Mitochondrial SCAR and SSR Markers for distinguishing cytoplasmic male sterile lines from their isogenic maintainer lines in cotton

With 8 figures and 3 tables Abstract Cytoplasmic male sterility (CMS) line P30A of Upland cotton has been used in commercial production of F1 seeds. However, cytoplasm-specific molecular markers in this three-line (CMS line P30A, maintainer line P30B and restorer line Y18R) system are mostly unknown. Twenty mitochondrial gene probes were used to identify the differences between P30B fertile (N-) and P30A sterile (S-) cytoplasm. Among six genes that revealed restriction fragment length polymorphisms (RFLPs), the gene for a-subunit of F1ATPase (atpA) revealed significant differences between N- and S-cytoplasm. All of the EcoRI restriction bands of atpA were amplified by inverse PCR (iPCR) technique, indicating that both N- and S-cytoplasm contained an intact and a 3' truncated atpA copy, but the truncating site (breakpoint) was different. According to the chimerical sequences following the breakpoints, three cytoplasm-specific sequence characterized amplified region (SCAR) markers were developed. In addition, a simple sequence repeat (SSR) locus in the 3' flanking sequences of the intact atpA gene was found between N- and S-cytoplasm. The four PCR markers were used to distinguish CMS lines from maintainer lines.