Pedigree Genotyping: A New Pedigree-Based Approach of QTL Identification and Allele Mining

Abstract

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 markerassisted 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. INTRODUCTIONTo date, molecular markers have been identified for many loci governing important horticultural traits. These markers have usually been identified in one single cross. As a consequence, only one or two favourable alleles of a locus are identified, whereas a breeding program usually includes many favourable alleles. If a breeder focuses his selection on these alleles, he would unnecessarily discard many favourable genotypes. This reduces the efficiency of the breeding program. Moreover, the genetic diversity of his material is unnecessarily narrowed. A new approach called 'Pedigree Genotyping' makes it possible to find markers for all favourable alleles present in a breeding program. The costs of this approach are low compared to traditional marker research, because it utilises data from the ongoing breeding program.

Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit: breeding insights from a multi-family study

“…rosbreed.org) and the participating Washington State University (WSU) Apple Breeding Program (Evans 2013). The pedigree-based analysis (PBA) approach (van de Weg et al 2004;Bink et al 2012Bink et al , 2014 has been established for the aforementioned breeding program in the RosBREED project, enabling efficient detection and validation of segregating alleles in multiple families (Peace et al 2014). The US apple Crop Reference Set (CR Set), representing alleles of important parents of US apple breeding germplasm, has been established (Peace et al 2014) and phenotyped for numerous traits, including fruit quality after storage, using standardized protocols (Evans et al 2012).…”

Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome

“…PBA includes the analysis of the segregation of specific chromosomal regions in genetically related cultivars, breeding selections, and small progenies through highly polymorphic codominant markers. This "identity by descent" approach allows the detection of QTLs (Bink et al 2002;van de Weg et al 2004).…”

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

“…Pedigree-based QTL analysis (PBA) (Van de Weg et al 2003) using DNA markers, pedigree information, and inter-related populations has been proposed as an approach to identify and characterize more QTL and more alleles at identified QTLs than are possible in biparental QTL studies. Recent advances have been made in PBA by the development of dedicated software including FlexQTL™ (Bink et al 2002(Bink et al , 2008www.flexqtl.nl), Pedimap (Voorrips et al 2012), and PediHaplotyper (Voorrips et al 2016).…”