QTL Analysis of Fruit Quality Traits in Peach [Prunus Persica (L.) Batsch] Using Dense SNP Maps

Abstract

Fruit quality is the main criterion used for selection of new varieties in peach, and it is usually defined by the conjunction of organoleptic and nutritional traits and postharvest behavior. The aim of this study was the identification of quantitative trait loci (QTL) for several fruit quality traits using an F1 segregating population of 75 seedlings derived from the cross between 'Venus' and 'Big Top' nectarine cultivars. The progeny was evaluated over several years for agronomic and pomological characteristics (including basic quality traits and antioxidant compounds content) and also genotyped using SNPs included in the 'IPSC 9K peach SNP array v1' developed by the International Peach SNP Consortium, which carries 8,144 SNPs. Two preliminary dense genetic linkage maps were constructed for 'Venus' and 'Big Top', with 160 and 208 markers placed onto 11 linkage groups, respectively. A second round was used to identify QTLs that were mapped over twelve LG representing seven peach chromosomes. Some of the QTLs mapped in the same position of previously reported QTLs, interestingly QTLs for fructose in LG 6 and phenolic compounds in LG2 were detected for the first time. LG4 in 'Venus' and LG5 in 'Big Top' maps presented the highest density of QTLs controlling several traits. This work represents the first study identifying QTLs for fruit quality traits using the high-density SNP array 'IPSC 9K peach SNP array v1' in an F1 nectarine family.

Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

“…Wide phenotypic variation was found for most of the traits studied in this progeny (Abidi et al 2011;Zeballos et al 2015), which supports the quantitative nature of these traits. Distribution of the traits has been …”

“…For the segregation deviation test, a Chi-square test was performed with p = 0.05 as the threshold (Zeballos et al 2015). In a second round, the markers were adjusted to a 1:1 segregation ratio with a p = 0.005 threshold.…”

“…A preliminary number of groups and linkage groups (LGs) were established using the recombination fraction criterion (see details in Zeballos et al 2015). A second mapping round was performed with the selected SNPs by including the SSR markers, the order of markers in each LG was established using the maximum likelihood mapping option, and map distances were calculated using Kosambi's mapping function.…”

“…LGs (Zeballos et al 2015). Final LG assignment was performed after comparison with the peach genome v1.0 physical map (GDR, 2015), and markers with identical segregation patterns that were previously excluded were included for the next step (Zeballos 2012 Table 3).…”

Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families

“…QTL identification in peaches conducted [ 5 ] for acidity, total sugar content, organic acids, fruit weight, bloom, and harvest dates [ 6 , 7 ], and chilling injury susceptibility [ 8 ] have been limited due to the low marker density of genetic maps [ 9 ]. Recently, these issues have been overcome due to the availability of the peach genome v1.0 and v2.0 [ 10 , 11 ] sequence and the development of the International Peach SNP Consortium peach 9 K SNP array [ 11 ].…”