{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T07:45:37Z","timestamp":1782287137448,"version":"3.54.5"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T00:00:00Z","timestamp":1695340800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFD1201502"],"award-info":[{"award-number":["2022YFD1201502"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. Addressing this biological complexity requires innovative and accurate tools for trait prediction. In response to this challenge, we have developed SoyDNGP, a deep learning-based model that offers significant advancements in the field of soybean trait prediction. Compared to existing methods, such as DeepGS and DNNGP, SoyDNGP boasts a distinct advantage due to its minimal increase in parameter volume and superior predictive accuracy. Through rigorous performance comparison, including prediction accuracy and model complexity, SoyDNGP represents improved performance to its counterparts. Furthermore, it effectively predicted complex traits with remarkable precision, demonstrating robust performance across different sample sizes and trait complexities. We also tested the versatility of SoyDNGP across multiple crop species, including cotton, maize, rice and tomato. Our results showed its consistent and comparable performance, emphasizing SoyDNGP's potential as a versatile tool for genomic prediction across a broad range of crops. To enhance its accessibility to users without extensive programming experience, we designed a user-friendly web server, available at http:\/\/xtlab.hzau.edu.cn\/SoyDNGP. The server provides two features: 'Trait Lookup', offering users the ability to access pre-existing trait predictions for over 500 soybean accessions, and 'Trait Prediction', allowing for the upload of VCF files for trait estimation. By providing a high-performing, accessible tool for trait prediction, SoyDNGP opens up new possibilities in the quest for optimized soybean breeding.<\/jats:p>","DOI":"10.1093\/bib\/bbad349","type":"journal-article","created":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T14:25:50Z","timestamp":1697120750000},"source":"Crossref","is-referenced-by-count":61,"title":["SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding"],"prefix":"10.1093","volume":"24","author":[{"given":"Pengfei","family":"Gao","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haonan","family":"Zhao","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zheng","family":"Luo","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Lin","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanjie","family":"Feng","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaling","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fanjiang","family":"Kong","sequence":"additional","affiliation":[{"name":"Guangzhou Key Laboratory of Crop Gene Editing , Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, , Guangzhou 510006 , China"},{"name":"Guangzhou University , Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, , Guangzhou 510006 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Fang","sequence":"additional","affiliation":[{"name":"Guangzhou Key Laboratory of Crop Gene Editing , Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, , Guangzhou 510006 , China"},{"name":"Guangzhou University , Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, , Guangzhou 510006 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xutong","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"},{"name":"Hubei Hongshan Laboratory , No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,10,11]]},"reference":[{"key":"2023101218254579400_ref1","first-page":"2021","volume-title":"The State of Food Security and Nutrition in the World 2021. 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