Initiation of genomics-assisted breeding in virginia-type peanuts through the generation of a de novo reference genome and informative markers

Authors: NEWMAN, CASSONDRA - North Carolina State University; ANDRES, RYAN - North Carolina State University; YOUNGBLOOD, RAMEY - Mississippi State University; Campbell, Jacqueline; Simpson, Sheron; Cannon, Steven; Scheffler, Brian; OAKLEY, ANDREW - North Carolina State University; Hulse-Kemp, Amanda; DUNNE, JEFFREY - North Carolina State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/28/2022
Publication Date: 1/27/2023
Citation: Newman, C.S., Andres, R.J., Youngblood, R.C., Campbell, J.D., Simpson, S.A., Cannon, S.B., Scheffler, B.E., Oakley, A.T., Hulse-Kemp, A.M., Dunne, J.C. 2023. Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers. Frontiers in Plant Science. 13.Article 1073542. https://doi.org/10.3389/fpls.2022.1073542.
DOI: https://doi.org/10.3389/fpls.2022.1073542

Interpretive Summary: Peanut is a staple crop that is cultivated and consumed globally as a high-quality source of protein and oil. Peanut is a sustainable source of protein as it is able to grow in poor and sandy soils, contributes to nitrogen fixation, and offers major water use savings when compared to most tree nuts. Virginia-type peanut, is the second largest market class of peanut cultivated in the United States. It is mainly used for large-seeded, in-shell products. Historically, Virginia-type peanut cultivars were developed through conventional plant breeding. Contemporary genomic technologies represent a tremendous opportunity to revolutionize traditional peanut breeding. While there are genomic tools available for wild and cultivated peanuts, none are tailored specifically to Virginia-type peanuts. Here, the first Virginia-type peanut reference genome, was assembled and 1.15 million genomic markers were discovered. Genomic marker data allowed important regions of the genome to be cataloged, some of which are known to confer resistance to one or more peanut pathogens. Furthermore, assays were designed for 111 of these genetic markers for rapid use by the scientific commuity. The findings and tools produced in this research will allow swift response to changing biotic and abiotic threats, and ultimately the development of superior peanuts for public use and consumption.

Technical Abstract: Introduction: Historically, Virginia-type peanut cultivars were developed through recurrent phenotypic selection. Contemporary genomic technologies represent a tremendous opportunity to revolutionize breeding pipeline. While there are genomic tools available for wild and cultivated peanuts, none are tailored specifically to Virginia-type peanuts. Tools to initiate marker assisted selection and genomic selection for Virginia-Type peanut are necessary. Methods: De novo genome assembly was done for flaship Virginia-Type peanut cultivar 'Bailey II'. Whole genome sequencing and variant calling was conducted on 66 relevant peanut lines. Wild species introgressions were cataloged. PCR Allele Competitive Extension assays were created for 111 positions. High quality variants were annotated for use in routine genotyping for genomic selection. Results: The complete Bailey II reference genome consists of 2.56 Gb of sequence in 1,004 contigs. Whole genome sequencing resulted idenitfying 1.15 million SNP markers. Thirty-four wild species introgression blocks were delimited. Forty-thousand markers were annotated as high quality and appropriate for use in genomic selection. Discussion: The first Virginia-type peanut reference genome was assembled, and it represents large improvements in sequence contiguity and quality. The PCR Allele Competitive Extension assays will allow for marker assisted selection of wild species introgression blocks. These markers can be used to rapidly track, delimit, and stack blocks for future research and breeding purposes. A subset of 40,009 high-quality markers were identified for use in a mid-density genotyping system for future genomic selection. With the findings of this study, applied genomics-informed breeding may commence in the NCSU Virginia-type peanut breeding program.