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 F1seeds. 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 α‐subunit of F1ATPase (atpA) revealed significant differences between N‐ and S‐cytoplasm. All of theEcoRI restriction bands ofatpAwere amplified by inverse PCR (iPCR) technique, indicating that both N‐ and S‐cytoplasm contained an intact and a 3′ truncatedatpAcopy, 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 intactatpAgene was found between N‐ and S‐cytoplasm. The four PCR markers were used to distinguish CMS lines from maintainer lines.