Editorial

Huatao Chen^1*Li Song²Henry T Nguyen³Donghe Xu⁴Chengfu Su⁵

• ¹Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing, China
• ²Yangzhou University, Yangzhou, Jiangsu Province, China
• ³University of Missouri, Columbia, Kentucky, United States
• ⁴Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
• ⁵Qingdao Agricultural University, Qingdao, Shandong Province, China

EditorialHuatao Chen1*, Li Song2, Henry T. Nguyen3, Donghe Xu4, Chengfu Su5 1Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing, China, 2Yangzhou University, Yangzhou, China, 3University of Missouri, Columbia, United States, 4Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan, 5Qingdao Agricultural University, Qingdao, ChinaSoybean, with its high - protein and oil - rich seeds, is a vital agricultural commodity. However, the growing global demand, spurred by population growth and dietary changes, poses significant challenges in meeting production demand. Abiotic and biotic stresses, such as drought, salinity, extreme temperatures, and flooding, are major hurdles in soybean breeding.To address these challenges, modern soybean breeding strategies aim to develop stress tolerant varieties. Advancements in molecular biology and biotechnology provide innovative approaches to this end. Techniques such as Kompetitive Allele-Specific PCR (KASP) molecular markers help breeders to accurately select stress - tolerant genes, while omics - based approaches provide insights into the molecular mechanisms underlying soybean's stress responses. These findings are presented in eleven papers in the special issue on the Research Topic “Soybean Breeding for Abiotic Stress Tolerance: Towards Sustainable Agriculture.”Salt toleranceWang et al. investigate the genetic basis of salt tolerance in soybeans, a crucial aspect considering the global issue of soil salinization. A natural population of 283 soybean germplasms was used for this study. After identifying 180 mM NaCl as the optimal stress concentration, germination traits such as germination rate, energy, and index were measured under salt stress conditions. Through a genome-wide association study (GWAS), 1841 significant SNPs associated with these traits were identified, leading to the identification of 12 candidate genes. KASP markers were developed for specific SNPs. These findings offer valuable insights into soybean salt tolerance and offer genetic resources and a theoretical foundation for breeding salt-tolerant soybean varieties.Xu et al. aimed to identify salt-tolerance-associated SNPs in soybean and evaluate genomic prediction for salt tolerance, using 563 germplasms from twenty-six countries. They identified four subpopulations (Q1-Q4) through relevant analyses. GWAS identified 10 SNPs on chromosomes 1, 2, 3, 7, and 16 that were significantly associated with salt tolerance, with eleven candidate genes located near 7 of these SNPs. Genomic prediction models including maBLUP, gBLUP, and sBLUP showed moderate - to - high r - values, and the GWAS-derived SNP marker set was effective for genomic selection. The genetic diversity analysis of salt-tolerant germplasms indicated a broad genetic background and highlighted the influence of geographic factors on salt tolerance in soybeans.Drought toleranceIn response to the challenge of drought affecting soybean production in China, Jia et al. focused on a natural population of 264 Chinese soybean accessions. They treated these accessions with 15% PEG - 6000 during germination and employed a series of evaluation indexes, identified 17 drought - tolerant germplasms. Utilizing Genome - Wide Association Studies (GWAS), 92 SNPs and 9 candidate genes related to drought tolerance were discovered. Moreover, two KASP markers associated with drought tolerance were developed, which not only augment the soybean germplasm pool but also establish a crucial basis for molecular breeding of drought-resistant soybean varieties.Flooding toleranceSoybean is highly sensitive to flooding stress, and the Hypoxia Inducible Gene Domain (HIGD) gene family may play a role in plant responses to hypoxia. Geng et al. identified six GmHIGD genes in the soybean genome. The genes have conserved genomic structures and motifs. Chromosomal location and collinearity analysis revealed their distribution and potential evolutionary relationships. Cis - element analysis of promoters and TF identification suggested their involvement in growth, development, and stress responses. Expression analyses across various tissues and stresses (flooding, hypoxia, drought, salt) were conducted. Notably, GmHIGD3 was found to be localized in mitochondria, and its overexpression in Arabidopsis affected catalase activity and ROS content. Overall, this research provides valuable insights into the characteristics and potential functions of the GmHIGD gene family in soybean.Shoot toleranceJia et al. (2024) investigate the impact of shade on soybean yield, with a focus on identifying shade-tolerant genomic loci and varieties. A natural population of 264 soybean accessions was subjected to a 30% light reduction treatment. GWAS was conducted on six agronomic traits and shade tolerance coefficients (STCs). Five high shade-tolerant germplasms were found, and a total of 733 significant SNPs associated with STCs of six traits were detected over two years. Four candidate genes related to shade tolerance were found. Additionally, KASP markers were developed for four SNPs, and haplotype analysis was performed. These results provide valuable genetic resources and new insights for soybean shade tolerance breeding and theoretical research.Root architectureIn soybean, root architecture traits are vital for plant performance. The root length locus qRL16.1 on chromosome 16 has been previously reported. Through transcriptome analysis of near - isogenic lines (NILs), Kumawat et al. characterized two candidate genes, Glyma.16g108500 and Glyma.16g108700, which exhibited higher expression in longer root accessions. The C-terminal domains of these genes are similar to those of C-terminally encoded peptides (CEPs) in Arabidopsis, known to regulate root length and nutrient response. Two polymorphisms located upstream of Glyma.16g108500 were associated with root length traits. Synthetic peptide assays showed a positive effect of the predicted CEP variants on primary root length. These genes are specifically expressed in the root during the early growth stage and shown differential expression pattern only in the primary root. They hold potential for improving soybean to develop a strong root system under low moisture and nutrient conditions.Seed traitsSoybean seed viability is crucial for both quality and production yet seed quality and germplasm preservation face challenges. Li et al. investigated the mechanisms of soybean seed aging by using aging-sensitive R31 and aging-tolerant R80 lines, subjecting them to artificial aging treatments of varying durations. Analyses of the transcriptome and metabolome revealed that the response to aging stress is associated with the phenylpropanoid metabolism pathway, in which caffeic acid plays a key role. Furthermore, soaking seeds in caffeic acid was found to enhance germination rates. These fundings provide a theoretical basis for future research on soybean seed aging mechanisms.RNA modificationDespite the known significance of N6 - methyladenosine (m6A) RNA modification in regulating biological processes, its genome - wide identification and functional characterization in legumes like soybean have been lacking. Liu et al. used bioinformatics to identify thirteen m6A writer complex genes in soybean, which grouped into four families. They analyzed the characteristics, enzymatic activities, and expression patterns of these genes under abiotic stresses conditions, highlighting the roles of GmMTAs and GmMTBs in soybean's response to abiotic stress. This study establishes a foundation for further exploration of the functions of m6A modification in soybean.ReferencesGeng X, Dong L, Zhu T, Yang C, Zhang J, Guo B, Chen H, Zhang Q, Song L. Genome-wide analysis of soybean hypoxia inducible gene domain containing genes: a functional investigation of GmHIGD3. Front Plant Sci. 2024, 15:1403841.Jia Q, Hu S, Li X, Wei L, Wang Q, Zhang W, Zhang H, Liu X, Chen X, Wang X, Chen H. Identification of candidate genes and development of KASP markers for soybean shade-tolerance using GWAS. Front Plant Sci. 2024, 15:1479536.Jia Q, Zhou M, Xiong Y, Wang J, Xu D, Zhang H, Liu X, Zhang W, Wang Q, Sun X, Chen H. Development of KASP markers assisted with soybean drought tolerance in the germination stage based on GWAS. Front Plant Sci. 2024, 15:1352379.Kumawat G, Cao D, Park C, Xu D. C-terminally encoded peptide-like genes are associated with the development of primary root at qRL16.1 in soybean. Front Plant Sci. 2024, 15:1387954.Li G, Xie J, Zhang W, Meng F, Yang M, Fan X, Sun X, Zheng Y, Zhang Y, Wang M, Chen Q, Wang S, Jiang H. Integrated examination of the transcriptome and metabolome of the gene expression response and metabolite accumulation in soybean seeds for seed storability under aging stress. Front Plant Sci. 2024, 15:1437107.Li H, Zhang X, Yang Q, Shangguan X, Ma Y. Genome-wide identification and tissue expression pattern analysis of TPS gene family in soybean (Glycine max). Front Plant Sci. 2024, 1487092.Liu G, Fang Y, Liu X, Jiang J, Ding G, Wang Y, Zhao X, Xu X, Liu M, Wang Y, Yang C. Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean. Front Plant Sci. 2024, 15:1369650.Liu P, Liu H, Zhao J, Yang T, Guo S, Chang L, Xiao T, Xu A, Liu X, Zhu C, Gan L, Chen M. Genome-wide identification and functional analysis of mRNA m6A writers in soybean under abiotic stress. Front Plant Sci. 2024, 15:1446591.Raza MM, Jia H, Razzaq MK, Li B, Li K, Gai J. Identification and functional validation of a new gene conferring resistance to Soybean Mosaic Virus strains SC4 and SC20 in soybean. Front Plant Sci. 2025, 15:1518829.Wang J, Zhou M, Zhang H, Liu X, Zhang W, Wang Q, Jia Q, Xu D, Chen H, Su C. A genome-wide association analysis for salt tolerance during the soybean germination stage and development of KASP markers. Front Plant Sci. 2024, 15:1352465.Xu R, Yang Q, Liu Z, Shi X, Wu X, Chen Y, Du X, Gao Q, He D, Shi A, Tao P, Yan L. Genome-wide association analysis and genomic prediction of salt tolerance trait in soybean germplasm. Front Plant Sci. 2024, 15:1494551.