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The content of protein and oil in soybeans is an important trait for evaluating quality and is regulated by genetic and environmental factors, lacking comprehensive identification under a variety of ecological conditions. Therefore, evaluating the stability of soybean quality traits under different environmental conditions has great significance for various applications. In this study, we compare 150 soybean varieties from Northeast China (Group A and Group B) and the Huang-Huai-Hai region (Group C). As the release time progressed, the oil content in the soybean varieties showed an upward trend in both Northeast China and the Huang-Huai-Hai region, while the protein content showed a downward trend. Additionally, the oil contents were negatively correlated with the protein contents and the sum of protein and oil contents, while the protein contents were positively correlated with the sum of protein and oil contents, with the correlation becoming stronger as the latitude decreased. Moreover, there were obvious variations in quality stability among different varieties. Hefeng 45, Jilinxiaolidou 4, and Zhonghuang 19 had relatively high protein contents and exhibited good stability across different environments, while Kenjiandou 25, Changnong 17, Dongnong 46, Kennong 17, Liaodou 14, and GR8836 had relatively high oil contents with good stability performance in varying environments. [ABSTRACT FROM AUTHOR]

The application of heterosis is a promising approach for greatly increasing yield in soybean (Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Here we report the cloning of the gene underlying the soybean male‐sterile mutant ms‐1, which has been widely used for recurrent selection in soybean breeding programs. We initially delimited the ms1 locus to a 16.15 kb region on chromosome 13, based on SLAF_BSA sequencing followed by genotyping of an F2 population segregating for the locus. Compared with the same region in fertile plants, the mutant region lacks a sequence of approximately 38.7 kb containing five protein‐coding genes, including an ortholog of the kinesin‐like protein gene NACK2, named GmMs1. The GmMs1 knockout plants generated via CRISPR/Cas‐mediated gene editing displayed a complete male‐sterile phenotype. Metabolic profiling showed that fertile anthers accumulated starch and sucrose normally, whereas sterile anthers had higher anthocyanin levels and lower flavonoid levels and lower antioxidant enzyme activities. These results provide insights into the molecular mechanisms governing male sterility and demonstrate that GmMs1 could be used to create male‐sterile lines through targeted mutagenesis. These findings pave the way for designing seed production technology and an intelligent male‐sterile line system to utilize heterosis in soybean. [ABSTRACT FROM AUTHOR]

Improved soybean cultivars have been adapted to grow at a wide range of latitudes, enabling expansion of cultivation worldwide. However, the genetic basis of this broad adaptation is still not clear. Here, we report the identification of GmPRR3b as a major flowering time regulatory gene that has been selected during domestication and genetic improvement for geographic expansion. Through a genome-wide association study of a diverse soybean landrace panel consisting of 279 accessions, we identified 16 candidate quantitative loci associated with flowering time and maturity time. The strongest signal resides in the known flowering gene E2 , verifying the effectiveness of our approach. We detected strong signals associated with both flowering and maturity time in a genomic region containing GmPRR3b. Haplotype analysis revealed that GmPRR3b H6 is the major form of GmPRR3b that has been utilized during recent breeding of modern cultivars. mRNA profiling analysis showed that GmPRR3b H6 displays rhythmic and photoperiod-dependent expression and is preferentially induced under long-day conditions. Overexpression of GmPRR3b H6 increased main stem node number and yield, while knockout of GmPRR3b H6 using CRISPR/Cas9 technology delayed growth and the floral transition. GmPRR3bH6 appears to act as a transcriptional repressor of multiple predicted circadian clock genes, including GmCCA1a , which directly upregulates J/GmELF3a to modulate flowering time. The causal SNP (Chr12:5520945) likely endows GmPRR3bH6 a moderate but appropriate level of activity, leading to early flowering and vigorous growth traits preferentially selected during broad adaptation of landraces and improvement of cultivars. Natural variation in flowering time is critical for geographic adaptation of soybean. A circadian clock gene, GmPRR3b , was identified as a major flowering time QTL through a genome-wide association study. GmPRR3b haplotype 6 is identified to be associated with early flowering and vigorous growth traits, which has been extensively utilized during domestication and breeding of modern cultivars. [ABSTRACT FROM AUTHOR]

Key message: GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean.Abstract: Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length. The bioactive GA1 (gibberellin A1) and GA4 (gibberellin A4) were not detectable in the stem of dw, and the dwarf phenotype could be rescued by treatment with exogenous GA3. Genetic analysis showed that the dwarf trait of dw was controlled by a recessive nuclear gene. By combining linkage analysis and mapping-by-sequencing, we mapped the GmDW1 gene to an approximately 460-kb region on chromosome (Chr.) 8, containing 36 annotated genes in the reference Willliams 82 genome. Of these genes, we identified two nonsynonymous single nucleotide polymorphisms (SNPs) that are present in the encoding regions of Gmdw1 and Glyma.08G165100 in dw, respectively. However, only the SNP mutation (T>A) at nucleotide 1224 in Gmdw1 cosegregated with the dwarf phenotype. GmDW1 encodes an ent-kaurene synthase, and was expressed in various tissues including root, stem, and leaf. Further phenotypic analysis of the allelic variations in soybean accessions strongly indicated that GmDW1 is responsible for the dwarf phenotype in dw. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. [ABSTRACT FROM AUTHOR]

Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS)-induced soybean ( Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over 1,000 M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, g yl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to MinnGold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene ( ChlI1a) results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean. [ABSTRACT FROM AUTHOR]

Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping. [ABSTRACT FROM AUTHOR]

In order to ensure an ongoing and long-term breeding progress of soybean, stable sources of major quality traits across multi-environments need to be identified. Here, a panel of 135 soybean genotypes was tested in three different Chinese environments, including Beijing, Anhui, and Hainan during the 2017 and 2018 growing seasons to identify stable genotypes for cultivation under varying environmental conditions. The weighted average of absolute scores biplot (WAASB) for the best linear unbiased predictions of the genotype-environment interaction and multi-trait stability index (MTSI) were utilized to determine the stability of the soybeans for seven seed composition traits viz; protein content, oil content, and five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic acids). Based on the WAASB index, the following genotypes were identified as stable genotypes for some specific traits; ZDD12828 and ZDD12832 for protein content, WDD01583 and WDD03025 for oil content, ZDD23040 for palmitic acid, WDD00033 for stearic acid, ZDD23822 for oleic acid, ZDD11183 for linoleic acid, and ZDD08489 for linolenic acid. Furthermore, based on MTSI at a selection intensity of 10%, 14 soybean genotypes were selected for their average performance and stability. Overall, the MTSI was shown to be a powerful and simple tool for identifying superior genotypes in terms of both performance and stability, hence, identifying stable soybean genotypes for future breeding programs of quality traits. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max L. Merr.) is one of the most important crops in the world. Its major content of vegetable oil made it widely used for human consumption and several food industries. To investigate the variation in seed fatty acid composition of soybeans from different origins, a set of 633 soybean accessions originated from four diverse germplasm collections—including China, United States of America (USA), Japan, and Russia—were grown in three locations, Beijing, Anhui, and Hainan for two years. The results showed significant differences (P < 0.001) among the four germplasm origins for all fatty acid contents investigated. Higher levels, on average, of palmitic acid (PA) and linolenic acid (LNA) were observed in Russian germplasm (12.31% and 8.15%, respectively), whereas higher levels of stearic acid (SA) and oleic acid (OA) were observed in Chinese germplasm (3.95% and 21.95%, respectively). The highest level of linoleic acid (LA) was noticed in the USA germplasm accessions (56.34%). The largest variation in fatty acid composition was found in LNA, while a large variation was observed between Chinese and USA germplasms for LA level. Maturity group (MG) significantly (P < 0.0001) affected all fatty acids and higher levels of PA, SA, and OA were observed in early maturing accessions, while higher levels of LA and LNA were observed in late maturing accessions. The trends of fatty acids concentrations with different MG in this study further provide an evidence of the importance of MG in breeding for such soybean seed components. Collectively, the unique accessions identified in this study can be used to strengthen the soybean breeding programs for meeting various human nutrition patterns around the globe. [ABSTRACT FROM AUTHOR]

Germination of soybean seed is the imminent vital process after sowing. The status of plumular axis and radicle determine whether soybean seed can emerge normally. Epicotyl, an organ between cotyledons and first functional leaves, is essential for soybean seed germination, seedling growth and early morphogenesis. Epicotyl length (EL) is a quantitative trait controlled by multiple genes/QTLs. Here, the present study analyzes the phenotypic diversity and genetic basis of EL using 951 soybean improved cultivars and landraces from Asia, America, Europe and Africa. 3VmrMLM was used to analyze the associations between EL in 2016 and 2020 and 1,639,846 SNPs for the identification of QTNs and QTN-by-environment interactions (QEIs)".A total of 180 QTNs and QEIs associated with EL were detected. Among them, 74 QTNs (ELS&#95;Q) and 16 QEIs (ELS&#95;QE) were identified to be associated with ELS (epicotyl length of single plant emergence), and 60 QTNs (ELT&#95;Q) and 30 QEIs (ELT&#95;QE) were identified to be associated with ELT (epicotyl length of three seedlings). Based on transcript abundance analysis, GO (Gene Ontology) enrichment and haplotype analysis, ten candidate genes were predicted within nine genic SNPs located in introns, upstream or downstream, which were supposed to be directly or indirectly involved in the process of seed germination and seedling development., Of 10 candidate genes, two of them (Glyma.04G122400 and Glyma.18G183600) could possibly affect epicotyl length elongation. These results indicate the genetic basis of EL and provides a valuable basis for specific functional studies of epicotyl traits., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Hong, Li, Chen, Wang, Wang, Guo, Gao, Ren, Yuan, Han and Qiu.)

The electron-phonon (e-ph) interaction in lead halide perovskites (LHPs) plays a role in a variety of physical phenomena. Unveiling how the local lattice distortion responds to charge carriers is a critical step toward understanding the e-ph interaction in LHPs. Herein, we advance a fundamental understanding of the e-ph interaction in LHPs from the perspective of stereochemical activity of 6s 2 lone-pair electrons on the Pb 2+ cation. We demonstrate a model system based on three LHPs with distinctive lone-pair activities for studying the structure-property relationships. By tuning the A-cation chemistry, we synthesized single-crystal CsPbBr 3 , (MA 0.13 EA 0.87 )PbBr 3 (MA + = methylammonium; EA + = ethylammonium), and (MHy)PbBr 3 (MHy + = methylhydrazinium), which exhibit stereo-inactive, dynamic stereo-active, and static stereo-active lone pairs, respectively. This gives rise to distinctive local lattice distortions and low-frequency vibrational modes. We find that the e-ph interaction leads to a blue shift of the band gap as temperature increases in the structure with the dynamic stereo-active lone pair but to a red shift in the structure with the static stereo-active lone pair. Furthermore, analyses of the temperature-dependent low-energy photoluminescence tails reveal that the strength of the e-ph interaction increases with increasing lone-pair activity, leading to a transition from a large polaron to a small polaron, which has significant influence on the emission spectra and charge carrier dynamics. Our results highlight the role of the lone-pair activity in controlling the band gap, phonon, and polaronic effect in LHPs and provide guidelines for optimizing the optoelectronic properties, especially for tin-based and germanium-based halide perovskites, where stereo-active lone pairs are more prominent than their lead counterparts.

Soybean (Glycine max L. Merrill) isoflavones are secondary metabolites of great interest because of their beneficial impact on human health. We profiled the seed isoflavone composition of 1168 soybean accessions collected from diverse ecoregions of China in three locations over two years. We observed significant differences in isoflavone content among the accessions, accession types, years of growth and ecoregions of origin. Total isoflavone (TIF) concentration of the soybean accessions ranged from 745 μg g -1 to 5253.98 μg g -1 , which represents a 7-fold difference. The highest mean TIF concentration (2689.27 μg g -1 ) was observed in the Huang Huai Hai Valley Region (HR) accessions, followed by accessions from the Southern Region (SR) and Northern Region (NR) with TIF concentration of 2518.91 μg g -1 and 1942.78 μg g -1 , respectively. Thirty-five accessions were identified as elite soybean resources based on their higher TIF concentration (4024.74 μg g -1 to 5253.98 μg g -1 ). Pairwise correlation analysis showed significant positive correlations between individual isoflavones and TIF concentrations. Malonyldaidzin and malonylgenistin showed the highest correlations with TIF concentration (r = 0.90 and r = 0.92, respectively), whereas acetyldaidzin showed the lowest correlation. The main isoflavone components had significant negative correlations with latitude and longitude, indicating that the geographical origin of the accessions influenced their seed isoflavone composition. Based on principal component analysis, glycosides and malonylglycosides of isoflavones were the major discriminative components for the soybean accessions. The present study demonstrated the geographical distribution of soybean seed isoflavone concentrations across the main ecoregion of China. The identified soybean accessions with both high and low TIF concentrations, which are desirable materials for industrial uses and could also be used as parents to breed soybean lines with improved isoflavone quantity and composition in the seeds., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Soil salinity reduces soybean growth and yield. The recently identified GmSALT3 ( Glycine max salt Tolerance-associated gene on chromosome 3) has the potential to improve soybean yields in salinized conditions. Here we evaluate the impact of GmSALT3 on soybean performance under saline or non-saline conditions. Three sets of near isogenic lines (NILs), with genetic similarity of 95.6-99.3% between each pair of NIL-T and NIL-S, were generated from a cross between two varieties 85-140 (salt-sensitive, S) and Tiefeng 8 (salt-tolerant, T) by using marker-assisted selection. Each NIL-T; 782-T, 820-T and 860-T, contained a common ~1000 kb fragment on chromosome 3 where GmSALT3 was located. We show that GmSALT3 does not contribute to an improvement in seedling emergence rate or early vigor under salt stress. However, when 12-day-old seedlings were exposed to NaCl stress, the NIL-T lines accumulated significantly less leaf Na + compared with their corresponding NIL-S, while no significant difference of K + concentration was observed between NIL-T and NIL-S; the magnitude of Na + accumulation within each NIL-T set was influenced by the different genetic backgrounds. In addition, NIL-T lines accumulated less Cl - in the leaf and more in the root prior to any difference in Na + ; in the field they accumulated less pod wall Cl - than the corresponding NIL-S lines. Under non-saline field conditions, no significant differences were observed for yield related traits within each pair of NIL-T and NIL-S lines, indicating there was no yield penalty for having the GmSALT3 gene. In contrast, under saline field conditions the NIL-T lines had significantly greater plant seed weight and 100-seed weight than the corresponding NIL-S lines, meaning GmSALT3 conferred a yield advantage to soybean plants in salinized fields. Our results indicated that GmSALT3 mediated regulation of both Na + and Cl - accumulation in soybean, and contributes to improved soybean yield through maintaining a higher seed weight under saline stress.

Molecular characterization of sequence flanking exogenous fragment insertion is essential for safety assessment and labeling of genetically modified organism (GMO). In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS) method. More than 22.4 Gb sequence data (∼21 × coverage) for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundaries of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of genomic insertion sites of G2-EPSPS and GAT transgenes will facilitate the utilization of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS was a cost-effective and rapid method for identifying sites of T-DNA insertions and flanking sequences in soybean.

Glyphosate is a widely used non-selective herbicide with broad spectrum of weed control around the world. At present, most of the commercial glyphosate tolerant soybeans utilize glyphosate tolerant gene CP4-EPSPS or glyphosate acetyltransferase gene GAT separately. In this study, both glyphosate tolerant gene G2-EPSPS and glyphosate degraded gene GAT were co-transferred into soybean and transgenic plants showed high tolerance to glyphosate. Molecular analysis including PCR, Sothern blot, qRT-PCR, and Western blot revealed that target genes have been integrated into genome and expressed effectively at both mRNA and protein levels. Furthermore, the glyphosate tolerance analysis showed that no typical symptom was observed when compared with a glyphosate tolerant line HJ06-698 derived from GR1 transgenic soybean even at fourfold labeled rate of Roundup. Chlorophyll and shikimic acid content analysis of transgenic plant also revealed that these two indexes were not significantly altered after glyphosate application. These results indicated that co-expression of G2-EPSPS and GAT conferred high tolerance to the herbicide glyphosate in soybean. Therefore, combination of tolerant and degraded genes provides a new strategy for developing glyphosate tolerant transgenic crops.