Genome-wide association studies using chromosome-scale genomes of male and female lines redefines two sex-linked loci in linkage disequilibrium in Ficus carica L.

Abstract

Despite its significance in breeding and agricultural practices, the genetic mechanisms that determine sex in the fig (Ficus carica) are not clearly understood, highlighting the need for comprehensive genomic and genetic research to clarify these complex processes. With the aim to accurately identifying the genetic loci involved in sex-related traits of the fig, two chromosome-scale genome sequences for ‘Horaishi’ (a female line) and ‘Caprifig 6085′ (a male line) were determined, and a genome-wide association study (GWAS) was subsequently conducted using single nucleotide polymorphisms (SNPs) obtained from whole genome sequencing across genetically diverse lines and a biparental mapping population derived from a cross between the two lines. As a result, two major GWAS signals were detected. Of these, only the SNPs on FcRAN1 were found to perfectly associate with the sex phenotype, which was suggested as a sex determinant in our previous study. On the other hand, the SNP pattern of FcAG did not perfectly match the sex phenotype, but FcAG was located near and showed another strong GWAS signal, and in contrast, the polymorphisms in the deletion of FcAG did not contradict the sex phenotype or the SNP pattern of FcRAN1. These results suggest that the candidate genes for the sex-linked traits in figs are narrowed down to both FcRAN1 and FcAG, indicating that they are not limited to one or the other. Furthermore, they suggest some potential scenarios, including the possibility that the sex-linked traits are controlled either complementarily or collaboratively by these two genes, which are in linkage disequilibrium. In addition, we confirmed that a non-recombining sex-linked region exists between these two gene loci. The genome information and the finding for sex-related traits would be helpful to understand sex determination mechanisms in Ficus plants as well as the fig breeding programs.