Identification of a novel haplotype of the Ms locus controlling restoration of male-fertility and its implication in origination of cytoplasmic male-sterility in onion (Allium cepa L.)

Seeds of F₁ hybrid cultivars of onions have been exclusively produced by utilising cytoplasmic male-sterility (CMS). A single locus, <i>Ms</i>, controls restoration of male-fertility of CMS onions. When a molecular marker tagging the <i>AcPMS1</i> gene, a candidate gene for the <i>Ms</i> locus, was used to genotype diverse breeding lines, an unusual marker genotype showing an intermediate size of PCR product was identified in one breeding line (ORI854). The male-fertility phenotype of ORI854 was all male-sterile. Full-length genomic DNA sequence (16,464 bp) of this novel <i>AcPMS1</i> allele from ORI854 was more closely related to a recessive <i>AcPMS1</i> allele than to a dominant allele. However, there were more than 200 polymorphic sequences between this novel allele and the recessive allele, indicating that this novel <i>AcPMS1</i> allele might not have recently diverged from the recessive allele. Phylogenetic analysis implied that onion male-sterility might have first appeared in a common ancestor before divergence of this novel allele and recessive allele of <i>AcPMS1</i>. Analysis of full-length cDNA sequences of additional 12 genes showing almost perfect linkage disequilibrium with the <i>Ms</i> locus indicated that no recombination might have happened among 13 genes including <i>AcPMS1</i> in the novel <i>Ms</i> haplotype after divergence from the recessive <i>Ms</i> haplotype.