Molecular genetic linkage maps have become a major tool in genetics, genomics and breeding of plant and animal species. Linkage maps provide opportunities for unlocking the complex genetics of quantitatively inherited traits through the localization of quantitative trait loci (QTL), identification and positional cloning of individual genes, development of genome-wide physical maps, assembly and annotation of whole genome sequence, and serve as a repository of markers useful in marker-assisted breeding (MAB) of crop and animal species. Among the most informative maps for MAB are those constructed using parent genotypes directly involved in breeding programs.
Peach is one of the best genetically characterized species in the Rosaceae family [1
], and the most economically important crop in Prunus
], a genus that also includes nectarine, plum, apricot, cherry, and almond. The small genome size and expanding genomic resources of peach highlight peach as a model species for genomics studies of tree fruits [1
]. Details of these genetic and genomic resources are updated and described on the Genomic Database for Rosaceae (GDR) [5
While numerous Prunus
species linkage maps have been published, the interspecific linkage map (T × E) developed from an interspecific cross of almond ("Texas") with peach ("Earlygold") is the most saturated of all these linkage maps [6
]. Due to this saturation, a high degree of polymorphism, and extensive co-linearity and synteny among Prunus
], research community consensus has established the T × E map as the reference map for all Prunus
species. The most recent published version of the T × E map contains 562 markers spanning 519 cM with an average density of 0.9 cM per marker [8
]. Building on the reference status of T × E, a bin-mapping strategy was developed [11
]. In this technique, recombination patterns in six progeny of the T × E mapping population were used to reduce the Prunus
genome to 67 "bins" of 7.8 cM average length and to further populate the reference map with an additional 264 microsatellite-derived markers [11
]. Other interspecific Prunus
linkage maps were derived from almond 'Padre' × peach selection 54P545 [12
], and myrobalan plum clone P.2175 × almond-peach hybrid clone GN22 [14
]. Interspecific maps are easily saturated with markers due to the high level of polymorphism between parent genotypes. However, they are limited in their immediate applicability to cultivar improvement via MAS when compared to intraspecific maps because markers that are polymorphic between species are often not polymorphic within species. This is especially true for peach which has a narrow genetic base [15
]. Reported intraspecific Prunus
linkage maps include those of almond [16
], apricot [19
], sweet cherry [23
], and peach [15
]. The ultimate stated goal of most linkage map construction efforts for Prunus
crop species is the development of breeder-friendly MAB tools. Potential benefits of MAB are particularly great for these crop species because of their long juvenility and requirements for large field planting spaces.
The concept of fruit quality of Prunus fruit crops includes both its attainment, such changes in color, flavor, and texture as fruit develop, grow, and ripen, and its maintenance following harvest from the tree as the perishable tissues senesce. Prunus fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption.
The goal of the present study was to develop a genomic resource to facilitate the genetic dissection of Prunus fruit quality traits. This paper reports the genetic mapping in the Prunus genome of candidate genes for fruit texture, pigmentation, flavor, and cold-responsiveness of peach, using both an intraspecific peach population to create a linkage map for genetic analyses of fruit quality and chilling injury (CI), and the interspecific Prunus reference map. The utility of the "fruit quality gene map" developed here for Prunus is demonstrated by highlighting co-localization of fruit quality QTLs with mapped fruit quality candidate genes.