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.

Soybean (Glycine max) is an important and valuable crop, providing oil and proteins for both humans and animals. Seed weight is a key trait that determines soybean yields; however, the genes and mechanisms controlling seed weight remain poorly understood. Here, we used genome-wide association study (GWAS) and joint linkage mapping to identify a ubiquitin-specific protease, GmSW17.1, which regulates 100-seed weight in soybean. Two natural allelic variants of GmSW17.1 resulted in significantly different 100-seed weight, with GmSW17.1^T conferring heavier seeds. We used CRISPR/Cas9 technology to knock out GmSW17.1, resulting in lighter and smaller seeds; however, these mutants produced more seeds than the wild type, resulting in similar overall yields. Owing to the increased number of seeds, we determined that GmSW17.1 is highly transcribed in developing seeds, and its encoded protein physically interacts in the nucleus with GmSGF11, which plays a crucial role in the deubiquitinating pathway. Analysis of genomic sequences from more than 1714 soybean accessions suggested that the natural allele GmSW17.1^T was selected during the domestication and genetic improvement, resulting in its rapid expansion in cultivated soybean. These findings provide important insights into the role of GmSW17.1 in 100-seed weight and offer valuable clues for the molecular breeding of soybean.

Flowering time is important for adaptation of soybean (Glycine max) to different environments. Here, we conducted a genome-wide association study of flowering time using a panel of 1490 cultivated soybean accessions. We identified three strong signals at the qFT02-2 locus (Chr02: 12037319–12238569), which were associated with flowering time in three environments: Gongzhuling, Mengcheng, and Nanchang. By analyzing linkage disequilibrium, gene expression patterns, gene annotation, and the diversity of variants, we identified an AP1 homolog as the candidate gene for the qFT02-2 locus, which we named GmAP1d. Only one nonsynonymous polymorphism existed among 1490 soybean accessions at position Chr02:12087053. Accessions carrying the Chr02:12087053-T allele flowered significantly earlier than those carrying the Chr02:12087053-A allele. Thus, we developed a cleaved amplified polymorphic sequence (CAPS) marker for the SNP at Chr02:12087053, which is suitable for marker-assisted breeding of flowering time. Knockout of GmAP1d in the ‘Williams 82’ background by gene editing promoted flowering under long-day conditions, confirming that GmAP1d is the causal gene for qFT02-2. An analysis of the region surrounding GmAP1d revealed that GmAP1d was artificially selected during the genetic improvement of soybean. Through stepwise selection, the proportion of modern cultivars carrying the Chr02:12087053-T allele has increased, and this allele has become nearly fixed (95%) in northern China. These findings provide a theoretical basis for better understanding the molecular regulatory mechanism of flowering time in soybean and a target gene that can be used for breeding modern soybean cultivars adapted to different latitudes.

Soybean (Glycine max L.) is a protein and oil crop grown worldwide. Its fitness may be reduced by deleterious mutations, whose identification and purging is desirable for crop breeding. In the published whole-genome re-sequenced data of 2214 soybean accessions, including 221 wild soybean, 1132 landrace cultivars and 861 improved soybean lines, we identified 115,275 deleterious single-nucleotide polymorphisms (SNPs). Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines. Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes. Deleterious mutations explained 4.3%–48% more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2 (SCN2), soybean cyst nematode race 3 (SCN3) and soybean mosaic virus race 3 (SMV3). These findings illustrate how mutation load has shifted during soybean domestication, expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most economically destructive pathogens. The soybean line Zhongpin03-5373 (ZP), which combines resistance genes from several donors, is highly resistant to SCN race 3 (SCN3). In our previous study, two QTL (rhg1 and GmSNAP11) were identified in a population of recombinant inbred lines derived from a cross between ZP and the susceptible parent Zhonghuang 13. The two QTL explained around one-third of the resistance, suggesting the presence of further QTL contributing to SCN resistance. In the present study, we used an improved version of the genetic map comprising the previously applied 1062 molecular markers and 47 newly developed InDel (insertion-deletion) markers. The improved map revealed a novel locus contributing to SCN3 resistance: qSCN3-1, flanked by InDel marker InDel1-7 and SNP marker Map-0047, explained 4.55% of the phenotypic variance for resistance to SCN3 and was not involved in digenic epistatic interaction with rhg1 and GmSNAP11. Haplotypes of Map-0047_CAPS (a CAPS marker developed for Map-0047) and InDel1-7 were significantly associated with SCN3 resistance in a panel of 209 resistant and susceptible accessions. Using further allele-combination analysis for three functional markers representing three cloned resistance genes (rhg1, Rhg4, and GmSNAP11) and two markers flanking qSCN3-1, we found that adding the resistance allele of qSCN3-1 greatly increased soybean resistance to SCN, even in diverse genetic backgrounds. The qSCN3-1 locus will be useful for marker-assisted polygene pyramid breeding and should be targeted for the future identification of candidate genes.

Soybean cyst nematode (SCN) is a highly destructive pathogen. The soybean host genome harbors at least two major genes for resistance (rhg1 and Rhg4), as well as a minor locus (SCN3-11). In the present study, a splicing site in GmSNAP11, the potential causal gene of SCN3-11, was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean accessions. The sequence information was used to design a codominant CAPS marker, GmSNAP11-2565, which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance. Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect (nonsynonymous) locus, GmSNAP11-2307, previously identified in GmSNAP11, revealed linkage disequilibrium (P < 0.0001) between the two loci, suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11. GmSNAP11-2565 was accordingly used, along with established markers for GmSNAP18 (rhg1) and GmSHMT (Rhg4), to characterize the panel accessions. The mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance (20.3%) was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18 (12.4%), while the index for accessions carrying alleles for resistance at all of GmSNAP11, GmSNAP18, and GmSHMT was very low (1.9%). Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3.

The concept of core collection (CC) provides a new way of management and utilization of plant germplasm resources. In this study, an integrated applied core collection (IACC) of soybean was developed based on evaluation data for desirable agronomic and nutritional traits of available soybean germplasm resources including accessions with cold tolerance, drought tolerance, salt tolerance, soybean cyst nematode resistance, soybean mosaic virus resistance, high protein content, and high fat content. The newly formed collection encompasses accessions with high genetic diversity and desirable agronomic traits. The genetic diversity of the newly formed IACC was compared with that of the established mini core collection (MCC) of soybean with the aid of simple sequence repeat (SSR) markers and phenotypic traits. The results showed that at the molecular level, soybean IACC harbored a similar level of genetic diversity as the established MCC, and that at the phenotypic level the IACC encompasses more accessions with desirable traits than does the established MCC. The development of soybean IACC lays a foundation for breeding projects to meet different objectives in different eco-regions.