{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T22:45:53Z","timestamp":1776206753011,"version":"3.50.1"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T00:00:00Z","timestamp":1736121600000},"content-version":"vor","delay-in-days":45,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Higher Education Science Research Project of Anhui Province (Natural Sciences Category","award":["2023AH040132"],"award-info":[{"award-number":["2023AH040132"]}]},{"name":"Introduction and Stabilization of Talent Project of Anhui Agricultural University","award":["yj2019-32"],"award-info":[{"award-number":["yj2019-32"]}]},{"name":"Open Fund of Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information","award":["BDSY2023001"],"award-info":[{"award-number":["BDSY2023001"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62102004"],"award-info":[{"award-number":["62102004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Given the adverse effects faced by rice due to abiotic stresses, the precise and rapid identification of single nucleotide polymorphisms (SNPs) associated with abiotic stress traits (ABST-SNPs) in rice is crucial for developing resistant rice varieties. The scarcity of high-quality data related to abiotic stress in rice has hindered the development of computational models and constrained research efforts aimed at rice improvement and breeding. Genome-wide association studies provide a better statistical power to consider ABST-SNPs in rice. Meanwhile, deep learning methods have shown their capability in predicting disease- or phenotype-associated loci, but have primarily focused on human species. Therefore, developing predictive models for identifying ABST-SNPs in rice is both urgent and valuable. In this paper, a model called RiceSNP-ABST is proposed for predicting ABST-SNPs in rice. Firstly, six training datasets were generated using a novel strategy for negative sample construction. Secondly, four feature encoding methods were proposed based on DNA sequence fragments, followed by feature selection. Finally, convolutional neural networks with residual connections were used to determine whether the sequences contained rice ABST-SNPs. RiceSNP-ABST outperformed traditional machine learning and state-of-the-art methods on the benchmark dataset and demonstrated consistent generalization on an independent dataset and cross-species datasets. Notably, multi-granularity causal structure learning was employed to elucidate the relationships among DNA structural features, aiming to identify key genetic variants more effectively. The web-based tool for the RiceSNP-ABST can be accessed at http:\/\/rice-snp-abst.aielab.cc.<\/jats:p>","DOI":"10.1093\/bib\/bbae702","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T05:15:33Z","timestamp":1736140533000},"source":"Crossref","is-referenced-by-count":6,"title":["RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-6802-0443","authenticated-orcid":false,"given":"Quan","family":"Lu","sequence":"first","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-0712-0167","authenticated-orcid":false,"given":"Jiajun","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renyi","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hangcheng","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meng","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoshuang","family":"Liu","sequence":"additional","affiliation":[{"name":"Research Center for Biological Breeding Technology , Advance Academy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui Province 230036,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9370-2540","authenticated-orcid":false,"given":"Zhenyu","family":"Yue","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Research Center for Biological Breeding Technology , Advance Academy, , 130, Changjiang West Road, Hefei, Anhui Province 230036 ,","place":["China"]},{"name":"Anhui Agricultural University , Advance Academy, , 130, Changjiang West Road, Hefei, Anhui Province 230036 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