ATP binding, and catalytic domains. Northern blot and RT-PCR analysis revealed that the GhCDKA transcript was high in 5–10 DPA fibers, moderate in 15 and 20 DPA fibers and roots, and low in flowers and leaves. GhCDKA protein levels in fibers increased from 5–15 DPA, peaked at 15 DPA, and decreased from 15 t0 20 DPA. The differential expression of GhCDKA suggested that the gene might play an important role in fiber development. The GhCDKA sequence data was used to develop single nucleotide polymorphism (SNP) markers specific for the CDKA gene in cotton. A primer specific to one of the SNPs was used to locate the CDKA gene to chromosome 16 by deletion analysis using a series of hypoaneuploid interspecific hybrids. 1. Introduction Cotton fibers are unicellular seed trichomes differentiated from the outer integument of a developing seed. The regulation of cell division is thus an important aspect of fiber initiation and development. About 25% of commercial cotton ovule epidermal cells stops division and develops to produce fibers [1]. It has been reported that the cell cycle in fiber cells is arrested in the G1 phase during the early stages of fiber development [2]. A central role in the regulation of the cell division is played by cyclin-dependent kinases (CDKs) and their regulatory cyclin subunits [3–5]. Eleven types of cyclins (A, B, C, D, H, CycJ18, L, T, U, SDS (solo dancers), and P) have been identified in plants [6, 7]. Plant CDKs, identified in 23 species of algae, gymnosperms, and angiosperms, contain three functional domains: an ATP-binding domain, a cyclin-binding domain, and a catalytic domain. They are classified into five types (A, B, C, D, and E) based on their sequence differences in the cyclin-binding domain [8]. The A-type CDK (CDKA) proteins are characterized by the presence of the PSTAIRE motif, which is essential for cyclin binding [9]. Plant CDKAs, but not CDKBs, have been shown to complement yeast CDK mutants [10–13], suggesting that plant CDKAs are functional homologues of the yeast CDK. Plant CDKAs not only control cell cycle progression from the G1 to S phase and from the G2 to M phase [5, 14] but also participate in cell proliferation and maintenance of cell division competence in differentiated tissues during development [15]. Since the CDKA gene is expressed in both dividing and differential tissues [15, 16], it has been suggested that
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