Abstract
Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application in self-incompatible plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European pears (109), and interspecific hybrids (45) were investigated using genotyping-by-sequencing in this study. Fruit phenotypes including fruit weight, firmness, Brix, titratable acidity, and flavor volatiles were measured for genotype-phenotype analyses. The average number of ROH and the average total genomic length of ROH were 6 and 11 Mb, respectively, in Asian accessions, and 13 and 30 Mb, respectively, in European accessions. Significant associations between genomic inbreeding coefficients (FROH) and phenotypes were observed for 23 out of 32 traits analyzed. An overlap between ROH islands and significant markers from genome-wide association analyses was observed. Previously published quantitative trait loci for fruit traits and disease resistances also overlapped with some of the ROH islands. A prominent ROH island at the bottom of linkage group 17 overlapped with a recombination-supressed genomic region harboring the self-incompatibility locus. The observed ROH patterns suggested that systematic breeding of European pears would have started earlier than of Asian pears. Our research suggest that FROH would serve as a novel tool for managing inbreeding in gene-banks of self-incompatible plant species. ROH mapping provides a complementary strategy to unravel the genetic architecture of complex traits, and to evaluate differential selection in outbred plants. This seminal work would provide foundation for the ROH research in self-incompatible plants.
Highlights
Systematic genetic improvement of outbred plants for economically important traits such as yield, consumer acceptance and nutritional value, has led to the loss of genetic diversity within and among accessions in domesticated gene pools (Van de Wouw et al, 2010; Smýkal et al, 2018)
After quality controls, about 8500 single nucleotide polymorphisms (SNPs) distributed across the genome (Supplementary Figure S1) were retained for further analysis
Results from our study suggested that FROH derived from using a high-density genotyping platform would provide a novel tool for managing diversity of plant genetic resources
Summary
Systematic genetic improvement of outbred plants for economically important traits such as yield, consumer acceptance and nutritional value, has led to the loss of genetic diversity within and among accessions in domesticated gene pools (Van de Wouw et al, 2010; Smýkal et al, 2018). Mating among related individuals would lead to inbreeding, which increases the level of homozygosity and Homozygosity Mapping in Outbred Plants reduces recombination frequency in the genome (Charlesworth, 2003). Long tracts of consecutive homozygous segments in the genome can arise through mechanisms such as natural and artificial selection, genetic drift and population bottlenecks (Ceballos et al, 2018). Runs of homozygosity (ROH), first described by Gibson et al (2006), are successive homozygous segments of the genome where the two haplotypes inherited from the parents are identical-by-descent. Long ROH could still be observed in outbred accessions, perhaps due to unusual mutation and recombination suppression at certain genomic locations. ROH mapping allows a comparison of the degree of homozygosity among populations with varying degrees of isolation and inbreeding (Kirin et al, 2010)
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