A RAD-based linkage map of kiwifruit (Actinidia chinensis Pl.) as a tool to improve the genome assembly and to scan the genomic region of the gender determinant for the marker-assisted breeding

Abstract

Kiwifruit breeding still largely relies on phenotypic observation of cross progeny grown in the field to fruiting maturity, without any selection prior to the juvenility being overcome. Developing markers for the selection of traits of interest would greatly help breeders to rapidly screen breeding populations. With the aim of mapping several traits of interest in kiwifruit, a F1 population of diploid (2n= 58) Actinidia chinensis was produced by combining parents with contrasting phenotypic traits. Ninety-four individuals were preliminarily analyzed to obtain a saturated genetic map based on 167 SSRs from the literature and 12,586 segregating restriction-site-associated DNA (RAD) loci obtained through an approach known as genotyping-by-sequencing (GBS) based on haplotype calling of SNP markers identified by a modified double digest restriction-associated DNA sequencing (ddRADseq) protocol as proposed by Peterson et al. (2012). To improve the accuracy of genotype calling, restriction-site-associated reads were aligned to the scaffolds of the recently published kiwifruit genome (Huang et al. 2013). This strategy provided genetic anchoring to 557 Mbp (90 %) of the assembly, helping also to anchor some 120 unmapped Mbp and to identify some mis-joined scaffolds. The analysis of the region controlling the dioecy in kiwifruit, spanning 16 scaffolds in the pseudomolecule 25 of the genome assembly (approximately 4.9 Mbp), with RAD markers that co-segregated with the gender determinant, allowed to sort out markers suitable for marker-assisted selection for the gender in the mapping population with successful extension to further controlled crosses having parents at different ploidy level and belonging to the A. chinensis/Actinidia deliciosa complex.