Chromosome-level genome assembly of a high-yield Chinese soybean variety Mengdou1137 unlocks genetic potential of disease and lodging resistance

Rujian Sun, Bincheng Sun, Zihao Zheng, Qi Zhang, Xingguo Hu, Rongqi Guo, Lei Feng, Shen Chai, Jingshun Wang, Ping Qiu, Ping Yu, Ying Liu, Wei Song, Yinghui Li, Lijuan Qiu

Theoretial and Applied Genetics; May 15 2025; vol.138; article 119

Abstract

As a cornerstone in the global agricultural landscape, soybean stands as a pivotal oilseed crop, underpinning both nutritional and industrial applications. The burgeoning development of novel soybean varieties significantly propels the crop’s industrialization, offering enhanced traits that cater to diverse agricultural and commercial needs. In this study, we present the de novo assembly of the genome a high-yield Chinese soybean variety Mengdou1137, employing an integrated approach of both long-read and short-read sequencing technologies to achieve comprehensive genomic insights. Achieving a notable assembly with a genome size of 999.99 Mb, our work features a contig N50 of 14.92 Mb and a scaffold N50 of 50.26 Mb, successfully anchoring 98.24% of sequences across the 20 chromosomes. Through meticulous comparative analysis with existing soybean genomes, our research unveiled 115 Mengdou1137-specific disease resistance genes alongside a substantial array of agronomical trait-associated genomic variants. Among the salient genomic features, we identified a favorable haplotype of the dwarf gene PH13, a critical determinant of plant stature, underscoring its potential for breeding compact soybean varieties with lodging resistance. This high-quality assembly of the Mengdou1137 genome not only enriches the repository of soybean genetic resources but also paves the way for future innovations in soybean breeding and trait improvement, offering valuable insights for the enhancement of this crucial agricultural commodity.

See https://link.springer.com/article/10.1007/s00122-025-04881-4

Figure 2

Assembly and annotation: a synteny blocks between Mengdou1137 and Wm82 were used to anchor scaffolds to each chromosome. b A physical map illustrating the 20 chromosomes for Mengdou1137, featuring: (A) TE density, (B) Copia density, (C) Gypsy density, (D) gene density, (E) GC content and (F) SV number. c Results of functional annotations of protein-coding genes using four distinct databases