Pedigree genotyping: a new pedigree-based approach of QTL identification and allele mining

To date, molecular markers are available for many economically important traits. Unfortunately, lack of knowledge of the allelic variation of the related genes 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 exploitable for marker-assisted breeding (MAB), whereas a breeding program may include several alleles. Selection for just 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 most alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, thus 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 analyses. 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) intra- as well as inter-QTL interactions can be explored. Fruit firmness in apple will be used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation

[1]  D. Byrne,et al.  CYTOLOGICAL DIPLOIDIZATION IN THE CULTIVATED OCTOPLOID STRAWBERRY FRAGARIA × ANANASSA , 1976 .

[2]  C. Durel,et al.  ESTIMATION OF FIRE BLIGHT RESISTANCE HERITABILITY IN THE FRENCH PEAR BREEDING PROGRAM USING A PEDIGREE-BASED APPROACH , 2004 .

[3]  M. Soller,et al.  Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. , 1993, Genetics.

[4]  E. Schrevens,et al.  Quantitative genetic analysis and comparison of physical and sensory descriptors relating to fruit flesh firmness in apple (Malus pumila Mill.) , 2000, Theoretical and Applied Genetics.

[5]  L. Gianfranceschi,et al.  THE EUROPEAN PROJECT HIDRAS: INNOVATIVE MULTIDISCIPLINARY APPROACHES TO BREEDING HIGH QUALITY DISEASE RESISTANT APPLES , 2004 .

[6]  Agim Ballvora,et al.  Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type , 2004, Molecular Breeding.

[7]  Y. Lespinasse,et al.  Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple , 1998, Theoretical and Applied Genetics.

[8]  Daniel Gianola,et al.  Combining gene expression and molecular marker information for mapping complex trait genes: a simulation study. , 2003, Genetics.

[9]  M. Lynch,et al.  Genetics and Analysis of Quantitative Traits , 1996 .

[10]  M. Sillanpää,et al.  Bayesian versus frequentist analysis of multiple quantitative trait loci with an application to an outbred apple cross , 2001, Theoretical and Applied Genetics.

[11]  C. Gessler,et al.  Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.) , 2002, Molecular Breeding.

[12]  D. Balding,et al.  Handbook of statistical genetics , 2004 .

[13]  M. Bink,et al.  On flexible finite polygenic models for multiple-trait evaluation. , 2002, Genetical research.

[14]  R. Jansen,et al.  Mapping quantitative trait loci in plant breeding populations , 2003 .

[15]  M. Sillanpää,et al.  Multiple QTL mapping in related plant populations via a pedigree-analysis approach , 2002, Theoretical and Applied Genetics.

[16]  A. Long,et al.  The Lowdown on Linkage Disequilibrium , 2003, The Plant Cell Online.

[17]  D. Sargent,et al.  Development and characterization of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry , 2003 .