The Soybean-Specific Maturity Gene E1 Family of Floral Repressors Controls Night-Break Responses through Down-Regulation of FLOWERING LOCUS T Orthologs

Environmental and genetic regulation of plant height in soybean

BACKGROUND

Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce.

RESULTS

In this study, 308 representative soybean lines from a core collection and 168 F9 soybean progeny were planted at distinct field sites. The results demonstrated the presence of significant genotype × environment interaction (G × E) effects on traits associated with plant height in a natural soybean population. In total, 19 loci containing 51 QTLs (quantitative trait locus) for plant height were identified across four environments, with 23, 13 and 15 being QTLs for SH (shoot height), SNN (stem node number) and AIL (average internode length), respectively. Significant LOD ranging from 2.50 to 16.46 explained 2.80-26.10% of phenotypic variation. Intriguingly, only two loci, Loc11 and Loc19-1, containing 20 QTLs, were simultaneously detected across all environments. Results from Pearson correlation analysis and PCA (principal component analysis) revealed that each of the five agro-meteorological factors and four soil properties significantly affected soybean plant height traits, and that the corresponding QTLs had additive effects. Among significant environmental factors, AD (average day-length), AMaT (average maximum temperature), pH, and AN (available nitrogen) had the largest impacts on soybean plant height. Therefore, in spite of uncontrollable agro-meteorological factors, soybean shoot architecture might be remolded through combined efforts to produce superior soybean genetic materials while also optimizing soil properties.

CONCLUSIONS

Overall, the comprehensive set of relationships outlined herein among environment factors, soybean genotypes and QTLs in effects on plant height opens new avenues to explore in work aiming to increase soybean yield through improvements in shoot architecture.

The Candidate Photoperiod Gene MtFE Promotes Growth and Flowering in Medicago truncatula

Flowering time influences the yield and productivity of legume crops. Medicago truncatula is a reference temperate legume that, like the winter annual Arabidopsis thaliana, shows accelerated flowering in response to vernalization (extended cold) and long-day (LD) photoperiods (VLD). However, unlike A. thaliana, M. truncatula appears to lack functional homologs of core flowering time regulators CONSTANS (CO) and FLOWERING LOCUS C (FLC) which act upstream of the mobile florigen FLOWERING LOCUS T (FT). Medicago truncatula has three LD-induced FT-like genes (MtFTa1, MtFTb1, and MtFTb2) with MtFTa1 promoting M. truncatula flowering in response to VLD. Another photoperiodic regulator in A. thaliana, FE, acts to induce FT expression. It also regulates the FT transport pathway and is required for phloem development. Our study identifies a M. truncatula FE homolog Medtr6g444980 (MtFE) which complements the late flowering fe-1 mutant when expressed from the phloem-specific SUCROSE-PROTON SYMPORTER 2 (SUC2) promoter. Analysis of two M. truncatula Tnt1 insertional mutants indicate that MtFE promotes flowering in LD and VLD and growth in all conditions tested. Expression of MtFTa1, MtFTb1, and MtFTb2 are reduced in Mtfe mutant (NF5076), correlating with its delayed flowering. The NF5076 mutant plants are much smaller than wild type indicating that MtFE is important for normal plant growth. The second mutant (NF18291) displays seedling lethality, like strong fe mutants. We searched for mutants in MtFTb1 and MtFTb2 identifying a Mtftb2 knock out Tnt1 mutant (NF20803). However, it did not flower significantly later than wild type. Previously, yeast-two-hybrid assays (Y2H) suggested that Arabidopsis FE interacted with CO and NUCLEAR FACTOR-Y (NF-Y)-like proteins to regulate FT. We found that MtFE interacts with CO and also M. truncatula NF-Y-like proteins in Y2H experiments. Our study indicates that despite the apparent absence of a functional MtCO-like gene, M. truncatula FE likely influences photoperiodic FT expression and flowering time in M. truncatula via a partially conserved mechanism with A. thaliana.

Allele combinations of maturity genes E1-E4 affect adaptation of soybean to diverse geographic regions and farming systems in China

Appropriate flowering and maturity time are important for soybean production. Four maturity genes E1, E2, E3 and E4 have been molecularly identified and found to play major roles in the control of flowering and maturity of soybean. Here, to further investigate the effect of different allele combinations of E1-E4, we performed Kompetitive Allele Specific PCR (KASP) assays based on single nucleotide polymorphisms (SNPs) at these four E loci, and genotyped E1-E4 genes across 308 Chinese cultivars with a wide range of maturity groups. In total, twenty-one allele combinations for E1-E4 genes were identified across these Chinese cultivars. Various combinations of mutations at four E loci gave rise to the diversity of flowering and maturity time, which were associated with the adaptation of soybean cultivars to diverse geographic regions and farming systems. In particular, the cultivars with mutations at all four E loci reached flowering and maturity very early, and adapted to high-latitude cold regions. The allele combinations e1-as/e2-ns/e3-tr/E4, E1/e2-ns/E3/E4 and E1/E2/E3/E4 played important roles in the Northeast China, Huang-Huai-Hai (HHH) Rivers Valley and South China regions, respectively. Notably, E1 and E2, especially E2, affected flowering and maturity time of soybean significantly. Our study will be beneficial for germplasm evaluation, cultivar improvement and regionalization of cultivation in soybean production.

A Soybean Deletion Mutant That Moderates the Repression of Flowering by Cool Temperatures

Ambient growing temperature and photoperiod are major environmental stimuli that summer annual crops use to adjust their reproductive phenology so as to maximize yield. Variation in flowering time among soybean (Glycine max) cultivars results mainly from allelic diversity at loci that control photoperiod sensitivity and FLOWERING LOCUS T (FT) orthologs. However, variation in the thermal regulation of flowering and its underlying mechanisms are poorly understood. In this study, we identified a novel mutant (ef1) that confers altered thermal regulation of flowering in response to cool ambient temperatures. Mapping analysis with simple sequence repeat (SSR) markers located the mutation in the upper part of chromosome 19, where no QTL for flowering has been previously reported. Fine-mapping and re-sequencing revealed that the mutation was caused by deletion of a 214 kbp genomic region that contains 11 annotated genes, including CONSTANS-LIKE 2b (COL2b), a soybean ortholog of Arabidopsis CONSTANS. Comparison of flowering times under different photo-thermal conditions revealed that early flowering in the mutant lines was most distinct under cool ambient temperatures. The expression of two FT orthologs, FT2a and FT5a, was dramatically downregulated by cool temperature, but the magnitude of the downregulation was lower in the mutant lines. Cool temperatures upregulated COL2b expression or delayed peak expression, particularly at the fourth trifoliate-leaf stage. Intriguingly, they also upregulated E1, a soybean-specific repressor of FT orthologs. Our results suggest that the ef1 mutation is involved in thermal regulation of flowering in response to cool ambient temperature, and the lack of COL2b in the mutant likely alleviates the repression of flowering by cool temperature. The ef1 mutant can be used as a novel gene resource in breeding soybean cultivars adapted to cool climate and in research to improve our understanding of thermal regulation of flowering in soybean.

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.)

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

Characterization and quantitative trait locus mapping of late-flowering from a Thai soybean cultivar introduced into a photoperiod-insensitive genetic background

The timing of both flowering and maturation determine crop adaptability and productivity. Soybean (Glycine max) is cultivated across a wide range of latitudes. The molecular-genetic mechanisms for flowering in soybean have been determined for photoperiodic responses to long days (LDs), but remain only partially determined for the delay of flowering under short-day conditions, an adaptive trait of cultivars grown in lower latitudes. Here, we characterized the late-flowering (LF) habit introduced from the Thai cultivar K3 into a photoperiod-insensitive genetic background under different photo-thermal conditions, and we analyzed the genetic basis using quantitative trait locus (QTL) mapping. The LF habit resulted from a basic difference in the floral induction activity and from the suppression of flowering, which was caused by red light-enriched LD lengths and higher temperatures, during which FLOWERING LOCUS T (FT) orthologs, FT2a and FT5a, were strongly down-regulated. QTL mapping using gene-specific markers for flowering genes E2, FT2a and FT5a and 829 single nucleotide polymorphisms obtained from restriction-site associated DNA sequencing detected three QTLs controlling the LF habit. Of these, a QTL harboring FT2a exhibited large and stable effects under all the conditions tested. A resequencing analysis detected a nonsynonymous substitution in exon 4 of FT2a from K3, which converted the glycine conserved in FT-like proteins to the aspartic acid conserved in TERMINAL FLOWER 1-like proteins (floral repressors), suggesting a functional depression in the FT2a protein from K3. The effects of the remaining two QTLs, likely corresponding to E2 and FT5a, were environment dependent. Thus, the LF habit from K3 may be caused by the functional depression of FT2a and the down-regulation of two FT genes by red light-enriched LD conditions and high temperatures.

Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study

A core collection is a subset that represents genetic diversity of the total collection. Soybean (Glycine max (L.) Merr.) is one of major food and feed crops. It is the world's most cultivated annual herbaceous legume. Constructing a core collection for soybean could play a pivotal role in conserving and utilizing its genetic variability for research and breeding programs. To construct and evaluate a Korean soybean core collection, genotypic and phenotypic data as well as population structure, were analyzed. The Korean soybean core collection consisted of 430 accessions selected from 2,872 collections based on Affymetrix Axiom® 180k SoyaSNP array data. The core collection represented 99% of genotypic diversity of the total collection. Analysis of population structure clustered the core collection into five subpopulations. Accessions from South Korea and North Korea were distributed across five subpopulations. Analysis of molecular variance indicated that only 2.01% of genetic variation could be explained by geographic origins while 16.18% of genetic variation was accounted for by subpopulations. Genome-wide association study (GWAS) for days to flowering, flower color, pubescent color, and growth habit confirmed that the core collection had the same genetic diversity for tested traits as the total collection. The Korean soybean core collection was constructed based on genotypic information of the 180k SNP data. Size and phenotypic diversity of the core collection accounted for approximately 14.9% and 18.1% of the total collection, respectively. GWAS of core and total collections successfully confirmed loci associated with tested traits. Consequently, the present study showed that the Korean soybean core collection could provide fundamental and practical material and information for both soybean genetic research and breeding programs.

Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and Its Roles in Photoperiodic Flowering of Soybean

Photoperiodic flowering, a plant response to seasonal photoperiod changes in the control of reproductive transition, is an important agronomic trait that has been a central target of crop domestication and modern breeding programs. However, our understanding about the molecular mechanisms of photoperiodic flowering regulation in crop species is lagging behind. To better understand the regulatory gene networks controlling photoperiodic flowering of soybeans, we elucidated global gene expression patterns under different photoperiod regimes using the near isogenic lines (NILs) of maturity loci (E loci). Transcriptome signatures identified the unique roles of the E loci in photoperiodic flowering and a set of genes controlled by these loci. To elucidate the regulatory gene networks underlying photoperiodic flowering regulation, we developed the network inference algorithmic package CausNet that integrates sparse linear regression and Granger causality heuristics, with Gaussian approximation of bootstrapping to provide reliability scores for predicted regulatory interactions. Using the transcriptome data, CausNet inferred regulatory interactions among soybean flowering genes. Published reports in the literature provided empirical verification for several of CausNet's inferred regulatory interactions. We further confirmed the inferred regulatory roles of the flowering suppressors GmCOL1a and GmCOL1b using GmCOL1 RNAi transgenic soybean plants. Combinations of the alleles of GmCOL1 and the major maturity locus E1 demonstrated positive interaction between these genes, leading to enhanced suppression of flowering transition. Our work provides novel insights and testable hypotheses in the complex molecular mechanisms of photoperiodic flowering control in soybean and lays a framework for de novo prediction of biological networks controlling important agronomic traits in crops.

Loss of Function of the E1-Like-b Gene Associates With Early Flowering Under Long-Day Conditions in Soybean

Photoperiod response of flowering determines plant adaptation to different latitudes. Soybean, a short-day plant, has gained the ability to flower under long-day conditions during the growing season at higher latitudes, mainly through dysfunction of phytochrome A genes (E3 and E4) and the floral repressor E1. In this study, we identified a novel molecular genetic basis of photoperiod insensitivity in Far-Eastern Russian soybean cultivars. By testcrossing these cultivars with a Canadian cultivar Harosoy near-isogenic line for a recessive e3 allele, followed by association tests and fine mapping, we determined that the insensitivity was inherited as a single recessive gene located in an 842-kb interval in the pericentromeric region of chromosome 4, where E1-Like b (E1Lb), a homoeolog of E1, is located. Sequencing analysis detected a single-nucleotide deletion in the coding sequence of the gene in insensitive cultivars, which generated a premature stop codon. Near-isogenic lines (NILs) for the loss-of-function allele (designated e1lb) exhibited upregulated expression of soybean FLOWERING LOCUS T (FT) orthologs, FT2a and FT5a, and flowered earlier than those for E1Lb under long-day conditions in both the e3/E4 and E3/E4 genetic backgrounds. These NILs further lacked the inhibitory effect on flowering by far-red light-enriched long-day conditions, which is mediated by E4, but not that of red-light-enriched long-day conditions, which is mediated by E3. These findings suggest that E1Lb retards flowering under long-day conditions by repressing the expression of FT2a and FT5a independently of E1. This loss-of-function allele can be used as a new resource in breeding of photoperiod-insensitive cultivars, and may improve our understanding of the function of the E1 family genes in the photoperiod responses of flowering in soybean.

Photoperiodism dynamics during the domestication and improvement of soybean

Soybean (Glycine max) is a facultative short-day plant with a sensitive photoperiod perception and reaction system, which allows it to adjust its physiological state and gene regulatory networks to seasonal and diurnal changes in environmental conditions. In the past few decades, soybean cultivation has spread from East Asia to areas throughout the world. Biologists and breeders must now confront the challenge of understanding the molecular mechanism of soybean photoperiodism and improving agronomic traits to enable this important crop to adapt to geographical and environmental changes. In this review, we summarize the genetic regulatory network underlying photoperiodic responses in soybean. Genomic and genetic studies have revealed that the circadian clock, in conjunction with the light perception pathways, regulates photoperiodic flowering. Here, we provide an annotated list of 844 candidate flowering genes in soybean, with their putative biological functions. Many photoperiod-related genes have been intensively selected during domestication and crop improvement. Finally, we describe recent progress in engineering photoperiod-responsive genes for improving agronomic traits to enhance geographic adaptation in soybean, as well as future prospects for research on soybean photoperiodic responses.

Molecular mechanisms of flowering under long days and stem growth habit in soybean

Precise timing of flowering is critical to crop adaptation and productivity in a given environment. A number of classical E genes controlling flowering time and maturity have been identified in soybean [Glycine max (L.) Merr.]. The public availability of the soybean genome sequence has accelerated the identification of orthologues of Arabidopsis flowering genes and their functional analysis, and has allowed notable progress towards understanding the molecular mechanisms of flowering in soybean. Great progress has been made particularly in identifying genes and modules that inhibit flowering in long-day conditions, because a reduced or absent inhibition of flowering by long daylengths is an essential trait for soybean, a short-day (SD) plant, to expand its adaptability toward higher latitude environments. In contrast, the molecular mechanism of floral induction by SDs remains elusive in soybean. Here we present an update on recent work on molecular mechanisms of flowering under long days and of stem growth habit, outlining the progress in the identification of genes responsible, the interplay between photoperiod and age-dependent miRNA-mediated modules, and the conservation and divergence in photoperiodic flowering and stem growth habit in soybean relative to other legumes, Arabidopsis, and rice (Oryza sativa L.).

Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean

KEY MESSAGE

E10 is a new maturity locus in soybean and FT4 is the predicted/potential functional gene underlying the locus. Flowering and maturity time traits play crucial roles in economic soybean production. Early maturity is critical for north and west expansion of soybean in Canada. To date, 11 genes/loci have been identified which control time to flowering and maturity; however, the molecular bases of almost half of them are not yet clear. We have identified a new maturity locus called "E10" located at the end of chromosome Gm08. The gene symbol E10e10 has been approved by the Soybean Genetics Committee. The e10e10 genotype results in 5-10 days earlier maturity than E10E10. A set of presumed E10E10 and e10e10 genotypes was used to identify contrasting SSR and SNP haplotypes. These haplotypes, and their association with maturity, were maintained through five backcross generations. A functional genomics approach using a predicted protein-protein interaction (PPI) approach (Protein-protein Interaction Prediction Engine, PIPE) was used to investigate approximately 75 genes located in the genomic region that SSR and SNP analyses identified as the location of the E10 locus. The PPI analysis identified FT4 as the most likely candidate gene underlying the E10 locus. Sequence analysis of the two FT4 alleles identified three SNPs, in the 5'UTR, 3'UTR and fourth exon in the coding region, which result in differential mRNA structures. Allele-specific markers were developed for this locus and are available for soybean breeders to efficiently develop earlier maturing cultivars using molecular marker assisted breeding.

Genetic separation of southern and northern soybean breeding programs in North America and their associated allelic variation at four maturity loci

North American soybean breeders have successfully developed a large number of elite cultivars with diverse maturity groups (MG) from a small number of ancestral landraces. To understand molecular and genetic basis underlying the large variation in their maturity and flowering times, we integrated pedigree and maturity data of 166 cultivars representing North American soybean breeding. Network analysis and visualization of their pedigree relationships revealed a clear separation of southern and northern soybean breeding programs, suggesting that little genetic exchange occurred between northern (MG 0-IV) and southern cultivars (MG V-VIII). We also analyzed the transcript sequence and expression levels of four major maturity genes (E1 to E4) and revealed their allelic variants in 75 major ancestral landraces and milestone cultivars. We observed that e1-as was the predominant e mutant allele in northern genotypes, followed by e2 and e3. There was no allelic variation at E4. Transcript accumulation of the e2 mutant allele was significantly reduced, which might be caused by its premature stop codon triggering the nonsense-mediated mRNA decay pathway. The large DNA deletion generating the e3 mutant allele also created a gene fusion transcript. The e alleles found in milestone cultivars were traced through pedigrees to their ancestral landraces and geographic origins. Our analysis revealed an approximate correlation between dysfunctional alleles and maturity groups for most of the 75 cultivars. However, single e mutant alleles and their combinations were not sufficient to fully explain their maturity diversity, suggesting that additional genes/alleles are likely involved in regulating maturity time.

The loss of vernalization requirement in narrow-leafed lupin is associated with a deletion in the promoter and de-repressed expression of a Flowering Locus T (FT) homologue

Adaptation of Lupinus angustifolius (narrow-leafed lupin) to cropping in southern Australian and northern Europe was transformed by a dominant mutation (Ku) that removed vernalization requirement for flowering. The Ku mutation is now widely used in lupin breeding to confer early flowering and maturity. We report here the identity of the Ku mutation. We used a range of genetic, genomic and gene expression approaches to determine whether Flowering Locus T (FT) homologues are associated with the Ku locus. One of four FT homologues present in the narrow-leafed lupin genome, LanFTc1, perfectly co-segregated with the Ku locus in a reference mapping population. Expression of LanFTc1 in the ku (late-flowering) parent was strongly induced by vernalization, in contrast to the Ku (early-flowering) parent, which showed constitutively high LanFTc1 expression. Co-segregation of this expression phenotype with the LanFTc1 genotype indicated that the Ku mutation impairs cis-regulation of LanFTc1. Sequencing of LanFTc1 revealed a 1.4-kb deletion in the promoter region, which was perfectly predictive of vernalization response in 216 wild and domesticated accessions. Linkage disequilibrium rapidly decayed around LanFTc1, suggesting that this deletion caused the loss of vernalization response. This is the first time a legume FTc subclade gene has been implicated in the vernalization response.

Assessment of Soybean Flowering and Seed Maturation Time in Different Latitude Regions of Kazakhstan

Soybean is still a minor crop in Kazakhstan despite an increase in planting area from 4,500 to 11,400 km2 between 2006 and 2014. However, the Government's recently accepted crop diversification policy projects the expansion of soybean cultivation area to more than 40,000 km2 by 2020. The policy is targeting significant expansion of soybean production in South-eastern, Eastern, and Northern regions of Kazakhstan. Successful realization of this policy requires a comprehensive characterization of plant growth parameters to identify optimal genotypes with appropriate adaptive phenotypic traits. In this study 120 soybean accessions from different parts of the World, including 18 accessions from Kazakhstan, were field tested in South-eastern, Eastern, and Northern regions of the country. These studies revealed positive correlation of yield with flowering time in Northern Kazakhstan, with seed maturity time in Eastern Kazakhstan, and with both these growth stages in South-eastern Kazakhstan. It was determined that in South-eastern, Eastern and Northern regions of Kazakhstan the majority of productive genotypes were in maturity groups MGI, MG0, and MG00, respectively. The accessions were genotyped for four major maturity genes (E1, E2, E3, and E4) in order to assess the relationship between E loci and agronomic traits. The allele composition of the majority of accessions was e1-as/e2/E3/E4 (specific frequencies 57.5%, 91.6%, 65.0%, and 63.3%, respectively). Accessions with dominant alleles in either E3 or E4 genes showed higher yield in all three regions, although the specific genotype associated with greatest productivity was different for each site. Genotype-environment interaction studies based on yield performances suggest that South-east and East regions formed one mega-environment, which was well separated from North Kazakhstan where significantly earlier time to maturation is required. The results provide important insights into the relationship between genetic and phenotypic patterns in new soybean growing territories in Kazakhstan.

A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog

FLOWERING LOCUS T (FT) is an important floral integrator whose functions are conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a major role in initiating flowering. Their expression in response to different photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, generating variation in flowering time among cultivars. We determined the molecular basis of a quantitative trait locus (QTL) for flowering time in linkage group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an intron, and the 3' untranslated region of FT5a, although the FT5a coding regions were identical. Transcript abundance of FT5a was higher in near-isogenic lines for ef than in those for lf, suggesting that different transcriptional activities or mRNA stability caused the flowering time difference. Single-nucleotide polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild soybean accessions indicated that ef is a rare haplotype that is distinct from common haplotypes including lf The ef allele at FT5a may play an adaptive role at latitudes where early flowering is desirable.

Functional conservation and diversification of the soybean maturity gene E1 and its homologs in legumes

Gene regulatory networks involved in flowering time and photoperiodic responses in legumes remain unknown. Although the major maturity gene E1 has been successfully deciphered in soybean, knowledge on the functional conservation of this gene is limited to a certain extent to E1 homologs in legumes. The ectopic expression of Phvul.009G204600 (PvE1L), an E1 homolog from common bean, delayed the onset of flowering in soybean. By contrast, the ectopic expression of Medtr2g058520 (MtE1L) from Medicago truncatula did not affect the flowering of soybean. Characterization of the late-flowering mte1l mutant indicated that MtE1L promoted flowering in Medicago truncatula. Moreover, all transgenic E1, PvE1L and MtE1L soybean lines exhibited phenotypic changes in terms of plant height. Transgenic E1 or PvE1L plants were taller than the wild-type, whereas transgenic MtE1L plants produced dwarf phenotype with few nodes and short internode. Thus, functional conservation and diversification of E1 family genes from legumes in the regulation of flowering and plant growth may be associated with lineage specification and genomic duplication.

Functional conservation and diversification of the soybean maturity gene E1 and its homologs in legumes

Gene regulatory networks involved in flowering time and photoperiodic responses in legumes remain unknown. Although the major maturity gene E1 has been successfully deciphered in soybean, knowledge on the functional conservation of this gene is limited to a certain extent to E1 homologs in legumes. The ectopic expression of Phvul.009G204600 (PvE1L), an E1 homolog from common bean, delayed the onset of flowering in soybean. By contrast, the ectopic expression of Medtr2g058520 (MtE1L) from Medicago truncatula did not affect the flowering of soybean. Characterization of the late-flowering mte1l mutant indicated that MtE1L promoted flowering in Medicago truncatula. Moreover, all transgenic E1, PvE1L and MtE1L soybean lines exhibited phenotypic changes in terms of plant height. Transgenic E1 or PvE1L plants were taller than the wild-type, whereas transgenic MtE1L plants produced dwarf phenotype with few nodes and short internode. Thus, functional conservation and diversification of E1 family genes from legumes in the regulation of flowering and plant growth may be associated with lineage specification and genomic duplication.

A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog

BACKGROUND

Understanding the molecular mechanisms of flowering and maturity is important for improving the adaptability and yield of seed crops in different environments. In soybean, a facultative short-day plant, genetic variation at four maturity genes, E1 to E4, plays an important role in adaptation to environments with different photoperiods. However, the molecular basis of natural variation in time to flowering and maturity is poorly understood. Using a cross between early-maturing soybean cultivars, we performed a genetic and molecular study of flowering genes. The progeny of this cross segregated for two maturity loci, E1 and E9. The latter locus was subjected to detailed molecular analysis to identify the responsible gene.

RESULTS

Fine mapping, sequencing, and expression analysis revealed that E9 is FT2a, an ortholog of Arabidopsis FLOWERING LOCUS T. Regardless of daylength conditions, the e9 allele was transcribed at a very low level in comparison with the E9 allele and delayed flowering. Despite identical coding sequences, a number of single nucleotide polymorphisms and insertions/deletions were detected in the promoter, untranslated regions, and introns between the two cultivars. Furthermore, the e9 allele had a Ty1/copia-like retrotransposon, SORE-1, inserted in the first intron. Comparison of the expression levels of different alleles among near-isogenic lines and photoperiod-insensitive cultivars indicated that the SORE-1 insertion attenuated FT2a expression by its allele-specific transcriptional repression. SORE-1 was highly methylated, and did not appear to disrupt FT2a RNA processing.

CONCLUSIONS

The soybean maturity gene E9 is FT2a, and its recessive allele delays flowering because of lower transcript abundance that is caused by allele-specific transcriptional repression due to the insertion of SORE-1. The FT2a transcript abundance is thus directly associated with the variation in flowering time in soybean. The e9 allele may maintain vegetative growth in early-flowering genetic backgrounds, and also be useful as a long-juvenile allele, which causes late flowering under short-daylength conditions, in low-latitude regions.