Structural variation in Heinong 531 soybean genome underlies yield and resistance traits

Soybean (Glycine max) is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals. Cultivated soybean varieties exhibit considerable genetic diversity depending on their geographical origin. Heinong 531 (HN531) is an elite cultivar that was released in China in June 2021 with 22.34% seed oil, high resistance to soybean cyst nematode (SCN) race 3, and enhanced yield. However, the genetic basis for these desirable agronomic traits is unclear. In this study, we generated a high-quality genome assembly for HN531 and used it to systematically analyze genes related to agronomic traits such as resistance to SCN. The assembled genome spans 981.20 Mb, featuring a contig N50 of 19.47 Mb, and contains 58,151 predicted gene models. Pan-genomic comparison with 27 previously reported soybean genomes revealed 95,071 structural variants (SVs) of > 50 bp, of which 602 were HN531-specific. Furthermore, we identified a copy number variation at rhg1 that underlies resistance to SCN, and we found elite alleles of functional genes underlying important agronomic traits such as seed oil content, adaptability, and yield. This high-quality HN531 genome can be used to explore the genetic basis for the excellent agronomic traits of this cultivar, and is a valuable resource for breeders aiming to improve HN531 and related cultivars.