Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding
Open Access
- 5 July 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Communications
- Vol. 12 (1), 1-12
- https://doi.org/10.1038/s41467-021-24328-w
Abstract
Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.This publication has 88 references indexed in Scilit:
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution, 2013
- STAR: ultrafast universal RNA-seq alignerBioinformatics, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- The Arabidopsis Information Resource (TAIR): improved gene annotation and new toolsNucleic Acids Research, 2011
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing dataBioinformatics, 2011
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- The Sorghum bicolor genome and the diversification of grassesNature, 2009
- Improving the Arabidopsis genome annotation using maximal transcript alignment assembliesNucleic Acids Research, 2003
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002