A RAD-based linkage map of kiwifruit (Actinidia chinensis Pl.) and map position of genetic determinants of traits of interest to breeders

Kiwifruit breeding still largely relies on phenotypic observation of cross progeny grown in the field to fruiting maturity, without any selection prior to juvenility being overcome. Developing marker-assisted selection for traits of interest would greatly help breeders to screen rapidly breeding populations, thereby saving costs and labor. With the aim of mapping several characters of interest in kiwifruit, a pseudo test-cross population of diploid Actinidia chinensis was produced by crossing parents with contrasting phenotypic traits. Ninety-four individuals were analysed to obtain a saturated genetic map based on 167 SSRs retrieved from the literature and 9,397 segregating loci obtained through haplotype calling of SNP markers identified by a modified ddRAD 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 557M bp (90%) of the available assembly, helping also to anchor some unmapped 120 Mbp and to identify some mis-joined scaffolds. Phenotypic traits, such as gender, bud burst, flowering time, fruit weight, flesh color, sugar content, pH and flesh acidity, were recorded during two consecutive seasons in individual seedlings of both populations. Several genetic determinants of traits were mapped and markers for selection are being identified. The methodological approach to the production of linkage maps based on genotyping-by-sequencing strategy together with the mapping of genetic determinants of several phenotypic traits are presented and discussed.