Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

Authors: GRABOWSKI, PAUL - Hudsonalpha Institute For Biotechnology; Dang, Phat; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; SREEDASYAM, AVINASH - Hudsonalpha Institute For Biotechnology; WEBBER, JENELL - Hudsonalpha Institute For Biotechnology; Lamb, Marshall; ZHANG, QIONG - Auburn University; SANZ-SAEZ, ALVARO - Auburn University; FENG, YUCHENG - Auburn University; BUNTING, VICTORIA - University Of Arizona; TALAG, JAYSON - University Of Arizona; CLEVENGER, JOSHUA - Hudsonalpha Institute For Biotechnology; OZIAS-AKINS, PEGGY - University Of Georgia; Holbrook, Carl - Corley; CHU, YE - University Of Georgia; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; CHEN, CHARLES - Auburn University; LOVELL, JOHN - Hudsonalpha Institute For Biotechnology

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/26/2024
Publication Date: 9/1/2024
Citation: Grabowski, P., Dang, P.M., Jenkins, J., Sreedasyam, A., Webber, J., Lamb, M.C., Zhang, Q., Sanz-Saez, A., Feng, Y., Bunting, V., Talag, J., Clevenger, J., Ozias-Akins, P., Holbrook Jr, C.C., Chu, Y., Grimwood, J., Schmutz, J., Chen, C., Lovell, J. 2024. Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar. G3, Genes/Genomes/Genetics. 14(11).Article jkae208. https://doi.org/10.1093/g3journal/jkae208.
DOI: https://doi.org/10.1093/g3journal/jkae208

Interpretive Summary: Peanut is a globally important oil and food crop frequently grown in dry environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here we present the genome sequencing, assembly, and gene association for 'Line8', a peanut line bred from drought tolerant cultivars. Our assembly and annotation have the longest sequencing stretches and the most complete peanut genome resources available. The high quality and length of sequencing of the Line8 assembly allowed us to explore genome structural variation both between peanut lines and within their respective genomes. We detect several large deoxyribonucleic acid (DNA) segment exchanges between Line8 and other peanut genome assemblies, and there is a trend for increased exchange rate between more genetically diverged peanut lines. Unexpectedly, we discovered that Line8 harbors a large section of DNA exchange from Arachis cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both genetically different peanut lines in this observed genetic exchange provide the first characterization of Arachis cardenasii candidate genetic variations 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.

Technical Abstract: Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid and semi-arid 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 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 discovered that Line8 harbors an introgression from Arachis 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 Arachis 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.