{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,3]],"date-time":"2026-05-03T11:11:23Z","timestamp":1777806683438,"version":"3.51.4"},"reference-count":34,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2023,10,9]],"date-time":"2023-10-09T00:00:00Z","timestamp":1696809600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["advanced.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Advanced Intelligent Systems"],"published-print":{"date-parts":[[2023,12]]},"abstract":"<jats:p>\nMachine learning (ML) is one of the core driving forces for the next breeding stage, and Breeding 4.0. Genotype matrix based on single\u2010nucleotide polymorphisms (SNPs) is often used in ML for genome\u2010to\u2010phenotype prediction. Genotype matrix has an inherent defect, as the feature spaces it generates across different individuals or groups are inconsistent, and this hinders the application of ML. To overcome the challenge, a genome descriptor, Genic SNPs Composition Tool (GSCtool) is developed, which counts the number of SNPs in each gene of the genome so the dimension of the feature vectors equals the number of annotated genes in a species. Compared to using the genotype matrix, using GSCtool significantly decreases the model training time and has a higher accuracy of phenotype prediction. GSCtool also achieves good performance in variety identification, which is useful in crop variety protection. In general, GSCtool will help facilitate the application and study of genomic ML. The source code and test data of GSCtool are freely available at https:\/\/github.com\/SZJhacker\/GSCtool and https:\/\/gitee.com\/shenzijie\/GSCtool.<\/jats:p>","DOI":"10.1002\/aisy.202300426","type":"journal-article","created":{"date-parts":[[2023,10,9]],"date-time":"2023-10-09T15:42:37Z","timestamp":1696866157000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["GSCtool: A Novel Descriptor that Characterizes the Genome for Applying Machine Learning in Genomics"],"prefix":"10.1002","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1410-3038","authenticated-orcid":false,"given":"Zijie","family":"Shen","sequence":"first","affiliation":[{"name":"Hainan Institute Zhejiang University  Sanya 572025 China"},{"name":"Institute of Crop Science &amp; Institute of Bioinformatics College of Agriculture &amp; Biotechnology Zhejiang University  Hangzhou 310058 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7587-5771","authenticated-orcid":false,"given":"Enhui","family":"Shen","sequence":"additional","affiliation":[{"name":"Institute of Crop Science &amp; Institute of Bioinformatics College of Agriculture &amp; Biotechnology Zhejiang University  Hangzhou 310058 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6505-7417","authenticated-orcid":false,"given":"Qian-Hao","family":"Zhu","sequence":"additional","affiliation":[{"name":"CSIRO Agriculture and Food  GPO Box 1700 Canberra ACT 2601 Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4846-0500","authenticated-orcid":false,"given":"Longjiang","family":"Fan","sequence":"additional","affiliation":[{"name":"Hainan Institute Zhejiang University  Sanya 572025 China"},{"name":"Institute of Crop Science &amp; Institute of Bioinformatics College of Agriculture &amp; Biotechnology Zhejiang University  Hangzhou 310058 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Yangtze Delta Region Institute (Quzhou) University of Electronic Science and Technology of China  Quzhou 324003 China"},{"name":"Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of China  Chengdu 610054 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chu-Yu","family":"Ye","sequence":"additional","affiliation":[{"name":"Institute of Crop Science &amp; Institute of Bioinformatics College of Agriculture &amp; Biotechnology Zhejiang University  Hangzhou 310058 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,10,9]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-120116-024846"},{"key":"e_1_2_8_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tplants.2022.08.018"},{"key":"e_1_2_8_2_3","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-07319-x"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s43016-021-00400-y"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/hdy.2017.4"},{"key":"e_1_2_8_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25893-w"},{"key":"e_1_2_8_4_3","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02492-y"},{"key":"e_1_2_8_4_4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0273293"},{"key":"e_1_2_8_4_5","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2020.03.002"},{"key":"e_1_2_8_4_6","doi-asserted-by":"publisher","DOI":"10.1534\/g3.119.400498"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.566796"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty140"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11427-019-1682-6"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3007"},{"key":"e_1_2_8_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7258"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab951"},{"key":"e_1_2_8_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1112"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01644"},{"key":"e_1_2_8_11_1","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2001-2-5-preprint0004","volume":"2","author":"Malek J. 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