Construction of a high-density genetic map and QTL mapping of growth traits in kiwifruit

Abstract Background Kiwifruit is a perennial vine with a long juvenile period. Trunk diameter (TD) and annual branch diameter (ABD) are closely related to the growth vigor, abiotic resistance and fruit yield of kiwifruit. They are quantitative traits that are controlled by more than one quantitative trait locus (QTL). QTLs for TD and ABD in kiwifruit remain unelucidated. Results In the present study, a cross of the diploid species Actinidia chinensis ‘Hongyang’בBiyu’♂ was generated to construct a high-density linkage map. We carried out restriction-site associated DNA sequencing of the parents and 173 F1 progeny to identify single-nucleotide polymorphisms (SNPs) in the population. A high-density linkage map spanning 2548.97 cM was developed using 6506 bin markers. This bin map consisted of 29 linkage group (LG), with an average genetic distance of 0.39 cM. A total of 11 QTLs were identified: 5 for the TD and 6 for the ABD. QTL effect sizes were small to moderate, with 1.58 to 13.42% of the variance explained by a single QTL. A total of 358 TD candidate genes and 181 ABD candidate genes were extracted from among the QTLs. Enrichment analysis of candidate genes was carried out using the Gene Ontology (GO) classification system and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In addition, we developed a TD marker in LG23 at position 1971916 bp and an ABD marker in LG10 at position 584605 bp. Genotyping assays revealed that two markers correlated significantly with growth vigor. A TD candidate gene (Actinidia22292) and an ABD candidate gene (Actinidia40478) were also identified near two markers. Conclusions This linkage map and QTLs identified will be useful to dissect the genetics of growth vigor. Furthermore, the molecular markers found in this study can be used in marker-assisted selection to screen kiwifruit seedlings for high growth vigor. These genetic findings deepen our understanding of the genetic basis of growth traits in kiwifruit, and the information obtained is applicable to facilitate kiwifruit breeding.