Identification of an AFLP marker and conversion to a SCAR marker to identify cytoplasmic male-sterile or normal cytoplasm in Welsh onion (Allium fistulosum L.)

Abstract

SummaryMarker-assisted selection (MAS) is useful for obtaining cytoplasmic male-sterile (CMS) and maintainer lines and has accelerated plant breeding in recent years. The mitochondrial DNA (mtDNA) of nine Welsh onion (Allium fistulosum L.) lines with normal (N) or male-sterile (S) cytoplasm was used to develop molecular markers using the amplified fragment length polymorphism (AFLP) method. A clear polymorphic AFLP band (k1) was screened following a survey of 256 AFLP primer combinations. k1 could be used as an AFLP marker to distinguish between CMS and fertile lines. Another AFLP band (k2) was close to k1. The sequences of these two bands indicated that k1 was 302 bp and k2 was 297 bp in length. Both had a 140-bp sequence identical to the A. cepa cox1 gene. The homologous sequence contained part of the cox1 coding sequence and the 3' untranslated region (3'-UTR). When compared with k2, k1 showed a 5 bp insertion in the 3'-UTR of cox1 in male-sterile Welsh onion mtDNA. The AFLP marker k1 was successfully converted to a sequence-characterised amplified region (SCAR) marker called SCAR1.SCAR1 could be used to distinguish between CMS and normal cytoplasm, and would allow breeders to extract maintainer lines from open-pollinated populations of Welsh onion.