Development of co-dominant markers linked to a hemizygous region that is related to the self-compatibility locus (S) in buckwheat (Fagopyrum esculentum)

Common buckwheat (Fagopyrum esculentum) is a hcterostylous self-incompatible (SI) species with two different flower morphologies, pin and thrum. The SI trait is controlled by a single gene complex locus, S. Self-compatible (SC) lines were developed by crossing F. esculentum and F. homotmpicum; these lines have an SC gene, S-h, which is dominant over the s allele and recessive to the S allele. S-ELF3 has been identified as a candidate gene in the S locus and is present in the S and S-h but not s alleles. A single-nucleotide deletion in the S-ELF3 gene of the S-h allele results in a frame shift. To develop co-dominant markers to distinguish between (SSh)-S-h and S(h)s plants, we perfonned a next-generation sequencing analysis in combination with bulked-segregant analysis. We developed four co-dominant markers linked to the S locus. We investigated the polymorphism frequency between a self-compatible line and leading Japanese buckwheat cultivars. Linkage between a developed sequence-tagged-site marker and flower morphology was confirmed using more than 1000 segregating plants and showed no recombination. The developed markers would be useful for buck-wheat breeding and also to produce lines for genetic analysis such as recombinant inbred lines.