@article{newman_andres_youngblood_campbell_simpson_cannon_scheffler_oakley_hulse-kemp_dunne_2023, title={Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.1073542}, abstractNote={IntroductionVirginia-type peanut, Arachis hypogaea subsp. hypogaea, 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 long-term recurrent phenotypic selection and wild species introgression projects. Contemporary genomic technologies represent a unique opportunity to revolutionize the traditional breeding pipeline. While there are genomic tools available for wild and cultivated peanuts, none are tailored specifically to applied Virginia-type cultivar development programs.Methods and respective resultsHere, the first Virginia-type peanut reference genome, “Bailey II”, was assembled. It has improved contiguity and reduced instances of manual curation in chromosome arms. Whole-genome sequencing and marker discovery was conducted on 66 peanut lines which resulted in 1.15 million markers. The high marker resolution achieved allowed 34 unique wild species introgression blocks to be cataloged in the A. hypogaea genome, some of which are known to confer resistance to one or more pathogens. To enable marker-assisted selection of the blocks, 111 PCR Allele Competitive Extension assays were designed. Forty thousand high quality markers were selected from the full set that are suitable for mid-density genotyping for genomic selection. Genomic data from representative advanced Virginia-type peanut lines suggests this is an appropriate base population for genomic selection.DiscussionThe findings and tools produced in this research will allow for rapid genetic gain in the Virginia-type peanut population. Genomics-assisted breeding will allow swift response to changing biotic and abiotic threats, and ultimately the development of superior cultivars for public use and consumption.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Newman, Cassondra S. S. and Andres, Ryan J. J. and Youngblood, Ramey C. C. and Campbell, Jacqueline D. D. and Simpson, Sheron A. A. and Cannon, Steven B. B. and Scheffler, Brian E. E. and Oakley, Andrew T. T. and Hulse-Kemp, Amanda M. M. and Dunne, Jeffrey C. C.}, year={2023}, month={Jan} }
 @article{fritz_dean_hendrix_andres_newman_oakley_clevenger_dunne_2022, title={Flavor quality and composition of accession resources in the North Carolina State University peanut breeding program}, volume={7}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20774}, abstractNote={AbstractPlant breeders often focus on production traits such as yield and disease resistance, whereas quality traits such as flavor are given low priority. Food manufacturers and consumers have expressed interest in superior flavor experiences suggesting that flavor attributes should play a more prominent role in selection. Flavor attributes were evaluated among a subset of the North Carolina State University (NCSU) peanut germplasm collection to simplify flavor analysis and selection, confirm a recent lack of progress in flavor improvement and identify new sources of flavor improvement in Virginia‐type peanut (Arachis hypogaea L.). Multivariate and principal component analysis identified 11 flavor attributes and five principal components that should facilitate selection of improved peanut flavor. Analysis of historical variety trial data identified a significant deterioration in the roast peanut flavor and a modest improvement in other critical flavor attributes over the last 20 yr. Based on these findings, the accessions ‘Chimera’ and ‘NC Bunch’ were chosen to initiate a crossing program to develop Virginia‐type peanut cultivars with improved roast peanut flavor.}, journal={CROP SCIENCE}, author={Fritz, Katelyn R. and Dean, Lisa L. and Hendrix, Keith W. and Andres, Ryan J. and Newman, Cassondra S. and Oakley, Andrew T. and Clevenger, Josh P. and Dunne, Jeffrey C.}, year={2022}, month={Jul} }