QTL Mapping In Multiple, Pedigreed Populations: Proof Of Concept Delivered By Results From 27 Progenies For Quantitative Fruit Quality Traits In Apple

Multiple populations are essential for the building of robust genetic models explaining the inheritance of quantitative traits. They are needed to draw proper conclusions on (i) the number of genomic positions (Quantitative Trait Loci) that control the variation of these traits, (ii) their functional allelic diversity, (iii) their contributions to the trait, (iv) their mode of action (additive, interactive, epistatic), and (v) the influence of genetic background. To allow integrated QTL analysis on multiple populations, we developed advanced statistical procedures. FlexQTLTM software was developed to identify putative QTL positions and to estimate the Identity By Descent (IBD) probabilities for specific chromosomal locations, which probabilities can be used to trace founder alleles through pedigrees. New GENSTAT software code uses these probabilities to estimate their mode of action and to examine the robustness of QTLs over years and environments. Furthermore, visualization software, called Pedimap, has been developed to easily trace markers and/or chromosomal segments through pedigrees. Here we will deliver the proof of concept of QTL mapping in multiple pedigreed populations and the methodology of the software by the analysis of 27 small, pre-selected progenies from various European apple breeding programs for the quantitative trait fruit firmness. Each identified QTL was detected in just a limited number of progenies. This research was performed in the framework of the European project HiDRAS (http://users.unimi.it/hidras/). All generated data (markers, phenotypes, pedigrees) have been stored and documented in the database (Bioinformatics 23:882-891). AppleBreed-DB will be gradually made public from January 2008 on (http://applebreed_db.cra.wallonie.be).