Together, these findings reveal the long-term consequences of repeated selection on standing variation during crop improvement and trace inheritance of ancestral genomic regions across historical and contemporary germplasm.
Abstract
Canola breeding has been shaped by strong selection for oil quality, yet the origins of the known oil quality alleles and genomic consequences of their selection are not fully resolved. By integrating pedigree reconstruction with graph pan-genomics we trace inheritance of ancestral genomic regions across historical and contemporary germplasm. Surrounding the low erucic acid allele in BnA08.FAE1, we identify a 17.23 Mb haplotype that approached fixation in Australian canola in the early 2000s. Contradicting the prevailing model, this haplotype predates modern breeding and was likely widespread in ancestral B. napus in the early 1900s. Genomic analyses implicate centromeric recombination suppression and structural variation in its long-term persistence, which has led to megabase-scale diversity loss through hitchhiking of neighbouring alleles. The haplotype contains extensive structural variation and multiple alleles associated with polygenic disease resistance. Together, these findings reveal the long-term consequences of repeated selection on standing variation during crop improvement.
A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning all 10 recognized tetraploid wheat subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.
This study elucidated the genetic basis of Tropical-Temperate Integration, and established a rigorous, structural-aware framework for decoding the hidden variations that drive modern crop improvement.
Tetraploid potato is the most important vegetable food crop in the world. However, genetic gains from modern breeding efforts have been limited due to tetrasomic inheritance, the accumulation of deleterious mutations during domestication, and subsequent clonal propagation during modern breeding. In this study, we analyzed previously identified evolutionarily constrained genomic regions in the potato genome relative to a breeding panel of tetraploid potato clones derived from elite cultivars (the MASPOT panel). We demonstrate a significant association between derived allele frequency (DAF) and both positive (constrained) and negative (excess of substitutions relative to neutrality, i.e., hypervariable) nucleotide conservation scores (GERP scores) in the breeding panel, indicating that negative GERP scores can annotate sites affected by positive selection or other non-neutral processes affecting population allele frequency. The deep phylogeny approach can be leveraged to alleviate inbreeding in potatoes through the qualification of causative alleles in tetraploids, offering a valuable resource for potato genetic improvement by molecular breeding. Estimates of genetic load within the tetraploid clones reveal that heterozygous loads vastly exceed homozygous loads for deleterious alleles, consistent with masking of recessive mutations. Deleterious load was significantly correlated with several trait phenotypes but did not improve prediction accuracy of any traits in the tetraploid panel. This could be due to the increased complexity of tetrasomic inheritance, including more effective load complementation, and/or a higher proportion of heterozygosity in tetraploid compared to diploid potato. Intriguingly, the hypervariable load correlated significantly with several phenotypes and improved genomic prediction accuracy of yield by 5% relative to a negative control (permuted loads). This indicates that the inferred hypervariable sites from Solanaceae evolutionary information may contain genetic information relevant for breeding, and that, in contrast to current practice, it is relevant to include and further explore sites with negative GERP scores in general.
Genetics may help address the biodiversity crisis by providing information about genetic diversity and temporal changes in demography for species of interest. Advances in whole-genome sequencing create new opportunities for demographic analysis, even based on the two copies of a genome found in a single diploid individual. The Vertebrate Genomes Project (VGP) is generating high-quality, chromosome-level reference genomes across the full range of extant vertebrate species, with its first phase delivering assemblies spanning approximately 95% of vertebrate orders. Using 512 diploid VGP genomes, we quantified intra-species heterozygosity, runs of homozygosity (ROH), and inferred past effective population sizes (Ne) with the Pairwise Sequentially Markovian Coalescent (PSMC). Threatened species are more likely to exhibit lower heterozygosity and longer ROH, though there is large variation in both measures across all IUCN categories. Interestingly, PSMC suggests that estimated historical Ne several thousand generations ago is a better predictor of threatened status than the present day estimate. Co-analysing with life history traits, we found that marine species tend to have lower ROH content, while fossorial species show significantly higher inbreeding levels. Indeed, habitat and foraging strata are much stronger predictors of IUCN status than genetics, with estimated historical Ne providing a small but significant amount of additional information. Together, these results suggest that, while measures of genetic diversity are correlated with IUCN status, much of that correlation may derive from ecological factors such as habitat, with only a relatively small direct contribution. Nevertheless, reference genomes like those generated by the VGP can yield valuable information, like historical Ne, while facilitating population monitoring and management for species of interest.
