Pedigree genotyping: a new pedigree-based approach of QTL identification and allele mining by exploiting breeding material

To date, molecular markers have been made available for many economically important traits. Unfortunately, lack of knowledge of their allelic variation hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and may be exploited for marker-assisted breeding (MAB), while a breeding program may include several alleles. Selection for only these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. A new approach, called pedigree genotyping, allows the identification and exploitation of the majority of alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, so covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity by Descent (IBD) is utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analysis. Co-dominant markers, like SSR (= microsatellite) markers, are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable (4) possibility to explore intra- as well as inter-QTL interactions. Fruit firmness in apple is used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation. Prospects for strawberry are also indicated