Development of simple PCR-based markers linked to the Ms locus, a restorer-of-fertility gene in onion (Allium cepa L.)

Abstract

In order to implement reliable markerassisted selection systems for the restorer-of-fertility locus (Ms) in onions (Allium cepa L.), simple PCRbased codominant markers linked to the Ms locus were developed. Based on the EST probe sequences of previously reported RFLP markers, full-length genomic sequences of the gene encoding putative oligopeptide transporter (OPT) was obtained by RACE. The first intron contained two 108 and 439-bp indel polymorphisms between the two Ms allele-linked OPT alleles. A simple PCR marker for OPT was developed by designing a primer pair on the flanking regions of the 108-bp indel which is created by two tandem repeats. The second simple PCR marker was developed from the EST probe encoding photosystem I subunit O (PsaO). Two 14 and 39-bp tandem repeats were identified from the 5 0 upstream sequences of the PsaO-coding gene, which were isolated by genome walking. Three different compositions of these tandem repeats were identified from diverse onion germplasm. A primer set binding to the flanking sequence of these polymorphic repeats was used to amplify three different marker haplotypes. The OPT marker was tightly linked to the Ms locus at a distance of 1.5 cM, but the analysis of the linkage relationship showed little linkage disequilibrium between the marker and the Ms locus. Even so, these simple PCR markers are valuable tools for the marker-assisted selection of segregating individuals in onion F 1 hybrid breeding programs.

Limitations of PCR‐based molecular markers to identify male‐sterile and maintainer plants from Indian onion (Allium cepa L.) populations

“…, Bang et al. ). Kim () employed these two SCAR markers and observed that marker genotyping was not clear due to the dominant nature of these two markers.…”

“…We started our experiments with PCR marker OPT1 (Bang et al. ) as this marker was found to be in linkage disequilibrium in our previous studies with long‐day onion (Saini et al. ).…”

“…PCR markers, for identification of restorer of fertility ( Ms ) locus, were gene encoding putative oligopeptide transporter (OPT) (Bang et al. ), jnurf13 (Kim ), AcSKP1 (Huo et al. ) and AcPMS1 (Kim et al.…”

“…Markers tightly associated with Ms locus were first reported by Gökçe and Havey () followed by other PCR markers (Bang et al. , Kim , Huo et al. , Kim et al.…”

Enhancing onion breeding using molecular tools

“…Later, Bang et al. () developed PCR‐based markers from existing RFLP clones and detected one marker tightly linked to Ms , which exhibited limited linkage disequilibrium. This marker can be used to select specific alleles at Ms loci in segregating population with linkage disequilibrium, but not in diverse onion germplasm.…”