From sequences to prebreeding: Chromosome-level genome assemblies, comparative annotation, and a public database for Minghui 86 and Minhui 3301

Innovative breeding technologies routinely require genome-wide information for selecting individuals to enhance the genetic gain for multiple traits. Minghui 86 (MH86) and Minhui 3301 (MH3301) are two widely utilized hybrid rice restorer lines serving as significant core parents in rice breeding programs. Decoding their genomic information will provide substantial convenience for subsequent breeding applications. This study successfully assembled the genomes of MH86 and MH3301 at the chromosomal level and annotated their genes. This work elucidated the genetic information underlying their germplasm characteristics and establishing a foundation for future breeding efforts. To facilitate the utilization of the genomic sequences and annotation data from MH86 and MH3301, a genomic database (http://cropdesign.cn/) was developed. This database integrates results from targeted resequencing analyses conducted on 1256 rice germplasm samples, facilitating genotype retrieval for molecular design breeding initiatives. Furthermore, it offers various functionalities including search capabilities, sequence alignment tools, and more.