A functionally divergent SOC1 homolog improves soybean yield and latitudinal adaptation

The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean

Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.

Floral-promoting GmFT homologs trigger photoperiodic after-effects: An important mechanism for early-maturing soybean varieties to regulate reproductive development and adapt to high latitudes

Soybean (Glycine max) is a typical short-day plant, but has been widely cultivated in high-latitude long-day (LD) regions because of the development of early-maturing genotypes which are photoperiod-insensitive. However, some early-maturing varieties exhibit significant responses to maturity under different daylengths but not for flowering, depicting an evident photoperiodic after-effect, a poorly understood mechanism. In this study, we investigated the postflowering responses of 11 early-maturing soybean varieties to various preflowering photoperiodic treatments. We confirmed that preflowering SD conditions greatly promoted maturity and other postflowering developmental stages. Soybean homologs of FLOWERING LOCUS T (FT), including GmFT2a, GmFT3a, GmFT3b and GmFT5a, were highly accumulated in leaves under preflowering SD treatment. More importantly, they maintained a high expression level after flowering even under LD conditions. E1 RNAi and GmFT2a overexpression lines showed extremely early maturity regardless of preflowering SD and LD treatments due to constitutively high levels of floral-promoting GmFT homolog expression throughout their life cycle. Collectively, our data indicate that high and stable expression of floral-promoting GmFT homologs play key roles in the maintenance of photoperiodic induction to promote postflowering reproductive development, which confers early-maturing varieties with appropriate vegetative growth and shortened reproductive growth periods for adaptation to high latitudes.

Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean

Soybean (Glycine max [L.] Merr.) is an important crop that provides protein and vegetable oil for human consumption. As soybean is a photoperiod-sensitive crop, its cultivation and yield are limited by the photoperiodic conditions in the field. In contrast to other major crops, soybean has a special plant architecture and a special symbiotic nitrogen fixation system, representing two unique breeding directions. Thus, flowering time, plant architecture, and symbiotic nitrogen fixation are three critical or unique yield-determining factors. This review summarizes the progress made in our understanding of these three critical yield-determining factors in soybean. Meanwhile, we propose potential research directions to increase soybean production, discuss the application of genomics and genomic-assisted breeding, and explore research directions to address future challenges, particularly those posed by global climate changes.

Editing the nuclear localization signals of E1 and E1Lb enables the production of tropical soybean in temperate growing regions

Soybean is a typical short-day crop, and most commercial soybean cultivars are restricted to a relatively narrow range of latitudes due to photoperiod sensitivity. Photoperiod sensitivity hinders the utilization of soybean germplasms across geographical regions. When grown in temperate regions, tropical soybean responds to prolonged day length by increasing the vegetative growth phase and delaying flowering and maturity, which often pushes the harvest window past the first frost date. In this study, we used CRISPR/LbCas12a to edit a North American subtropical soybean cultivar named 06KG218440 that belongs to maturity group 5.5. By designing one gRNA to edit the nuclear localization signal (NLS) regions of both E1 and E1Lb, we created a series of new germplasms with shortened flowering time and time to maturity and determined their favourable latitudinal zone for cultivation. The novel partial function alleles successfully achieve yield and early maturity trade-offs and exhibit good agronomic traits and high yields in temperate regions. This work offers a straightforward editing strategy to modify subtropical and tropical soybean cultivars for temperate growing regions, a strategy that could be used to enrich genetic diversity in temperate breeding programmes and facilitate the introduction of important crop traits such as disease tolerance or high yield.

Multi-locus genome-wide association studies reveal the dynamic genetic architecture of flowering time in chrysanthemum

KEY MESSAGE

The dynamic genetic architecture of flowering time in chrysanthemum was elucidated by GWAS. Thirty-six known genes and 14 candidate genes were identified around the stable QTNs and QEIs, among which ERF-1 was highlighted. Flowering time (FT) adaptation is one of the major breeding goals in chrysanthemum, a multipurpose ornamental plant. In order to reveal the dynamic genetic architecture of FT in chrysanthemum, phenotype investigation of ten FT-related traits was conducted on 169 entries in 2 environments. The broad-sense heritability of five non-conditional FT traits, i.e., budding (FBD), visible coloring (VC), early opening (EO), full-bloom (OF) and decay period (DP), ranged from 56.93 to 84.26%, which were higher than that of the five derived conditional FT traits (38.51-75.13%). The phenotypic variation coefficients of OF_EO and DP_OF were relatively large ranging from 30.59 to 36.17%. Based on 375,865 SNPs, the compressed variance component mixed linear model 3VmrMLM was applied for a multi-locus genome-wide association study (GWAS). As a result, 313 quantitative trait nucleotides (QTNs) were identified for the non-conditional FT traits in single-environment analysis, while 119 QTNs and 67 QTN-by-environment interactions (QEIs) were identified in multi-environment analysis. As for the conditional traits, 343 QTNs were detected in single-environment analysis, and 119 QTNs and 83 QEIs were identified in multi- environment analysis. Among the genes around stable QTNs and QEIs, 36 were orthologs of known FT genes in Arabidopsis and other plants; 14 candidates were mined by combining the transcriptomics data and functional annotation, including ERF-1, ACA10, and FOP1. Furthermore, the haplotype analysis of ERF-1 revealed six elite accessions with extreme FBD. Our findings contribute to the understanding of dynamic genetic architecture of FT and provide valuable resources for future chrysanthemum molecular breeding programs.

Gene-edited Mtsoc1 triple mutant Medicago plants do not flower

Optimized flowering time is an important trait that ensures successful plant adaptation and crop productivity. SOC1-like genes encode MADS transcription factors, which are known to play important roles in flowering control in many plants. This includes the best-characterized eudicot model Arabidopsis thaliana (Arabidopsis), where SOC1 promotes flowering and functions as a floral integrator gene integrating signals from different flowering-time regulatory pathways. Medicago truncatula (Medicago) is a temperate reference legume with strong genomic and genetic resources used to study flowering pathways in legumes. Interestingly, despite responding to similar floral-inductive cues of extended cold (vernalization) followed by warm long days (VLD), such as in winter annual Arabidopsis, Medicago lacks FLC and CO which are key regulators of flowering in Arabidopsis. Unlike Arabidopsis with one SOC1 gene, multiple gene duplication events have given rise to three MtSOC1 paralogs within the Medicago genus in legumes: one Fabaceae group A SOC1 gene, MtSOC1a, and two tandemly repeated Fabaceae group B SOC1 genes, MtSOC1b and MtSOC1c. Previously, we showed that MtSOC1a has unique functions in floral promotion in Medicago. The Mtsoc1a Tnt1 retroelement insertion single mutant showed moderately delayed flowering in long- and short-day photoperiods, with and without prior vernalization, compared to the wild-type. In contrast, Mtsoc1b Tnt1 single mutants did not have altered flowering time or flower development, indicating that it was redundant in an otherwise wild-type background. Here, we describe the generation of Mtsoc1a Mtsoc1b Mtsoc1c triple mutant lines using CRISPR-Cas9 gene editing. We studied two independent triple mutant lines that segregated plants that did not flower and were bushy under floral inductive VLD. Genotyping indicated that these non-flowering plants were homozygous for the predicted strong mutant alleles of the three MtSOC1 genes. Gene expression analyses using RNA-seq and RT-qPCR indicated that these plants remained vegetative. Overall, the non-flowering triple mutants were dramatically different from the single Mtsoc1a mutant and the Arabidopsis soc1 mutant; implicating multiple MtSOC1 genes in critical overlapping roles in the transition to flowering in Medicago.

Dynamic Expressions of Yellow Stripe-Like (YSL) Genes During Pod Development Shed Light on Associations with Iron Distribution in Phaseolus vulgaris

The global prevalence of iron deficiency-induced "hidden hunger" highlights a critical health concern, underscoring the pressing need to improve iron nutrition through safe and efficient means, such as increasing iron intake from plant-based foods. Yellow Stripe-Like (YSL) genes play a crucial role in long-distance iron transport between source and sink tissues in plants. Here, we report on the analysis of YSL family genes in the common bean (Phaseolus vulgaris L.), an iron-rich legume crop. We identified 9 YSL genes in the common bean genome using BLAST and HMM methods. Gene duplication analysis revealed that PvYSL7a and PvYSL7b originated through tandem duplication events. Structural analysis noted an absence of conservative motifs in PvYSL3b and PvYSL7a, which led to distinct predicted 3D protein structures. Leveraging publicly available RNA-seq data from developing bean pods, the expression patterns of PvYSL genes alongside pod and seed development were analyzed. Notably, PvYSL7a and PvYSL7b, as well as PvYSL1a and PvYSL1b, exhibited diverged expression patterns in seeds, signifying their functional divergence in this tissue. Moreover, PvYSL3a and PvYSL3b exhibited divergent expression patterns in both pod walls and seeds during pod development, underscoring their distinct roles in facilitating iron transportation between pods and seeds. This study provides valuable insights into the gene regulatory basis of iron accumulation in bean pods and seeds.

Dissection of the E8 locus in two early maturing Canadian soybean populations

Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.

Multi-locus genome-wide association study and genomic prediction for flowering time in chrysanthemum

MAIN CONCLUSION

Multi-locus GWAS detected several known and candidate genes responsible for flowering time in chrysanthemum. The associations could greatly increase the predictive ability of genome selection that accelerates the possible application of GS in chrysanthemum breeding. Timely flowering is critical for successful reproduction and determines the economic value for ornamental plants. To investigate the genetic architecture of flowering time in chrysanthemum, a multi-locus genome-wide association study (GWAS) was performed using a collection of 200 accessions and 330,710 single-nucleotide polymorphisms (SNPs) via 3VmrMLM method. Five flowering time traits including budding (FBD), visible colouring (VC), early opening (EO), full-bloom (OF) and senescing (SF) stages, plus five derived conditional traits were recorded in two environments. Extensive phenotypic variations were observed for these flowering time traits with coefficients of variation ranging from 6.42 to 38.27%, and their broad-sense heritability ranged from 71.47 to 96.78%. GWAS revealed 88 stable quantitative trait nucleotides (QTNs) and 93 QTN-by-environment interactions (QEIs) associated with flowering time traits, accounting for 0.50-8.01% and 0.30-10.42% of the phenotypic variation, respectively. Amongst the genes around these stable QTNs and QEIs, 21 and 10 were homologous to known flowering genes in Arabidopsis; 20 and 11 candidate genes were mined by combining the functional annotation and transcriptomics data, respectively, such as MYB55, FRIGIDA-like, WRKY75 and ANT. Furthermore, genomic selection (GS) was assessed using three models and seven unique marker datasets. We found the prediction accuracy (PA) using significant SNPs identified by GWAS under SVM model exhibited the best performance with PA ranging from 0.90 to 0.95. Our findings provide new insights into the dynamic genetic architecture of flowering time and the identified significant SNPs and candidate genes will accelerate the future molecular improvement of chrysanthemum.

Soybean WRINKLED1 protein GmWRI1a promotes flowering under long-day conditions via regulating expressions of flowering-related genes

Flowering time is an important agronomic character that influences the adaptability and yield of soybean [Glycine max (L.) Merrill]. WRINKLED 1 (WRI1) plays an important regulatory role in plant growth and development. In this study, we found that the expression of GmWIR1a could be induced by long days. Compared with the wild type, transgenic soybean overexpressing GmWRI1a showed earlier flowering and maturity under long days but no significant changes under short days. Overexpression of GmWRI1a led to up-regulated expression of genes involved in the regulation of flowering time. The GmWRI1a protein was able to directly bind to the promoter regions of GmAP1, GmFUL1a, GmFUL2 and up-regulated their expression. GmCOL3 was identified by yeast one-hybrid library screening using the GmWRI1a promoter as bait. GmCOL3 was revealed to be a nucleus-localized protein that represses the transcription of GmWRI1a. Expression of GmCOL3 was induced by short days. Taken together, the results show that overexpression of GmWRI1a promotes flowering under long days by promoting the transcriptional activity of flowering-related genes in soybean, and that GmCOL3 binds to the GmWRI1a promoter and directly down-regulates its transcription. This discovery reveals a new function for GmWRI1a, which regulates flowering and maturity in soybean.

Online data resource for exploring transposon insertion polymorphisms in public soybean germplasm accessions

Soybean (Glycine max L. Merrill) is one of the most important economical crops. A large number of whole-genome resequencing datasets have been generated and are increasingly expanded for exploring genetic diversity and mining important quantitative trait loci. Most genome-wide association studies have focused on single-nucleotide polymorphisms, short insertions, and deletions. Nevertheless, structure variants mainly caused by transposon element mobilization are not fully considered. To fill this gap, we uniformly processed the publicly available whole-genome resequencing data from 5,521 soybean germplasm accessions and built an online soybean transposon insertion polymorphisms database named Soybean Transposon Insertion Polymorphisms Database (SoyTIPdb) (https://biotec.njau.edu.cn/soytipdb). The collected germplasm accessions derived from more than 45 countries and 160 regions representing the most comprehensive genetic diversity of soybean. SoyTIPdb implements easy-to-use query, analysis, and browse functions to help understand and find meaningful structural variations from TE insertions. In conclusion, SoyTIPdb is a valuable data resource and will help soybean breeders/researchers take advantage of the whole-genome sequencing datasets available in the public depositories.

CpCAF1 from Chimonanthus praecox Promotes Flowering and Low-Temperature Tolerance When Expressed in Arabidopsis thaliana

CCR4-associated factor I (CAF1) is a deadenylase that plays a critical role in the initial step of mRNA degradation in most eukaryotic cells, and in plant growth and development. Knowledge of CAF1 proteins in woody plants remains limited. Wintersweet (Chimonanthus praecox) is a highly ornamental woody plant. In this study, CpCAF1 was isolated from wintersweet. CpCAF1 belongs to the DEDDh (Asp-Glu-Asp-Asp-His) subfamily of the DEDD (Asp-Glu-Asp-Asp) nuclease family. The amino acid sequence showed highest similarity to the homologous gene of Arabidopsis thaliana. In transgenic Arabidopsis overexpressing CpCAF1, the timing of bolting, formation of the first rosette, and other growth stages were earlier than those of the wild-type plants. Root, lateral branch, rosette leaf, and silique growth were positively correlated with CpCAF1 expression. FLOWERING LOCUS T (FT) and SUPPRESSOROF OVEREXPRESSION OF CO 1 (SOC1) gene expression was higher while EARLY FLOWERING3 (ELF3) and FLOWERING LOCUS C (FLC) gene expression of transgenic Arabidopsis was lower than the wild type grown for 4 weeks. Plant growth and flowering occurrences were earlier in transgenic Arabidopsis overexpressing CpCAF1 than in the wild-type plants. The abundance of the CpCAF1 transcript grew steadily, and significantly exceeded the initial level under 4 °C in wintersweet after initially decreasing. After low-temperature exposure, transgenic Arabidopsis had higher proline content and stronger superoxide dismutase activity than the wild type, and the malondialdehyde level in transgenic Arabidopsis was decreased significantly by 12 h and then increased in low temperature, whereas it was directly increased in the wild type. A higher potassium ion flux in the root was detected in transgenic plants than in the wild type with potassium deficiency. The CpCAF1 promoter was a constitutive promoter that contained multiple cis-acting regulatory elements. The DRE, LTR, and MYB elements, which play important roles in response to low temperature, were identified in the CpCAF1 promoter. These findings indicate that CpCAF1 is involved in flowering and low-temperature tolerance in wintersweet, and provide a basis for future genetic and breeding research on wintersweet.

A novel MORN-motif type gene GmMRF2 controls flowering time and plant height of soybean

The flowering time of soybean is a highly important agronomic characteristic, which affects the adaptability and yield. AtMRF1, a MORN-repeat motif gene, acts as a floral promoter in Arabidopsis, its functions in soybean are not yet understood. Here, we employed qRT-PCR to analyze the tissue expression patten of MRF1 homologs in soybean and determined that the GmMRF2 gene, containing a MORN-motif, highly expressed in the shoot and responded to photoperiod. GmMRF2 overexpression soybean lines exhibited earlier flowering time under long-day (LD) conditions, and increased plant height under both LD and short-day (SD) conditions compared to wild-type (WT) plants. The expression levels of gibberellic acid (GA) pathway genes that positively regulate plant height genes and flowering-promoting genes were up-regulated in the GmMRF2 overexpression lines, were up-regulated in the GmMRF2 overexpression lines. Further study revealed that GmMRF2 interacted with GmTCP15 to co-induce the expression of GmSOC1b. Together, our results preliminarily reveal the functions and mechanisms of GmMRF2 in regulating flowering time and plant height, provide a new promising gene for soybean crop improvement.

Molecular breeding for improvement of photothermal adaptability in soybean

Soybean (Glycine max (L.) Merr.) is a typical short-day and temperate crop that is sensitive to photoperiod and temperature. Responses of soybean to photothermal conditions determine plant growth and development, which affect its architecture, yield formation, and capacity for geographic adaptation. Flowering time, maturity, and other traits associated with photothermal adaptability are controlled by multiple major-effect and minor-effect genes and genotype-by-environment interactions. Genetic studies have identified at least 11 loci (E1-E4, E6-E11, and J) that participate in photoperiodic regulation of flowering time and maturity in soybean. Molecular cloning and characterization of major-effect flowering genes have clarified the photoperiod-dependent flowering pathway, in which the photoreceptor gene phytochrome A, circadian evening complex (EC) components, central flowering repressor E1, and FLOWERING LOCUS T family genes play key roles in regulation of flowering time, maturity, and adaptability to photothermal conditions. Here, we provide an overview of recent progress in genetic and molecular analysis of traits associated with photothermal adaptability, summarizing advances in molecular breeding practices and tools for improving these traits. Furthermore, we discuss methods for breeding soybean varieties with better adaptability to specific ecological regions, with emphasis on a novel strategy, the Potalaization model, which allows breeding of widely adapted soybean varieties through the use of multiple molecular tools in existing elite widely adapted varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01406-z.

TM3 and STM3 Promote Flowering Together with FUL2 and MBP20, but Act Antagonistically in Inflorescence Branching in Tomato

The moment at which a plant transitions to reproductive development is paramount to its life cycle and is strictly controlled by many genes. The transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) plays a central role in this process in Arabidopsis. However, the role of SOC1 in tomato (Solanum lycopersicum) has been sparsely studied. Here, we investigated the function of four tomato SOC1 homologs in the floral transition and inflorescence development. We thoroughly characterized the SOC1-like clade throughout the Solanaceae and selected four tomato homologs that are dynamically expressed upon the floral transition. We show that of these homologs, TOMATO MADS 3 (TM3) and SISTER OF TM3 (STM3) promote the primary and sympodial transition to flowering, while MADS-BOX PROTEIN 23 (MBP23) and MBP18 hardly contribute to flowering initiation in the indeterminate cultivar Moneyberg. Protein-protein interaction assays and whole-transcriptome analysis during reproductive meristem development revealed that TM3 and STM3 interact and share many targets with FRUITFULL (FUL) homologs, including cytokinin regulators. Furthermore, we observed that mutating TM3/STM3 affects inflorescence development, but counteracts the inflorescence-branching phenotype of ful2 mbp20. Collectively, this indicates that TM3/STM3 promote the floral transition together with FUL2/MBP20, while these transcription factors have opposite functions in inflorescence development.

SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics

Soybean (Glycine max (L.) Merr.) is a globally significant crop, widely cultivated for oilseed production and animal feeds. In recent years, the rapid growth of multi-omics data from thousands of soybean accessions has provided unprecedented opportunities for researchers to explore genomes, genetic variations, and gene functions. To facilitate the utilization of these abundant data for soybean breeding and genetic improvement, the SoybeanGDB database (https://venyao.xyz/SoybeanGDB/) was developed as a comprehensive platform. SoybeanGDB integrates high-quality de novo assemblies of 39 soybean genomes and genomic variations among thousands of soybean accessions. Genomic information and variations in user-specified genomic regions can be searched and downloaded from SoybeanGDB, in a user-friendly manner. To facilitate research on genetic resources and elucidate the biological significance of genes, SoybeanGDB also incorporates a variety of bioinformatics analysis modules with graphical interfaces, such as linkage disequilibrium analysis, nucleotide diversity analysis, allele frequency analysis, gene expression analysis, primer design, gene set enrichment analysis, etc. In summary, SoybeanGDB is an essential and valuable resource that provides an open and free platform to accelerate global soybean research.

The genetic architecture of soybean photothermal adaptation to high latitudes

Soybean is a major plant protein source for both human food and animal feed, but to meet global demands as well as a trend towards regional production, soybean cultivation needs to be expanded to higher latitudes. In this study, we developed a large diversity panel consisting of 1503 early-maturing soybean lines and used genome-wide association mapping to dissect the genetic architecture underlying two crucial adaptation traits, flowering time and maturity. This revealed several known maturity loci, E1, E2, E3, and E4, and the growth habit locus Dt2 as causal candidate loci, and also a novel putative causal locus, GmFRL1, encoding a homolog of the vernalization pathway gene FRIGIDA-like 1. In addition, the scan for quantitative trait locus (QTL)-by-environment interactions identified GmAPETALA1d as a candidate gene for a QTL with environment-dependent reversed allelic effects. The polymorphisms of these candidate genes were identified using whole-genome resequencing data of 338 soybeans, which also revealed a novel E4 variant, e4-par, carried by 11 lines, with nine of them originating from Central Europe. Collectively, our results illustrate how combinations of QTL and their interactions with the environment facilitate the photothermal adaptation of soybean to regions far beyond its center of origin.

The Transcription Factors WRKY41 and WRKY53 Mediate Early Flowering Induced by the Novel Plant Growth Regulator Guvermectin in Arabidopsis thaliana

Flowering is a crucial stage for plant reproductive success; therefore, the regulation of plant flowering has been widely researched. Although multiple well-defined endogenous and exogenous flowering regulators have been reported, new ones are constantly being discovered. Here, we confirm that a novel plant growth regulator guvermectin (GV) induces early flowering in Arabidopsis. Interestingly, our genetic experiments newly demonstrated that WRKY41 and its homolog WRKY53 were involved in GV-accelerated flowering as positive flowering regulators. Overexpression of WRKY41 or WRKY53 resulted in an early flowering phenotype compared to the wild type (WT). In contrast, the w41/w53 double mutants showed a delay in GV-accelerated flowering. Gene expression analysis showed that flowering regulatory genes SOC1 and LFY were upregulated in GV-treated WT, 35S:WRKY41, and 35S:WRKY53 plants, but both declined in w41/w53 mutants with or without GV treatment. Meanwhile, biochemical assays confirmed that SOC1 and LFY were both direct targets of WRKY41 and WRKY53. Furthermore, the early flowering phenotype of 35S:WRKY41 lines was abolished in the soc1 or lfy background. Together, our results suggest that GV plays a function in promoting flowering, which was co-mediated by WRKY41 and WRKY53 acting as new flowering regulators by directly activating the transcription of SOC1 and LFY in Arabidopsis.

Natural variation of FKF1 controls flowering and adaptation during soybean domestication and improvement

Soybean (Glycine max) is a major source of protein and edible oil world-wide and is cultivated in a wide range of latitudes. However, it is extremely sensitive to photoperiod, which influences flowering time, maturity, and yield, and severely limits soybean latitude adaptation. In this study, a genome-wide association study (GWAS) identified a novel locus in accessions harboring the E1 allele, called Time of flowering 8 (Tof8), which promotes flowering and enhances adaptation to high latitude in cultivated soybean. Gene functional analyses showed that Tof8 is an ortholog of Arabidopsis FKF1. We identified two FKF1 homologs in the soybean genome. Both FKF1 homologs are genetically dependent on E1 by binding to E1 promoter to activate E1 transcription, thus repressing FLOWERING LOCUS T 2a (FT2a) and FT5a transcription, which modulate flowering and maturity through the E1 pathway. We also demonstrate that the natural allele FKF1b^H3 facilitated adaptation of soybean to high-latitude environments and was selected during domestication and improvement, leading to its rapid expansion in cultivated soybean. These findings provide novel insights into the roles of FKF1 in controlling flowering time and maturity in soybean and offer new means to fine-tune adaptation to high latitudes and increase grain yield.

Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean

Soybean (Glycine max) is an economically important crop worldwide, serving as a major source of oil and protein for human consumption and animal feed. Cultivated soybean was domesticated from wild soybean (Glycine soja) which both species are highly sensitive to photoperiod and can grow over a wide geographical range. The extensive ecological adaptation of wild and cultivated soybean has been facilitated by a series of genes represented as quantitative trait loci (QTLs) that control photoperiodic flowering and maturation. Here, we review the molecular and genetic basis underlying the regulation of photoperiodic flowering in soybean. Soybean has experienced both natural and artificial selection during adaptation to different latitudes, resulting in differential molecular and evolutionary mechanisms between wild and cultivated soybean. The in-depth study of natural and artificial selection for the photoperiodic adaptability of wild and cultivated soybean provides an important theoretical and practical basis for enhancing soybean adaptability and yield via molecular breeding. In addition, we discuss the possible origin of wild soybean, current challenges, and future research directions in this important topic.

Diverse flowering responses subjecting to ambient high temperature in soybean under short-day conditions

Flowering time is one of important agronomic traits determining the crop yield and affected by high temperature. When facing high ambient temperature, plants often initiate early flowering as an adaptive strategy to escape the stress and ensure successful reproduction. However, here we find opposing ways in the short-day crop soybean to respond to different levels of high temperatures, in which flowering accelerates when temperature changes from 25 to 30 °C, but delays when temperature reaches 35 °C under short day. phyA-E1, possibly photoperiodic pathway, is crucial for 35 °C-mediated late flowering, however, does not contribute to promoting flowering at 30 °C. 30 °C-induced up-regulation of FT2a and FT5a leads to early flowering, independent of E1. Therefore, distinct responsive mechanisms are adopted by soybean when facing different levels of high temperatures for successful flowering and reproduction.

GhAP1-D3 positively regulates flowering time and early maturity with no yield and fiber quality penalties in upland cotton

Flowering time (FTi) is a major factor determining how quickly cotton plants reach maturity. Early maturity greatly affects lint yield and fiber quality and is crucial for mechanical harvesting of cotton in northwestern China. Yet, few quantitative trait loci (QTLs) or genes regulating early maturity have been reported in cotton, and the underlying regulatory mechanisms are largely unknown. In this study, we characterized 152, 68, and 101 loci that were significantly associated with the three key early maturity traits-FTi, flower and boll period (FBP) and whole growth period (WGP), respectively, via four genome-wide association study methods in upland cotton (Gossypium hirsutum). We focused on one major early maturity-related genomic region containing three single nucleotide polymorphisms on chromosome D03, and determined that GhAP1-D3, a gene homologous to Arabidopsis thaliana APETALA1 (AP1), is the causal locus in this region. Transgenic plants overexpressing GhAP1-D3 showed significantly early flowering and early maturity without penalties for yield and fiber quality compared to wild-type (WT) plants. By contrast, the mutant lines of GhAP1-D3 generated by genome editing displayed markedly later flowering than the WT. GhAP1-D3 interacted with GhSOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1), a pivotal regulator of FTi, both in vitro and in vivo. Changes in GhAP1-D3 transcript levels clearly affected the expression of multiple key flowering regulatory genes. Additionally, DNA hypomethylation and high levels of H3K9ac affected strong expression of GhAP1-D3 in early-maturing cotton cultivars. We propose that epigenetic modifications modulate GhAP1-D3 expression to positively regulate FTi in cotton through interaction of the encoded GhAP1 with GhSOC1 and affecting the transcription of multiple flowering-related genes. These findings may also lay a foundation for breeding early-maturing cotton varieties in the future.

Overexpression of the aldehyde dehydrogenase AhALDH3H1 from Arachis hypogaea in soybean increases saline-alkali stress tolerance

Soybean production is severely hampered by saline-alkaline stress caused by saline-alkalization. Plants have aldehydrogenase (ALDH) family members that convert reactive aldehydes to carboxylic acids to remove active aldehyde molecules. However, little is known about the increased saline-alkali tolerance caused by the ALDH function in soybean. Here, we introduced a previously identified ALDH coding gene AhALDH3H1 from Arachis hypogaea into the soybean genome to investigate its critical role in response to saline-alkali stress. Transgenic soybean with increased aldehyde dehydrogenase activity showed significant tolerance to saline-alkali stress. It reduced malondialdehyde (MDA) content compared to its receptor, suggesting that over-expression of AhALDH3H1 accelerated soybean tolerance to saline-alkali stress by increasing aldehyde dehydrogenase activity, which is responsible for scavenging toxic MDA. To further analyze the inner mechanisms that allow transgenic plants to tolerate saline-alkali stress, we sequenced the transcriptome and metabolome of P3 (wild type, WT) and transgenic lines which were separately treated with water and a saline-alkali solution. When subjected to saline-alkali stress, the integrated analysis of the transcriptome and metabolome suggested that several genes related to cell wall structure crucial for preserving cell wall extensibility and plasticity were largely responsible for restoring homeostasis within the transgenic cells compared to WT. Metabolites, including both necessary ingredients for cell wall genesis and harmful production produced during the saline-alkali stress response, could be transported efficiently with the help of the ABC transporter, reducing the negative effects of saline-alkali stress. These findings suggest that introducing AhALDH3H1 increases transgenic soybean tolerance to saline-alkali stress may through cell wall structure maintenance and metabolites transport.

Understandings and future challenges in soybean functional genomics and molecular breeding

Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.

Plant genetics: Mechanisms of wild soybean adaptation

A new study shows that natural variation in the flowering repressor E1-like-a (Tof4/E1La) promoted wild soybean adaptation to high latitudes. This lost early-flowering allele can be reintroduced into cultivated soybean for developing early-maturing cultivars.

The genetic basis of high-latitude adaptation in wild soybean

In many plants, flowering time is influenced by daylength as an adaptive response. In soybean (Glycine max) cultivars, however, photoperiodic flowering reduces crop yield and quality in high-latitude regions. Understanding the genetic basis of wild soybean (Glycine soja) adaptation to high latitudes could aid breeding of improved cultivars. Here, we identify the Tof4 (Time of flowering 4) locus, which encodes by an E1-like protein, E1La, that represses flowering and enhances adaptation to high latitudes in wild soybean. Moreover, we found that Tof4 physically associates with the promoters of two important FLOWERING LOCUS T (FT2a and FT5a) and with Tof5 to inhibit their transcription under long photoperiods. The effect of Tof4 on flowering and maturity is mediated by FT2a and FT5a proteins. Intriguingly, Tof4 and the key flowering repressor E1 independently but additively regulate flowering time, maturity, and grain yield in soybean. We determined that weak alleles of Tof4 have undergone natural selection, facilitating adaptation to high latitudes in wild soybean. Notably, over 71.5% of wild soybean accessions harbor the mutated alleles of Tof4 or a previously reported gain-of-function allele Tof5^H2, suggesting that these two loci are the genetic basis of wild soybean adaptation to high latitudes. Almost no cultivated soybean carries the mutated tof4 allele. Introgression of the tof4-1 and Tof5^H2 alleles into modern soybean or editing E1 family genes thus represents promising avenues to obtain early-maturity soybean, thereby improving productivity in high latitudes.

Altered regulation of flowering expands growth ranges and maximizes yields in major crops

Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.

Establishment of a novel experimental system for studying the photoperiodic response of short-day dicots using soybean 'cotyledon-only plant' as material

Soybean is an important model crop for photoperiodic response studies in plants and contributes significantly to the study of plant development and physiology in the past century. Because soybean plant is much bigger in size and longer in life cycle than Arabidopsis, it needs much more space for growth and time for investigation, which significantly hamper the efficiency of research. In the current study, we tested the photoperiodic response of a distinctive artificially-made cotyledon-only plant (COP) using a photoperiod-sensitive soybean variety Zigongdongdou (ZGDD) and other varieties with diverse sensitivity to photoperiod. ZGDD COPs flowered 39.4 ± 2.5 d after emergence under short-day conditions but maintained vegetative growth under long-day and night break conditions, which is similar to the case in the intact ZGDD plants. The COPs of early-maturing and medium-maturing soybean varieties also grew and flowered normally under natural day-length conditions. At the molecular level, the key genes in the photoperiodic pathway such as E1, GmFT1a, GmFT2a, and GmFT5a in the COPs also showed the same photoperiod sensitivity as in the intact plants. In addition, a simpler material of COP with only one cotyledon and root was generated and found to be sensitive to photoperiod as well. Notably, the COPs are only one-fifth the height of intact plants and one-third the maximum diameter of the intact plants grown in chambers 30 d after emergence. Based on COPs, we established a novel experimental system characterized by an entire photoperiodic response and longer longevity of cotyledons in addition to small plant size, ensuring the consistency, reliability, and stability of plant materials. COPs have the potential to be a novel model material for studies of the developmental biology of soybean and other dicots.

Candidate loci for breeding compact plant-type soybean varieties

Plant height and node number are important agronomic traits that influence yield in soybean (Glycine max L.). Here, to better understand the genetic basis of the traits, we used two recombinant inbred line (RIL) populations to detect quantitative trait loci (QTLs) associated with plant height and node number in different environments. This analysis detected 9 and 21 QTLs that control plant height and node number, respectively. Among them, we identified two genomic regions that overlap with Determinate stem 1 (Dt1) and Dt2, which are known to influence both plant height and node number. Furthermore, different combinations of Dt1 and Dt2 alleles were enriched in distinct latitudes. In addition, we determined that the QTLs qPH-13-SE and qPH-13-DW in the two RIL populations overlap with genomic intervals associated with plant height and the QTL qNN-04-DW overlaps with an interval associated with node number. Combining the dwarf allele of qPH-13-SE/qPH-13-DW and the multiple-node allele of qNN-04-DW produced plants with ideal plant architecture, i.e., shorter main stems with more nodes. This plant type may help increase yield at high planting density. This study thus provides candidate loci for breeding elite soybean cultivars for plant height and node number.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01352-2.

GIGANTEA orthologs, E2 members, redundantly determine photoperiodic flowering and yield in soybean

Soybean (Glycine max L.) is a typical photoperiod-sensitive crop, such that photoperiod determines its flowering time, maturity, grain yield, and phenological adaptability. During evolution, the soybean genome has undergone two duplication events, resulting in about 75% of all genes being represented by multiple copies, which is associated with rampant gene redundancy. Among duplicated genes, the important soybean maturity gene E2 has two homologs, E2-Like a (E2La) and E2-Like b (E2Lb), which encode orthologs of Arabidopsis GIGANTEA (GI). Although E2 was cloned a decade ago, we still know very little about its contribution to flowering time and even less about the function of its homologs. Here, we generated single and double mutants in E2, E2La, and E2Lb by genome editing and determined that E2 plays major roles in the regulation of flowering time and yield, with the two E2 homologs depending on E2 function. At high latitude regions, e2 single mutants showed earlier flowering and high grain yield. Remarkably, in terms of genetic relationship, genes from the legume-specific transcription factor family E1 were epistatic to E2. We established that E2 and E2-like proteins form homodimers or heterodimers to regulate the transcription of E1 family genes, with the homodimer exerting a greater function than the heterodimers. In addition, we established that the H3 haplotype of E2 is the ancestral allele and is mainly restricted to low latitude regions, from which the loss-of-function alleles of the H1 and H2 haplotypes were derived. Furthermore, we demonstrated that the function of the H3 allele is stronger than that of the H1 haplotype in the regulation of flowering time, which has not been shown before. Our findings provide excellent allelic combinations for classical breeding and targeted gene disruption or editing.

QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits

The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.

Natural variation of Dt2 determines branching in soybean

Shoot branching is fundamentally important in determining soybean yield. Here, through genome-wide association study, we identify one predominant association locus on chromosome 18 that confers soybean branch number in the natural population. Further analyses determine that Dt2 is the corresponding gene and the natural variations in Dt2 result in significant differential transcriptional levels between the two major haplotypes. Functional characterization reveals that Dt2 interacts with GmAgl22 and GmSoc1a to physically bind to the promoters of GmAp1a and GmAp1d and to activate their transcription. Population genetic investigation show that the genetic differentiation of Dt2 display significant geographic structure. Our study provides a predominant gene for soybean branch number and may facilitate the breeding of high-yield soybean varieties.

Novel and multifaceted regulations of photoperiodic flowering by phytochrome A in soybean

Plants know the exact time of flowering by sensing the photoperiod. Flowering time is an important agronomic trait in crops. In order to ensure that crops maintain high yields in different latitudes, cultivars need to accurately adjust the flowering time of plants according to local photoperiod and environmental conditions. In many plants, phytochromes have been found to be involved in photoperiodic flowering, but the molecular mechanisms of how they control photoperiod flowering are not fully understood. Through a series of biochemical, molecular, and genetic analyses of soybean phytochrome A, we reveal a photoperiod flowering mechanism in plants by which the phytochrome A regulates LUX and E1 activity.

Photoperiod is an important environmental cue. Plants can distinguish the seasons and flower at the right time through sensing the photoperiod. Soybean is a sensitive short-day crop, and the timing of flowering varies greatly at different latitudes, thus affecting yields. Soybean cultivars in high latitudes adapt to the long day by the impairment of two phytochrome genes, PHYA3 and PHYA2, and the legume-specific flowering suppressor, E1. However, the regulating mechanism underlying phyA and E1 in soybean remains largely unknown. Here, we classified the regulation of the E1 family by phyA2 and phyA3 at the transcriptional and posttranscriptional levels, revealing that phyA2 and phyA3 regulate E1 by directly binding to LUX proteins, the critical component of the evening complex, to regulate the stability of LUX proteins. In addition, phyA2 and phyA3 can also directly associate with E1 and its homologs to stabilize the E1 proteins. Therefore, phyA homologs control the core flowering suppressor E1 at both the transcriptional and posttranscriptional levels, to double ensure the E1 activity. Thus, our results disclose a photoperiod flowering mechanism in plants by which the phytochrome A regulates LUX and E1 activity.

Agronomical selection on loss-of-function of GIGANTEA simultaneously facilitates soybean salt tolerance and early maturity

Salt stress and flowering time are major factors limiting geographic adaptation and yield productivity in soybean (Glycine max). Although improving crop salt tolerance and latitude adaptation are essential for efficient agricultural production, whether and how these two traits are integrated remains largely unknown. Here, we used a genome-wide association study to identify a major salt-tolerance locus controlled by E2, an ortholog of Arabidopsis thaliana GIGANTEA (GI). Loss of E2 function not only shortened flowering time and maturity, but also enhanced salt-tolerance in soybean. E2 delayed soybean flowering by enhancing the transcription of the core flowering suppressor gene E1, thereby repressing Flowering Locus T (FT) expression. An E2 knockout mutant e2^CR displayed reduced accumulation of reactive oxygen species (ROS) during the response to salt stress by releasing peroxidase, which functions in ROS scavenging to avoid cytotoxicity. Evolutionary and population genetic analyses also suggested that loss-of-function e2 alleles have been artificially selected during breeding for soybean adaptation to high-latitude regions with greater salt stress. Our findings provide insights into the coupled selection for adaptation to both latitude and salt stress in soybean; and offer an ideal target for molecular breeding of early-maturing and salt-tolerant cultivars.

The Organ Size and Morphological Change During the Domestication Process of Soybean

Soybean is one of the most important legume crops that can provide the rich source of protein and oil for human beings and livestock. In the twenty-one century, the total production of soybean is seriously behind the needs of a growing world population. Cultivated soybean [Glycine max (L.) Merr.] was domesticated from wild soybean (G. soja Sieb. and Zucc.) with the significant morphology and organ size changes in China around 5,000 years ago, including twisted stems to erect stems, small seeds to large seeds. Then it was spread worldwide to become one of the most popular and important crops. The release of the reference soybean genome and omics data provides powerful tools for researchers and breeders to dissect the functional genes and apply the germplasm in their work. Here, we summarized the function genes related to yield traits and organ size in soybean, including stem growth habit, leaf size and shape, seed size and weight. In addition, we also summarized the selection of organ traits during soybean domestication. In the end, we also discussed the application of new technology including the gene editing on the basic research and breeding of soybean, and the challenges and research hotspots in the future.

Multi-Omics Techniques for Soybean Molecular Breeding

Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.

Flowering time: Soybean adapts to the tropics

Soybean plants - the source of tofu, as well as soybean milk and oil - flower quickly under short-day photoperiods typical of low latitudes. A new study characterises how natural variation in soybean SOC1 floral-promoting genes confers adaptation to different photoperiods.