@article{massa_sobolev_faustinelli_tallury_stalker_lamb_arias_2024, title={Genetic diversity, disease resistance, and environmental adaptation of <i>Arachis duranensis </i>L.: New insights from landscape genomics}, volume={19}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0299992}, abstractNote={The genetic diversity that exists in natural populations of Arachis duranensis , the wild diploid donor of the A subgenome of cultivated tetraploid peanut, has the potential to improve crop adaptability, resilience to major pests and diseases, and drought tolerance. Despite its potential value for peanut improvement, limited research has been focused on the association between allelic variation, environmental factors, and response to early (ELS) and late leaf spot (LLS) diseases. The present study implemented a landscape genomics approach to gain a better understanding of the genetic variability of A . duranensis represented in the ex-situ peanut germplasm collection maintained at the U.S. Department of Agriculture, which spans the entire geographic range of the species in its center of origin in South America. A set of 2810 single nucleotide polymorphism (SNP) markers allowed a high-resolution genome-wide characterization of natural populations. The analysis of population structure showed a complex pattern of genetic diversity with five putative groups. The incorporation of bioclimatic variables for genotype-environment associations, using the latent factor mixed model (LFMM2) method, provided insights into the genomic signatures of environmental adaptation, and led to the identification of SNP loci whose allele frequencies were correlated with elevation, temperature, and precipitation-related variables ( q < 0.05). The LFMM2 analysis for ELS and LLS detected candidate SNPs and genomic regions on chromosomes A02, A03, A04, A06, and A08. These findings highlight the importance of the application of landscape genomics in ex situ collections of peanut and other crop wild relatives to effectively identify favorable alleles and germplasm for incorporation into breeding programs. We report new sources of A . duranensis germplasm harboring adaptive allelic variation, which have the potential to be utilized in introgression breeding for a single or multiple environmental factors, as well as for resistance to leaf spot diseases.}, number={4}, journal={PLOS ONE}, author={Massa, Alicia N. and Sobolev, Victor S. and Faustinelli, Paola C. and Tallury, Shyamalrau P. and Stalker, H. Thomas and Lamb, Marshall C. and Arias, Renee S.}, year={2024}, month={Apr} }
 @article{leal-bertioli_blas_carolina chavarro_simpson_valls_tallury_moretzsohn_custodio_thomas stalker_seijo_et al._2024, title={Relationships of the wild peanut species, section <i>Arachis</i>: A resource for botanical classification, crop improvement, and germplasm management}, ISSN={["1537-2197"]}, DOI={10.1002/ajb2.16357}, abstractNote={Abstract Premise Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea . Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification. Methods Using a high‐density array, we genotyped 272 accessions encompassing all diploid species in section Arachis . Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators. Results Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto‐domesticate A. stenosperma . However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus . We suggest new species assignments for several accessions. Conclusions Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer.}, journal={AMERICAN JOURNAL OF BOTANY}, author={Leal-Bertioli, Soraya C. M. and Blas, Francisco J. and Carolina Chavarro, M. and Simpson, Charles E. and Valls, Jose F. M. and Tallury, Shyam P. and Moretzsohn, Marcio C. and Custodio, Adriana R. and Thomas Stalker, H. and Seijo, Guillermo and et al.}, year={2024}, month={Jun} }
 @article{levinson_bertioli_chu_hopkins_leal-bertioli_stalker_gao_ozias-akins_2021, title={Development and applications of KASP markers distinguishing A- and B/K-genomes of Arachis}, volume={217}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-021-02923-8}, number={10}, journal={EUPHYTICA}, author={Levinson, Chandler M. and Bertioli, David and Chu, Ye and Hopkins, Mark and Leal-Bertioli, Soraya C. M. and Stalker, H. Thomas and Gao, Dongying and Ozias-Akins, Peggy}, year={2021}, month={Oct} }
 @misc{stalker_warburton_harlan_2021, title={Harlan's Crops and Man}, ISBN={9780891186335 9780891186342}, ISSN={2691-2341}, url={http://dx.doi.org/10.1002/9780891186342}, DOI={10.1002/9780891186342}, journal={ASA, CSSA, and SSSA Books}, publisher={Wiley}, author={Stalker, H. Thomas and Warburton, Marilyn L. and Harlan, Jack R.}, year={2021}, month={Mar} }
 @article{chu_bertioli_levinson_stalker_holbrook_ozias-akins_2021, title={Homoeologous recombination is recurrent in the nascent synthetic allotetraploid Arachis ipaensis x Arachis correntina(4x) and its derivatives}, volume={11}, ISSN={["2160-1836"]}, DOI={10.1093/g3journal/jkab066}, abstractNote={Abstract}, number={4}, journal={G3-GENES GENOMES GENETICS}, author={Chu, Ye and Bertioli, David and Levinson, Chandler M. and Stalker, H. Thomas and Holbrook, C. Corley and Ozias-Akins, Peggy}, year={2021}, month={Apr} }
 @article{bertioli_clevenger_godoy_stalker_wood_santos_ballen-taborda_abernathy_azevedo_campbell_et al._2021, title={Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange}, volume={118}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.2104899118}, abstractNote={Significance}, number={38}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Bertioli, David J. and Clevenger, Josh and Godoy, Ignacio J. and Stalker, H. T. and Wood, Shona and Santos, Joao F. and Ballen-Taborda, Carolina and Abernathy, Brian and Azevedo, Vania and Campbell, Jacqueline and et al.}, year={2021}, month={Sep} }
 @article{levinson_chu_luo_stalker_gao_holbrook_ozias-akins_2021, title={Morphological and reproductive characterization of nascent allotetraploids cross-compatible with cultivated peanut (Arachis hypogaea L.)}, volume={68}, ISSN={["1573-5109"]}, DOI={10.1007/s10722-021-01161-0}, abstractNote={Abstract}, number={7}, journal={GENETIC RESOURCES AND CROP EVOLUTION}, author={Levinson, Chandler and Chu, Ye and Luo, Xuelin and Stalker, H. Thomas and Gao, Dongying and Holbrook, C. Corley and Ozias-Akins, Peggy}, year={2021}, month={Oct}, pages={2883–2896} }
 @article{chu_stalker_marasigan_levinson_gao_bertioli_leal-bertioli_holbrook_jackson_ozias-akins_2021, title={Registration of three peanut allotetraploid interspecific hybrids resistant to late leaf spot disease and tomato spotted wilt}, ISSN={["1940-3496"]}, DOI={10.1002/plr2.20146}, abstractNote={Abstract}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Chu, Ye and Stalker, H. Thomas and Marasigan, Kathleen and Levinson, Chandler M. and Gao, Dongying and Bertioli, David J. and Leal-Bertioli, Soraya C. M. and Holbrook, C. Corley and Jackson, Scott A. and Ozias-Akins, Peggy}, year={2021}, month={Aug} }
 @article{jordan_dunne_stalker_shew_brandenburg_anco_mehl_taylor_balota_2020, title={Risk to sustainability of pest management tools in peanut}, volume={5}, ISSN={["2471-9625"]}, DOI={10.1002/ael2.20018}, abstractNote={Abstract}, number={1}, journal={AGRICULTURAL & ENVIRONMENTAL LETTERS}, author={Jordan, David L. and Dunne, Jeffrey and Stalker, H. Thomas and Shew, Barbara B. and Brandenburg, Rick L. and Anco, Dan and Mehl, Hillary and Taylor, Sally and Balota, Maria}, year={2020} }
 @article{tonnis_wang_tallury_tishchenko_stalker_2019, title={Identification of a mutant from Arachis veigae with enhanced seed oleic and very long-chain fatty acid content}, volume={62}, ISSN={["2468-0842"]}, DOI={10.1186/s13765-019-0420-x}, abstractNote={High oleate is an important seed quality trait frequently incorporated in peanut varieties. Crop wild relatives (CWR) are potentially useful genetic resources for cultivar improvement through genetic introgression; but for wild peanut species, many chemical or nutritional traits are not well characterized. A mutant from Arachis veigae S. H. Santana & Valls (2n = 2x = 20), with increased oleic and very long chain (C ≥ 22) fatty acid content was identified from screening 209 accessions of 45 species using gas chromatography (GC). The A. veigae (formerly A. sylvestris) accession, VVeSv 8373 (PI 688970) contained 55.5% oleic acid in seeds, significantly higher than the average (18.3%) of other accessions within the same species and also significantly higher than the average (37.0%) of all wild peanut accessions evaluated. A C37T substitution was identified by sequencing the coding region of FAD2H, resulting in the nonsense mutation of Q13* (a premature stop codon). This functional mutation may significantly reduce the fatty acid desaturase (FAD) activity and result in the enhanced oleate level. Arachis veigae also contained a high percentage of very long-chain (C ≥ 22) fatty acids, and their variation identified in this study is also discussed and compared with other species. The mutant with such an altered fatty acid composition may be useful for potentially improving seed or food nutrition quality.}, journal={APPLIED BIOLOGICAL CHEMISTRY}, author={Tonnis, Brandon and Wang, Ming Li and Tallury, Shyam and Tishchenko, Viktor and Stalker, H. Thomas}, year={2019}, month={Mar} }