A MADS-Box Gene-Based InDel Marker Discriminating Sex in Actinidia arguta

Abstract

Gene-based markers are valuable tools in breeding programs due to their direct linkage to traits of interest. In dioecious plants, such as kiwifruit (Actinidia spp.), sex-discriminating markers can shorten the breeding cycle by enabling the selection of preferred sexes at the juvenile stage. To develop a gene-based sex-discriminating marker, resequencing was conducted on female and male A. arguta accessions, and insertion and deletion (InDel) variations within sex-related genes were explored. A total of 203,116 InDels were detected between female and male A. arguta accessions, and 118,865 InDels were heterozygous between the two accessions. Sequence similarity between thirty-seven sex-related genes from seven dioecious species and the kiwifruit reference genome was investigated, revealing that ten genes exhibited similarities ranging from 59 to 79%. Among the 118,865 InDels, seven InDels were located on four sex-related genes encoding agamous-like MADS-box genes and hypothetical proteins. A 20 bp insertion in male A. arguta located in the agamous-like MADS-box gene was converted into an InDel marker, which clearly discriminates female and male A. arguta accessions and the interspecific hybrid cultivar. The InDel marker was designated CBk25id01 and produced approximately 350 bp amplicon only in the male A. arguta. The CBk25id01 linked to the agamous-like MADS-box gene involved in floral organ development may help understand sex differentiation and accelerate the breeding of kiwifruits.