@article{suppa_andres_dunne_arram_morgan_chen_2024, title={Autotetraploid Induction of Three A-Genome Wild Peanut Species, <i>Arachis cardenasii</i>, <i>A. correntina</i>, and <i>A. diogoi</i>}, volume={15}, ISSN={["2073-4425"]}, url={https://www.mdpi.com/2073-4425/15/3/303}, DOI={10.3390/genes15030303}, abstractNote={A-genome Arachis species (AA; 2n = 2x = 20) are commonly used as secondary germplasm sources in cultivated peanut breeding, Arachis hypogaea L. (AABB; 2n = 4x = 40), for the introgression of various biotic and abiotic stress resistance genes. Genome doubling is critical to overcoming the hybridization barrier of infertility that arises from ploidy-level differences between wild germplasm and cultivated peanuts. To develop improved genome doubling methods, four trials of various concentrations of the mitotic inhibitor treatments colchicine, oryzalin, and trifluralin were tested on the seedlings and seeds of three A-genome species, A. cardenasii, A. correntina, and A. diogoi. A total of 494 seeds/seedlings were treated in the present four trials, with trials 1 to 3 including different concentrations of the three chemical treatments on seedlings, and trial 4 focusing on the treatment period of 5 mM colchicine solution treatment of seeds. A small number of tetraploids were produced from the colchicine and oryzalin gel treatments of seedlings, but all these tetraploid seedlings reverted to diploid or mixoploid states within six months of treatment. In contrast, the 6-h colchicine solution treatment of seeds showed the highest tetraploid conversion rate (6–13% of total treated seeds or 25–40% of surviving seedlings), and the tetraploid plants were repeatedly tested as stable tetraploids. In addition, visibly and statistically larger leaves and flowers were produced by the tetraploid versions of these three species compared to their diploid versions. As a result, stable tetraploid plants of each A-genome species were produced, and a 5 mM colchicine seed treatment is recommended for A-genome and related wild Arachis species genome doubling.}, number={3}, journal={GENES}, author={Suppa, Robert W. and Andres, Ryan J. and Dunne, Jeffrey C. and Arram, Ramsey F. and Morgan, Thomas B. and Chen, Hsuan}, year={2024}, month={Mar} }
 @article{jones_andres_owen_dunne_contreras_cahoon_jennings_leon_everman_2023, title={Confirmation of a five-way herbicide-resistant Amaranthus tuberculatus population in North Carolina}, volume={7}, ISSN={["1365-3180"]}, url={https://doi.org/10.1111/wre.12590}, DOI={10.1111/wre.12590}, abstractNote={Abstract}, journal={WEED RESEARCH}, author={Jones, Eric A. L. and Andres, Ryan J. and Owen, Micheal D. K. and Dunne, Jeffrey C. and Contreras, Diego J. and Cahoon, Charles W. and Jennings, Katherine M. and Leon, Ramon G. and Everman, Wesley J.}, year={2023}, month={Jul} }
 @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.}, 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={Abstract}, 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} }
 @article{andres_dunne_2022, title={Understanding variation in oleic acid content of high-oleic virginia-type peanut}, volume={8}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-022-04190-0}, abstractNote={Contamination at the FAD2B locus due to inadequate screening protocols is the primary cause of sporadic, insufficient oleic acid content in Virginia-type peanut. The high oleic trait in peanut is conditioned by loss-of-function mutations in a pair of homeologous enzymes and is well known to improve the shelf life of peanut products. As such, the trait is given high priority in current and future cultivars by the North Carolina State University peanut breeding program. For unknown reasons, high oleic cultivars and breeding lines intermittently failed to meet self-imposed thresholds for oleic acid content in internal testing. To determine why, a manual seed chipper, crude DNA isolation protocol, genotyping assays for both mutations, and a web-based SNP calling application were developed. The primary cause was determined to be contamination with normal oleic seeds resulting from inadequate screening protocols. In order to correct the problem, a faster screening method was acquired to accommodate a higher oleic acid threshold. Additionally, results showed the mutation in one homeolog is fixed in the program, dig date had no significant effect on oleic acid content, and minor modifiers segregating within the program explained 6% of the variation in oleic acid content.}, journal={THEORETICAL AND APPLIED GENETICS}, author={Andres, R. J. and Dunne, J. C.}, year={2022}, month={Aug} }
 @article{zhu_andres_zhang_kuraparthy_2021, title={High-density linkage map construction and QTL analysis of fiber quality and lint percentage in tetraploid cotton}, volume={7}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20519}, abstractNote={Abstract}, journal={CROP SCIENCE}, author={Zhu, Linglong and Andres, Ryan J. and Zhang, Kuang and Kuraparthy, Vasu}, year={2021}, month={Jul} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2017, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, DOI={10.1101/062612}, abstractNote={Abstract}, number={1}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Andres, R. J. and Coneva, V. and Frank, M. H. and Tuttle, J. R. and Samayoa, L. F. and Han, S. W. and Kaur, B. and Zhu, L. L. and Fang, Hui and Bowman, D. T. and et al.}, year={2017}, pages={E57–66} }
 @article{kaur_andres_kuraparthy_2016, title={Major Leaf Shape Genes, Laciniate in Diploid Cotton and Okra in Polyploid Upland Cotton, Map to an Orthologous Genomic Region}, volume={56}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2015.10.0627}, abstractNote={Gossypium arboreum L, which produces spinnable cotton fibers, is an A‐genome diploid progenitor species of tetraploid cotton. With its diploid genome, publicly available genome sequence, adapted growth, and developmental and agronomic attributes, G. arboreum could make an ideal cotton species to study the genetic basis of biological traits that are controlled by orthologous loci in diploid and polyploid species. Leaf shape is an important agronomic trait in cotton. Normal, subokra, okra, and laciniate are the predominant leaf shapes in cotton cultivars. Laciniate in diploids is phenotypically similar to okra leaf shape in tetraploid. In the present study, a population of 135 F2 plants derived from accessions NC 501 and NC 505 was used for genetic and molecular mapping of laciniate leaf shape in diploid cotton (G. arboreum). An inheritance study showed that laciniate leaf shape was controlled by a single incompletely dominant gene (LL–A2). Molecular genetic mapping using simple‐sequence repeat (SSR) markers placed the leaf shape locus L‐A2 on chromosome 2. Targeted mapping using putative genes from the delineated region established that laciniate leaf shape in G. arboreum and okra leaf shape in Gossypium hirsutum L. were controlled by genes at orthologous loci. Collinearity was well conserved between the diploid A‐ (G. arboreum) and D‐ (G. raimondii Ulbr.) genomes in the targeted genomic region narrowing the candidate region for the leaf shape locus (L‐A2) to nine putative genes. Establishing the orthologous genomic region for the L loci could help use the diploid cotton resources toward map‐based cloning of leaf shape genes in Gossypium.}, number={3}, journal={CROP SCIENCE}, author={Kaur, Baljinder and Andres, Ryan and Kuraparthy, Vasu}, year={2016}, pages={1095–1105} }
 @article{andres_bowman_kaur_kuraparthy_2014, title={Mapping and genomic targeting of the major leaf shape gene (L) in Upland cotton (Gossypium hirsutum L.)}, volume={127}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-013-2208-4}, abstractNote={A major leaf shape locus (L) was mapped with molecular markers and genomically targeted to a small region in the D-genome of cotton. By using expression analysis and candidate gene mapping, two LMI1 -like genes are identified as possible candidates for leaf shape trait in cotton. Leaf shape in cotton is an important trait that influences yield, flowering rates, disease resistance, lint trash, and the efficacy of foliar chemical application. The leaves of okra leaf cotton display a significantly enhanced lobing pattern, as well as ectopic outgrowths along the lobe margins when compared with normal leaf cotton. These phenotypes are the hallmark characteristics of mutations in various known modifiers of leaf shape that culminate in the mis/over-expression of Class I KNOX genes. To better understand the molecular and genetic processes underlying leaf shape in cotton, a normal leaf accession (PI607650) was crossed to an okra leaf breeding line (NC05AZ21). An F2 population of 236 individuals confirmed the incompletely dominant single gene nature of the okra leaf shape trait in Gossypium hirsutum L. Molecular mapping with simple sequence repeat markers localized the leaf shape gene to 5.4 cM interval in the distal region of the short arm of chromosome 15. Orthologous mapping of the closely linked markers with the sequenced diploid D-genome (Gossypium raimondii) tentatively resolved the leaf shape locus to a small genomic region. RT-PCR-based expression analysis and candidate gene mapping indicated that the okra leaf shape gene (L (o) ) in cotton might be an upstream regulator of Class I KNOX genes. The linked molecular markers and delineated genomic region in the sequenced diploid D-genome will assist in the future high-resolution mapping and map-based cloning of the leaf shape gene in cotton.}, number={1}, journal={THEORETICAL AND APPLIED GENETICS}, author={Andres, Ryan J. and Bowman, Daryl T. and Kaur, Baljinder and Kuraparthy, Vasu}, year={2014}, month={Jan}, pages={167–177} }