Abstract
Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify and confirm direct parent–offspring relationships are routine, those for other types of close relationships have yet to be effectively and widely implemented with plants, due to complications such as asexual propagation and extensive inbreeding. The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes (referred to in this study as “summed potential lengths of shared haplotypes”, SPLoSH). A custom Python script, HapShared, was developed to generate SPLoSH data in apple and sweet cherry. HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops. These distributions were then used to estimate previously unknown relationships. Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data. For cherry, a full-sib relationship was deduced for ‘Emperor Francis, and ‘Schmidt’, a half-sib relationship for ‘Van’ and ‘Windsor’, and the paternal grandparents of ‘Stella’ were confirmed. For apple, 29 cultivars were found to share an unknown parent, the pedigree of the unknown parent of ‘Cox’s Pomona’ was reconstructed, and ‘Fameuse’ was deduced to be a likely grandparent of ‘McIntosh’. Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets, integrated genetic maps, and previously identified pedigree relationships. Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.
Highlights
Pedigree information is of fundamental importance in breeding, genetic studies, genebank germplasm management, and for resolving questions regarding cultivar histories
Reference summed potential lengths of shared haplotypes (SPLoSH) frequency distributions and models Distribution means of SPLoSH values for each examined relationship group in apple
Table S1) generally followed the trend of increasing SPLoSH value with increasingly close relationship levels, and distributions were mostly separated according to the different coefficients of relatedness (COR) values of each relationship level (Fig. 1 for the 25 cM threshold, Fig. S1 for all thresholds, and Table S2 for each SPLoSH value per cultivar pair)
Summary
Pedigree information is of fundamental importance in breeding, genetic studies, genebank germplasm management, and for resolving questions regarding cultivar histories. Many elite individuals and most diversity germplasm of genebank collections have unknown pedigrees. Recorded pedigree information is Howard et al Horticulture Research (2021)8:202 low costs in combination with their abundance, ubiquitous distribution across genomes, and low allele mutation rates. A summary of the methods typically used in pedigree reconstruction studies with SNP data was included in Huisman[7] and Flanagan and Jones[6]. These methods enable identification of parent–offspring relationships, of more distant pedigree relationships such as grandparent–
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