ArticleNature communications2021
Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- WalnutGDB: an integrated genomic portal for advancing Juglandaceae research and breeding.Horticulture research · 2026Article
- Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae).G3 (Bethesda, Md.) · 2026Article
- Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome.The New phytologist · 2026Article
- A public mid-density genotyping platform for pecan [Carya illinoinensis (Wangenh.) K. Koch].The plant genome · 2026Article
- Genome-wide identification of NAC gene family in pecan and its expression patterns during graft healing.BMC plant biology · 2026Article
- Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes.NAR genomics and bioinformatics · 2026Review
- Plant transcriptome data mining identified twenty-two putative novel taxa in the family Closteroviridae.Archives of virology · 2026Article
- Cell wall remodeling and inositol metabolism coexpression modules associated with nut size in Carya illinoinensis cvs. 'Mahan' and 'Tiny tim'.Scientific reports · 2026Article
- Lipid metabolic pathways and the roles of candidate transcription factors identified via lipidomic and transcriptomic analyses at various stages of seed development in Carya illinoinensis.BMC plant biology · 2026Article
- Chromosome-level genome assembly of the longfin barb (Acrossocheilus longipinnis).Scientific data · 2026Article
- Comprehensive genomic analysis of BAHD gene family: expression patterns during development and stress responses in pecan (Carya illinoinensis).BMC genomics · 2026Article
- Host genotype and environment shape rhizosphere and root microbiome composition of pecan rootstocks.Frontiers in microbiomes · 2026Article
- Comprehensive genomic analysis of the expansin gene family in pecan (Carya illinoinensis) and their transcriptional responses to stresses and fruit abscission.BMC plant biology · 2025Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts.Current biology : CB · 2025Article
- Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants.The Plant cell · 2025Review
- Chromosome-level genome assembly of Jaguar guapote (Parachromis manguensis) by massive parallel sequencing.Scientific data · 2025Article
- Weighted Gene Co-Expression Network Analysis Uncovers Core Drought Responsive Genes in Pecan (Plants (Basel, Switzerland) · 2025Article
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35 authors.
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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.
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