Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar
Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for "Line8," a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.
Authors
- Marshall C. Lamb (ORCID: https://orcid.org/0000-0001-5083-4132)
- John T. Lovell (ORCID: https://orcid.org/0000-0002-8938-1166)
- Avinash Sreedasyam (ORCID: https://orcid.org/0000-0001-7336-7012)
- Charles Y. Chen (ORCID: https://orcid.org/0000-0001-6677-7187)
- Jayson Talag (ORCID: https://orcid.org/0000-0001-6085-214X)
- Paul Grabowski (ORCID: https://orcid.org/0000-0002-4372-0847)
- Jerry Jenkins (ORCID: https://orcid.org/0000-0002-7943-3997)
- Josh Paul Clevenger (ORCID: https://orcid.org/0000-0002-9830-9481)
- C. Corley Holbrook (ORCID: https://orcid.org/0000-0002-7668-0378)
- Jane Grimwood (ORCID: https://orcid.org/0000-0002-8356-8325)
- Jeremy Schmutz (ORCID: https://orcid.org/0000-0001-8062-9172)
- Peggy Ozias‐Akins (ORCID: https://orcid.org/0000-0002-8864-2766)
- Álvaro Sanz‐Sáez (ORCID: https://orcid.org/0000-0002-7754-4618)
- Ye Chu (ORCID: https://orcid.org/0000-0002-8977-7945)
- Phat Dang (ORCID: https://orcid.org/0000-0002-3334-1384)
- Victoria Bunting
- Qiong Zhang (ORCID: https://orcid.org/0000-0001-5001-8434)
- Yucheng Feng (ORCID: https://orcid.org/0000-0001-7748-614X)
- Jenell Webber
Institutions
- Agricultural Research Service (US)
- University of Arizona (US)
- Georgia College & State University (US)
- University of Georgia (US)
- Joint Genome Institute (US)
- HudsonAlpha Institute for Biotechnology (US)
- National Peanut Research Laboratory (US)
- Auburn University (US)
Publication Details
- Journal
- G3 Genes Genomes Genetics
- Published
- 2024-09-01
- DOI
- https://doi.org/10.1093/g3journal/jkae208
- Citations
- 1
- Primary Topic
- Peanut Plant Research Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.60
Funders
- U.S. Department of Energy
- U.S. Department of Agriculture
- Auburn University
- Joint Genome Institute
- National Peanut Board
- National Institute of Food and Agriculture
- Agricultural Research Service