ENABLING MARKER-ASSISTED BREEDING (MAB) FOR BLUSH IN PEACH [Prunus persica (L.) Batsch]

ABSTRACT Phenotyping is a crucial component for using DNA-based tools in gene discovery and marker development. Phenotypic and genotypic data are essential for linking genetic variation with biological function, thus documenting gene function. However, phenotypic data gathering is not keeping pace with the immensely increasing amount of available genomic information, brought forth by current Next Generation Sequencing technologies. Standardized phenotyping protocols for peach [Prunus persica (L.) Batsch] have been developed for 6 productivity traits (on the tree) and 16 fruit quality traits. Documentation of fruit quality phenotypes has been performed applying developed standardized phenotyping protocol in two seasons, at nine locations, on 513 peach and almond accessions, cultivars, advanced selections, lines, and or populations. In this study blush (i.e. red skin pigmentation) inheritance and associated genes were investigated extensively. Blush is an important trait for marketing peaches. The red skin pigmentation develops through the flavonoid and anthocyanin pathways. Both genetic and environmental stimuli and their interaction (genotype x environment) control the regulation of this pathway. Sunlight induces the progression of red skin development. To study the genetic control of blush in peach a controlled cross between two cultivars with contrasting phenotypes, Zin Dai (~30% red) and Crimson Lady (~100% red), was made. One F1 hybrid, BY02p4019, with intermediate levels of blush (~65% red) was selfed to generate a segregating F2 blush population (ZC2). The segregating population was phenotyped for blush for four years (2007, 2008, 2010, 2011) using a visual rating scale (0-5) and in 2011 using a colorimeter (L*, a*, b*). Twenty-five individuals, exhibiting a blush range from 0 (0% red) to 5 (100% red) and a normal distribution for this trait, were genotyped with an IPSC 9K peach SNP array v1. A ZC2 genetic linkage map was constructed with 1,335 SNP markers, comprising 14 linkage groups. This map covers a genetic distance of ~452.51 cM with an average marker spacing of 2.38 cM/marker and an average number of 95 markers per LG. A major QTL for blush has been located on LG3, denoted Blush.Pp.ZC-3.1. This QTL spanned 21-41cM on LG3 and explained on average 72% of phenotypic variation for the trait. QTL analysis for four different seasons confirms the identification of this major QTL for blush in peach, and supports its stability. Three minor QTL\u27s were located on LG\u27s 4, and 7 indicating the presence of minor genes involved with blush development. Candidate genes involved in skin and flesh coloration of cherry (PavMYB10) and apple (MdMYB10) are located within the interval of the major QTL on LG3 suggesting the same genetic control for color development in the Rosaceae family. A standardized protocol for collecting phenotypic data in peach will facilitate discovery of genes associated with fruit quality and other agronomically important traits