Abstract
Information on crop pedigrees can be used to help maximise genetic gain in crop breeding and allow efficient management of genetic resources. We present a pedigree resource of 2,657 wheat (Triticum aestivum L.) genotypes originating from 38 countries, representing more than a century of breeding and variety development. Visualisation of the pedigree enables illustration of the key developments in United Kingdom wheat breeding, highlights the wide genetic background of the UK wheat gene pool, and facilitates tracing the origin of beneficial alleles. A relatively high correlation between pedigree- and marker-based kinship coefficients was found, which validated the pedigree and enabled identification of errors in the pedigree or marker data. Using simulations with a combination of pedigree and genotype data, we found evidence for significant effects of selection by breeders. Within crosses, genotypes are often more closely related than expected by simulations to one of the parents, which indicates selection for favourable alleles during the breeding process. Selection across the pedigree was demonstrated on a subset of the pedigree in which 110 genotyped varieties released before the year 2000 were used to simulate the distribution of marker alleles of 45 genotyped varieties released after the year 2000, in the absence of selection. Allelic diversity in the 45 varieties was found to deviate significantly from the simulated distributions at a number of loci, indicating regions under selection over this period. The identification of one of these regions as coinciding with a strong yield component quantitative trait locus (QTL) highlights both the potential of the remaining loci as wheat breeding targets for further investigation, as well as the utility of this pedigree-based methodology to identify important breeding targets in other crops. Further evidence for selection was found as greater linkage disequilibrium (LD) for observed versus simulated genotypes within all chromosomes. This difference was greater at shorter genetic distances, indicating that breeder selections have conserved beneficial linkage blocks. Collectively, this work highlights the benefits of generating detailed pedigree resources for crop species. The wheat pedigree database developed here represents a valuable community resource and will be updated as new varieties are released at https://www.niab.com/pages/id/501/UK_Wheat_varieties_Pedigree.
Highlights
Information of variety pedigree can be used by breeders to prioritise crosses between highly performing parents whilst maintaining genetic diversity in the offspring for selection
The resource developed here will serve as an evolving platform to inform and manage wheat genetic diversity in breeding programmes around the world and highlights the utility of developing and exploiting similar resources in other crop species
We show that (i) kinship coefficients calculated from markers or pedigree data show strong positive correlation and that large deviations from this correlation are due to erroneous pedigree or seed source data; (ii) within crosses, selection by breeders favours genetic material from the superior parent to which the selected variety will be disproportionally related; and (iii) higher than expected linkage disequilibrium (LD) in recent varieties and changes in allelic diversity provide evidence of selection by breeders over multiple generations of the pedigree
Summary
Information of variety pedigree (i.e., ancestry or genealogy) can be used by breeders to prioritise crosses between highly performing parents whilst maintaining genetic diversity in the offspring for selection. Its development would allow inheritance and origins of beneficial genes and alleles to be tracked through the pedigree to identify sources of traits and genetic variation for research and efficient exploitation. Crosses between genetically distant parents may present a wider genetic variance available for selection [5] and result in greater potential for heterosis and higher performance of F1 hybrid varieties [6,7,8]. Information on relatedness among available varieties could help farmers increase genetic diversity at a farm scale, resulting in resilient systems to deal with climate instability and biotic stresses [9]
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