Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

John T. Lovell (), Nolan B. Bentley, Gaurab Bhattarai, Jerry W. Jenkins, Avinash Sreedasyam, Yanina Alarcon, Clive Bock, Lori Beth Boston, Joseph Carlson, Kimberly Cervantes, Kristen Clermont, Sara Duke, Nick Krom, Keith Kubenka, Sujan Mamidi, Christopher P. Mattison, Maria J. Monteros, Cristina Pisani, Christopher Plott, Shanmugam Rajasekar, Hormat Shadgou Rhein, Charles Rohla, Mingzhou Song, Rolston St. Hilaire, Shengqiang Shu, Lenny Wells, Jenell Webber, Richard J. Heerema, Patricia E. Klein, Patrick Conner, Xinwang Wang, L. J. Grauke, Jane Grimwood, Jeremy Schmutz () and Jennifer J. Randall ()
Additional contact information
John T. Lovell: HudsonAlpha Institute for Biotechnology
Nolan B. Bentley: Texas A&M University
Gaurab Bhattarai: Genetics & Genomics, University of Georgia
Jerry W. Jenkins: HudsonAlpha Institute for Biotechnology
Avinash Sreedasyam: HudsonAlpha Institute for Biotechnology
Yanina Alarcon: Noble Research Institute
Clive Bock: USDA Southeastern Fruit and Tree Nut Research Laboratory
Lori Beth Boston: HudsonAlpha Institute for Biotechnology
Joseph Carlson: DOE Joint Genome Institute
Kimberly Cervantes: New Mexico State University
Kristen Clermont: USDA-ARS Food Processing and Sensory Quality Research
Sara Duke: USDA-ARS Plains Area Administrative Office
Nick Krom: Noble Research Institute
Keith Kubenka: USDA Pecan Breeding and Genetics
Sujan Mamidi: HudsonAlpha Institute for Biotechnology
Christopher P. Mattison: USDA-ARS Food Processing and Sensory Quality Research
Maria J. Monteros: Noble Research Institute
Cristina Pisani: USDA Southeastern Fruit and Tree Nut Research Laboratory
Christopher Plott: HudsonAlpha Institute for Biotechnology
Shanmugam Rajasekar: University of Arizona
Hormat Shadgou Rhein: New Mexico State University
Charles Rohla: Noble Research Institute
Mingzhou Song: New Mexico State University
Rolston St. Hilaire: New Mexico State University
Shengqiang Shu: DOE Joint Genome Institute
Lenny Wells: University of Georgia-Tifton Campus
Jenell Webber: HudsonAlpha Institute for Biotechnology
Richard J. Heerema: New Mexico State University
Patricia E. Klein: Texas A&M University
Patrick Conner: University of Georgia-Tifton Campus
Xinwang Wang: USDA Pecan Breeding and Genetics
L. J. Grauke: USDA Pecan Breeding and Genetics
Jane Grimwood: HudsonAlpha Institute for Biotechnology
Jeremy Schmutz: HudsonAlpha Institute for Biotechnology
Jennifer J. Randall: New Mexico State University

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-24328-w

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