Development of a CAPS Marker for Discriminating Sex in Actinidia arguta

Actinidia arguta is a Korean native kiwifruit with valuable traits for kiwifruit breeding, such as cold hardiness, disease tolerance, and high nutritional value. Early sex discrimination is a priority in kiwifruit breeding programs because Actinidia species are dioecious vines. A cleaved amplified polymorphic sequence (CAPS) marker discriminating sex was developed using genotyping-bysequencing (GBS)-derived single nucleotide polymorphisms (SNPs). Previously obtained GBS reads were re-aligned to the kiwifruit reference genome organized at the pseudo-chromosomal level. These GBS-SNPs could divide A. arguta accessions according to sex. Candidate CAPS markers were designed using these SNPs located on sex chromosomes. Among them, only the CAPS marker designed using the SNP located at 10,236,410 bp on sex chromosome was able to discriminate the sex of A. arguta accessions. This might be because the SNP located at 10,236,410 bp had higher read depth than other candidate SNPs. This CAPS marker, named CBk25ca01, produced DNA fragments of 300 and 147/153 bp in female and male A. arguta accessions, respectively. The CBk25ca01 marker will be useful to improve kiwifruit breeding programs by reducing the time needed to discriminate sex.