Computational tools for plant genomics and breeding

Hai Wang; Mengjiao Chen; Xin Wei; Rui Xia; Dong Pei; Xuehui Huang; Bin Han

doi:10.1007/s11427-024-2578-6

Computational tools for plant genomics and breeding

Sci China Life Sci. 2024 Apr 23. doi: 10.1007/s11427-024-2578-6. Online ahead of print.

Authors

Hai Wang^#^{1

2

3}, Mengjiao Chen^#⁴, Xin Wei⁵, Rui Xia⁶, Dong Pei⁴, Xuehui Huang⁵, Bin Han⁷

Affiliations

¹ State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China. wanghai@cau.edu.cn.
² Sanya Institute of China Agricultural University, Sanya, 572025, China. wanghai@cau.edu.cn.
³ Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China. wanghai@cau.edu.cn.
⁴ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
⁵ Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
⁶ College of Horticulture, South China Agricultural University, Guangzhou, 510640, China.
⁷ National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.

^# Contributed equally.

PMID: 38676814
DOI: 10.1007/s11427-024-2578-6

Abstract

Plant genomics and crop breeding are at the intersection of biotechnology and information technology. Driven by a combination of high-throughput sequencing, molecular biology and data science, great advances have been made in omics technologies at every step along the central dogma, especially in genome assembling, genome annotation, epigenomic profiling, and transcriptome profiling. These advances further revolutionized three directions of development. One is genetic dissection of complex traits in crops, along with genomic prediction and selection. The second is comparative genomics and evolution, which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant discovery. The third direction is the development of deep learning approaches for the rational design of biological sequences, especially proteins, for synthetic biology. All three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.

Keywords: bioinformatics; breeding by design; plant genomics.

Publication types

Review