Structural analysis of Actinidia arguta natural populations and preliminary application in association mapping of fruit traits

• Actinidia arguta can be classified into northern and central-southern geo-ecotypes. • 2496 alleles firstly identified in tetraploid A. arguta , located the associated traits. • A single nucleotide mutation found to control green/red fruit flesh color. • Enlargement of wild genetic pool of A. arguta increases variation for future breeding. The fruit of Actinidia arguta are currently receiving much attention owing to their various colors in green or purple and fully edible smooth skin with unique shapes, taste appeal and rich nutritional value. A. arguta is now, after A. chinensis var. chinensis and A. chinensis var. deliciosa , the third most widely planted member of the Actinidia genus in commercial orchards. In order to improve our understanding of A. arguta and to plan future use of the germplasm for breeding elite cultivars, 189 accessions (including 14 cultivars) collected were analyzed with 200 simple sequence repeats (SSR) to explore their molecular diversity and population structure, and to identify elite alleles. The results showed all these markers used were polymorphic and generated 2496 allele loci with a polymorphism information content (PIC) value of 0.658. Through population structure analysis, the accessions have been divided into four subpopulations (K = 4), each subpopulation corresponding well with the distance-based clustering. Eleven traits were associated using MLM (mixed linear model) with markers. Marker-trait association analysis identified 43 significant associations involving the 35 SSRs for the 11 traits, including some important and interesting traits in breeding such as gender and fruit quality like flesh color. Through transient expression, LR71 discovered in this study is a marker significantly associated with fruit flesh color, belongs to a gene encoding an MYB transcription factor that regulates the accumulation of anthocyanins, and causes red pigmentation. This study revealed the extent of genetic diversity and the population structure of A. arguta germplasm collected. The trait-marker pairs obtained from association mapping have potential value in molecular marker-assisted breeding, and genomics studies with gene mapping. The relationships among the natural populations touched and the origin of the cultivars mainly used are discussed, all of these help us to further understand and analyze the natural evolution of A. arguta .