GmTCP40 Promotes Soybean Flowering under Long-Day Conditions by Binding to the GmAP1a Promoter and Upregulating Its Expression.

Soybean [Glycine max (L.) Merr.] is a short-day (SD) plant that is sensitive to photoperiod, which influences flowering, maturity, and even adaptation. TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors have been shown to regulate photoperiodic flowering. However, the roles of TCPs in SD plants such as soybean, rice, and maize remain largely unknown. In this study, we cloned the GmTCP40 gene from soybean and investigated its expression pattern and function. Compared with wild-type (WT) plants, GmTCP40-overexpression plants flowered earlier under long-day (LD) conditions but not under SD conditions. Consistent with this, the overexpression lines showed upregulation of the flowering-related genes GmFT2a, GmFT2b, GmFT5a, GmFT6, GmAP1a, GmAP1b, GmAP1c, GmSOC1a, GmSOC1b, GmFULa, and GmAG under LD conditions. Further investigation revealed that GmTCP40 binds to the GmAP1a promoter and promotes its expression. Analysis of the GmTCP40 haplotypes and phenotypes of soybean accessions demonstrated that one GmTCP40 haplotype (Hap6) may contribute to delayed flowering at low latitudes. Taken together, our findings provide preliminary insights into the regulation of flowering time by GmTCP40 while laying a foundation for future research on other members of the GmTCP family and for efforts to enhance soybean adaptability.

Genome-wide association study for temperature response and photo-thermal interaction of flowering time in soybean using a panel of cultivars with diverse maturity groups.

KEY MESSAGE: A total of 101 QTNs were found to be associated with soybean flowering time responses to photo-thermal conditions; three candidate genes with non-synonymous substitutions were identified: Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). The flowering transition is a crucial component of soybean (Glycine max L. Merr.) development. The transition process is regulated by photoperiod, temperature, and their interaction. To examine the genetic architecture associated with temperature- and photo-thermal-mediated regulation of soybean flowering, we here performed a genome-wide association study using a panel of 201 soybean cultivars with maturity groups ranging from MG 000 to VIII. Each cultivar was grown in artificially controlled photoperiod and different seasons in 2017 and 2018 to assess the thermal response (TR) and the interactive photo-thermal response (IPT) of soybean flowering time. The panel contained 96,299 SNPs with minor allele frequencies > 5%; 33, 19, and 49 of these SNPs were significantly associated with only TR, only IPT, and both TR and IPT, respectively. Twenty-one SNPs were located in or near previously reported quantitative trait loci for first-flowering; 16 SNPs were located within 200 kb of the main-effect flowering genes GmFT2a, GmFT2b, GmFT3a, GmFT3b, GmFT5a, GmFT5b, GmCOL2b, GmPIF4b, and GmPIF4c, or near homologs of the known Arabidopsis thaliana flowering genes BBX19, VRN1, TFL1, FUL, AGL19, SPA1, HY5, PFT1, and EDF1. Natural non-synonymous allelic variations were identified in the candidate genes Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). Cultivars with different haplotypes showed significant variations in TR, IPT, and flowering time in multiple environments. The favorable alleles, candidate genes, and diagnostic SNP markers identified here provide valuable information for future improvement of soybean photo-thermal adaptability, enabling expansion of soybean production regions and improving plant resilience to global climate change.

Haplotype Analysis of GmSGF14 Gene Family Reveals Its Roles in Photoperiodic Flowering and Regional Adaptation of Soybean.

Flowering time and photoperiod sensitivity are fundamental traits that determine soybean adaptation to a given region or a wide range of geographic environments. The General Regulatory Factors (GRFs), also known as 14-3-3 family, are involved in protein-protein interactions in a phosphorylation-dependent manner, thus regulating ubiquitous biological processes, such as photoperiodic flowering, plant immunity and stress response. In this study, 20 soybean GmSGF14 genes were identified and divided into two categories according to phylogenetic relationships and structural characteristics. Real-time quantitative PCR analysis revealed that GmSGF14g, GmSGF14i, GmSGF14j, GmSGF14k, GmSGF14m and GmSGF14s were highly expressed in all tissues compared to other GmSGF14 genes. In addition, we found that the transcript levels of GmSGF14 family genes in leaves varied significantly under different photoperiodic conditions, indicating that their expression responds to photoperiod. To explore the role of GmSGF14 in the regulation of soybean flowering, the geographical distribution of major haplotypes and their association with flowering time in six environments among 207 soybean germplasms were studied. Haplotype analysis confirmed that the GmSGF14mH4 harboring a frameshift mutation in the 14-3-3 domain was associated with later flowering. Geographical distribution analysis demonstrated that the haplotypes related to early flowering were frequently found in high-latitude regions, while the haplotypes associated with late flowering were mostly distributed in low-latitude regions of China. Taken together, our results reveal that the GmSGF14 family genes play essential roles in photoperiodic flowering and geographical adaptation of soybean, providing theoretical support for further exploring the function of specific genes in this family and varietal improvement for wide adaptability.

Detection of type III effector-induced transcription factors that regulate phytohormone content during symbiosis establishment in soybean.

Soybean is a pivotal protein and oil crop that utilizes atmospheric nitrogen via symbiosis with rhizobium soil bacteria. Rhizobial type III effectors (T3Es) are essential regulators during symbiosis establishment. However, how the transcription factors involved in the interaction between phytohormone synthesis and type III effectors are connected is unclear. To detect the responses of phytohormone and transcription factor genes to rhizobial type III effector NopAA and type III secretion system, the candidate genes underlying soybean symbiosis were identified using RNA sequencing (RNA-seq) and phytohormone content analysis of soybean roots infected with wild-type Rhizobium and its derived T3E mutant. Via RNA-seq analysis the WRKY and ERF transcription factor families were identified as the most differentially expressed factors in the T3E mutant compared with the wild-type. Next, qRT-PCR was used to confirm the candidate genes Glyma.09g282900, Glyma.08g018300, Glyma.18g238200, Glyma.03g116300, Glyma.07g246600, Glyma.16g172400 induced by S. fredii HH103, S. fredii HH103ΩNopAA, and S. fredii HH103ΩRhcN. Since the WRKY and ERF families may regulate abscisic acid (ABA) content and underlying nodule formation, we performed phytohormone content analysis at 0.5 and 24 h post-inoculation (hpi). A significant change in ABA content was found between wild Rhizobium and type III effector mutant. Our results support that NopAA can promote the establishment of symbiosis by affecting the ABA signaling pathways by regulating WRKY and ERF which regulate the phytohormone signaling pathway. Specifically, our work provides insights into a signaling interaction of prokaryotic effector-induced phytohormone response involved in host signaling that regulates the establishment of symbiosis and increases nitrogen utilization efficiency in soybean plants.

Genome-Wide Identification of Candidate Genes Underlying Soluble Sugar Content in Vegetable Soybean (Glycine max L.) via Association and Expression Analysis.

Soluble sugar is a major indicator of the intrinsic quality of vegetable soybean [Glycine max (L.) Merr. ]. The improvement of soluble sugar content in soybean is very important due to its healthcare functions for humans. The genetic mechanism of soluble sugar in soybean is unclear. In this study, 278 diverse soybean accessions were utilized to identify the quantitative trait nucleotides (QTNs) for total soluble sugar content in soybean seeds based on a genome-wide association study (GWAS). A total of 25,921 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) ≥ 5% and missing data ≤ 10% were selected for GWAS. Totally, thirteen QTNs associated with total soluble sugar content were identified, which were distributed on ten chromosomes. One hundred and fifteen genes near the 200-kb flanking region of these identified QTNs were considered candidate genes associated with total soluble sugar content in soybean seed. Gene-based association analysis and haplotype analysis were utilized to further identify the effect of candidate genes on total soluble sugar content. Totally, 84 SNPs from seventeen genes across four chromosomes were significantly associated with the total soluble sugar content. Among them, three SNPs from Glyma.02G292900 were identified at two locations, and other eighty-one SNPs from sixteen genes were detected at three locations. Furthermore, expression level analysis of candidate genes revealed that Glyma.02G293200 and Glyma.02G294900 were significantly positively associated with soluble sugar content and Glyma.02G294000 was significantly negatively associated with soluble sugar content. Six genes (i.e., Glyma.02G292600, Glyma.02G292700, Glyma.02G294000, Glyma.02G294300, Glyma.02G294400, and Glyma.15G264200) identified by GWAS were also detected by the analysis of differential expression genes based on soybean germplasms with higher and lower soluble sugar content. Among them, Glyma.02G294000 is the only gene that was identified by gene-based association analysis with total soluble sugar content and was considered an important candidate gene for soluble sugar content. These candidate genes and beneficial alleles would be useful for improving the soluble sugar content of soybean.

Improving Ultra-Low Temperature Preservation Technologies of Soybean Pollen for Off-Season and Off-Site Hybridization.

Preserving viable pollen is of great interest to breeders to maintain desirable germplasm for future inbreeding. Ultra-low temperature preservation of pollen is an effective and safe way for long-term storage of plant germplasm resources. In this study, we improved methods for the preservation of soybean pollen at ultra-low temperature. Soybean flowers at the initially-open stage were collected at 6-10 a.m. during the fully-bloom stage of soybean plants and were dehydrated for 10 h and then frozen and stored at -196 or -80°C. In vitro culture experiments showed that the viability of preserved pollen remained as high as about 90%. The off-season (local site Heihe) and off-site (Beijing, after long-distance express delivery from Heihe) hybridization verification was conducted, and no significant difference in true hybrid rate was founded between the preserved pollen and the fresh pollen. The ultra-low temperature preservation technology for soybean pollen could break the spatiotemporal limit of soybean hybridization and facilitate the development of engineered soybean breeding.

Cotyledons facilitate the adaptation of early-maturing soybean varieties to high-latitude long-day environments.

Soybean (Glycine max), a typical short-day plant (SDP) domesticated in temperate regions, has expanded to high latitudes where daylengths are long from soybean emergence to bloom, but rapidly decrease from seed filling to maturity. Cotyledons are well known as the major storage organs in seeds, but it is unclear whether developing cotyledons store flowering substances at filling stage in SD for upcoming seedlings, or instead respond to photoperiod for floral induction after emergence of matured seeds in long-day (LD). Here, we report that cotyledons accelerate flowering of early-maturing varieties not resulting from stored floral stimuli but by perceiving photoperiod after emergence. We found that light signal is indispensable to activate cotyledons for floral induction, and flowering promoting gene GmFT2a is required for cotyledon-dependent floral induction via upregulation of floral identity gene GmAP1. Interestingly, cotyledons are competent to support the entire life cycle of a cotyledon-only plant to produce seeds, underlying a new photoperiod study system in soybean and other dicots. Taken together, these results demonstrate a substantial role for cotyledons in flowering process, whereby we propose a 'cotyledon-based self-reliance' model highlighting floral induction from emergence as a key ecological adaptation for rapid flowering of SDPs grown in LD environments at high latitudes.

Natural variation and CRISPR/Cas9-mediated mutation in GmPRR37 affect photoperiodic flowering and contribute to regional adaptation of soybean.

Flowering time is a critical determinant of the geographic distribution and regional adaptability of soybean (Glycine max) and is strongly regulated by photoperiod and temperature. In this study, quantitative trait locus (QTL) mapping and subsequent candidate gene analysis revealed that GmPRR37, encoding a pseudo-response regulator protein, is responsible for the major QTL qFT12-2, which was identified from a population of 308 recombinant inbred lines (RILs) derived from a cross between a very late-flowering soybean cultivar, 'Zigongdongdou (ZGDD)', and an extremely early-flowering cultivar, 'Heihe27 (HH27)', in multiple environments. Comparative analysis of parental sequencing data confirmed that HH27 contains a non-sense mutation that causes the loss of the CCT domain in the GmPRR37 protein. CRISPR/Cas9-induced Gmprr37-ZGDD mutants in soybean exhibited early flowering under natural long-day (NLD) conditions. Overexpression of GmPRR37 significantly delayed the flowering of transgenic soybean plants compared with wild-type under long photoperiod conditions. In addition, both the knockout and overexpression of GmPRR37 in soybean showed no significant phenotypic alterations in flowering time under short-day (SD) conditions. Furthermore, GmPRR37 down-regulated the expression of the flowering-promoting FT homologues GmFT2a and GmFT5a, and up-regulated flowering-inhibiting FT homologue GmFT1a expression under long-day (LD) conditions. We analysed haplotypes of GmPRR37 among 180 cultivars collected across China and found natural Gmprr37 mutants flower earlier and enable soybean to be cultivated at higher latitudes. This study demonstrates that GmPRR37 controls soybean photoperiodic flowering and provides opportunities to breed optimized cultivars with adaptation to specific regions and farming systems.

Genetic variation of maturity groups and four E genes in the Chinese soybean mini core collection.

The mini core collection (MCC) has been established by streamlining core collection (CC) chosen from China National Genebank including 23,587 soybean (Glycine max) accessions by morphological traits and simple sequence repeat (SSR) markers. Few studies have been focused on the maturity that has been considered as one of the most critical traits for the determination of the adaptation-growing region of the soybean. In the current study, two hundred and ninty-nine accessions of MCC planted for two years at four locations namely in Heihe, Harbin, Jining and Wuhan cities in China were used to assess the variation of maturity in MCC and identify the integrated effect of 4 E loci on flowering and maturity time in soybean. Forty-two North American varieties served as references of maturity groups (MG). Each accession in MCC was classified by comparing with the MG references in the days from VE (emergence) and physiological maturity (R7). The results showed that MCC covered a large range of MGs from MG000 to MGIX/X. Original locations and sowing types were revealed as the major affecting factors for maturity groups of the MCC accessions. The ratio of the reproductive period to the vegetative period (R/V) varied among MCC accessions. Genotyping of 4 maturity genes (i.e. E1, E2, E3 and E4) in 228 accessions indicated that recessive alleles e1, e2, e3 and e4 promoted earlier flowering and shortened the maturity time with different effects, while the dominate alleles were always detected in accessions with longer maturity. The allelic combinations determined the diversification of soybean maturity groups and adaptation to different regions. Our results indicated that the maturity of Chinese soybean MCC showed genetic diversities in phenotype and genotype, which provided information for further MG classification, geographic adaptation analysis of Chinese soybean cultivars, as well as developing new soybean varieties with adaptation to specific regions.

Maturity group classification and maturity locus genotyping of early-maturing soybean varieties from high-latitude cold regions.

BACKGROUND: With the migration of human beings, advances of agricultural sciences, evolution of planting patterns and global warming, soybeans have expanded to both tropical and high-latitude cold regions (HCRs). Unlike other regions, HCRs have much more significant and diverse photoperiods and temperature conditions over seasons or across latitudes, and HCR soybeans released there show rich diversity in maturity traits. However, HCR soybeans have not been as well classified into maturity groups (MGs) as other places. Therefore, it is necessary to identify MGs in HCRs and to genotype the maturity loci. METHODS: Local varieties were collected from the northern part of Northeast China and the far-eastern region of Russia. Maturity group reference (MGR) soybeans of MGs MG000, MG00, and MG0 were used as references during field experiments. Both local varieties and MGR soybeans were planted for two years (2010-2011) in Heihe (N 50°15', E 127°27', H 168.5 m), China. The days to VE (emergence), R1 (beginning bloom) and R7 (beginning maturity) were recorded and statistically analyzed. Furthermore, some varieties were further genotyped at four molecularly-identified maturity loci E1, E2, E3 and E4. RESULTS: The HCR varieties were classified into MG0 or even more early-maturing. In Heihe, some varieties matured much earlier than MG000, which is the most early-maturing known MG, and clustered into a separate group. We designated the group as MG0000, following the convention of MGs. HCR soybeans had relatively stable days to beginning bloom from emergence. The HCR varieties diversified into genotypes of E1, E2, E3 and E4. These loci had different effects on maturity. CONCLUSION: HCRs diversify early-maturing MGs of soybean. MG0000, a new MG that matures much earlier than known MGs, was developed. HCR soybean breeding should focus more on shortening post-flowering reproductive growth. E1, E2, E3, and E4 function differentially.