Variation in the durations of the photoperiod-sensitive and photoperiod-insensitive phases of development to flowering among eight maturity isolines of soyabean [Glycine max (L.) Merrill]

The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity

The general concept of photoperiodism, i.e., the photoperiodic induction of flowering, was established by Garner and Allard (1920). The genetic factor controlling flowering time, maturity, or photoperiodic responses was observed in soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named in 1971 and, thereafter, genetically characterized. At the centennial celebration of the discovery of photoperiodism in soybean, we recount our endeavors to successfully decipher the molecular bases for the major maturity loci E1, E2, and E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful identification of several circadian-related genes such as PRR3a, LUX, and J has enriched the known major E1-FTs pathway. Further research progresses on the identification of new flowering and maturity-related genes as well as coordinated regulation between flowering genes will enable us to understand profoundly flowering gene network and determinants of latitudinal adaptation in soybean.

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.

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.

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.

Soybean fruit development and set at the node level under combined photoperiod and radiation conditions

In soybean, long days during post-flowering increase seed number. This positive photoperiodic effect on seed number has been previously associated with increments in the amount of radiation accumulated during the crop cycle because long days extend the duration of the crop cycle. However, evidence of intra-nodal processes independent of the availability of assimilates suggests that photoperiodic effects at the node level might also contribute to pod set. This work aims to identify the main mechanisms responsible for the increase in pod number per node in response to long days; including the dynamics of flowering, pod development, growth and set at the node level. Long days increased pods per node on the main stems, by increasing pods on lateral racemes (usually dominated positions) at some main stem nodes. Long days lengthened the flowering period and thereby increased the number of opened flowers on lateral racemes. The flowering period was prolonged under long days because effective seed filling was delayed on primary racemes (dominant positions). Long days also delayed the development of flowers into pods with filling seeds, delaying the initiation of pod elongation without modifying pod elongation rate. The embryo development matched the external pod length irrespective of the pod's chronological age. These results suggest that long days during post-flowering enhance pod number per node through a relief of the competition between pods of different hierarchy within the node. The photoperiodic effect on the development of dominant pods, delaying their elongation and therefore postponing their active growth, extends flowering and allows pod set at positions that are usually dominated.

The alleles at the E1 locus impact the expression pattern of two soybean FT-like genes shown to induce flowering in Arabidopsis

A small gene family of phosphatidyl ethanolamine-binding proteins (PEBP) has been shown to function as key regulators in flowering; in Arabidopsis thaliana the FT protein promotes flowering whilst the closely related TFL1 protein represses flowering. Control of flowering time in soybean [Glycine max (L.) Merrill] is important for geographic adaptation and maximizing yield. Soybean breeders have identified a series of loci, the E-genes, that control photoperiod-mediated flowering time, yet how these loci control flowering is poorly understood. The objectives of this study were to evaluate the expression of GmFT-like genes in the E1 near-isogenic line (NIL) background. Of the 20 closely related PEBP proteins in the soybean genome, ten are similar to the Arabidopsis FT protein. Expression analysis of these ten GmFT-like genes confirmed that only two are detectable in the conditions tested. Further analysis of these two genes in the E1 NILs grown under short-day (SD) and long-day (LD) conditions showed a diurnal expression and tissue specificity expression commensurate with soybean flowering time under SD and LD conditions, suggesting that these were good candidates for flowering induction in soybean. Arabidopsis ft mutant lines flowered early when transformed with the two soybean genes, suggesting that the soybean genes can complement the Arabidopsis FT function. Flowering time in E1 NILs is consistent with the differential expression of the two GmFT-like genes under SD and LD conditions, suggesting that the E1 locus, at least in part, impacts time to flowering through the regulation of soybean FT expression.

Expression of flowering-time genes in soybean E1 near-isogenic lines under short and long day conditions

Control of soybean flowering time is important for geographic adaptation and maximizing yield. Plant breeders have identified a series of genes (E genes) that condition time to flowering; however, the molecular basis in the control of flowering by these E genes, in conjunction with canonical flowering-time genes, has not been studied. Time to flowering in near-isogenic lines (NILs) at the E1 locus was tested using a reciprocal transfer experiment under short day (SD) and long day (LD) conditions. Beginning 8 days after planting, three plant samples were harvested every 3 h for a 48-h period. RNA was isolated from these plants, and RNA samples were pooled for each line and each time period for cDNA synthesis. RT-PCR analysis was performed using primers synthesized for a number of putative flowering-time genes based on homology of soybean EST and genomic sequences to Arabidopsis genes. The results of the reciprocal transfer experiment suggest that the pre-inductive photoperiod-sensitive phase of the E1 NILs responsible for inducing flowering is perceived as early as 5-7-day post-planting. No gene expression differences were found between the E1 and e1 NILs, suggesting that the E1 gene does not directly affect the flowering-time genes during the time period tested; however, differences were observed in gene expression between SD and LD treatments for the putative soybean TOC1, CO, and FT genes. The gene expression results in this study were similar to those of flowering-time genes found in other SD species, suggesting that the selected genes correspond to the soybean flowering-time orthologs.

Comparison of environmental and mutational variation in flowering time in Arabidopsis

Developmental dynamics can be influenced by external and endogenous factors in a more or less analogous manner. To compare the phenotypic effects of (i) environmental [i.e. standard (stPhP) and extended (exPhP) photoperiods] changes in Arabidopsis wild types and (ii) endogenous genetic variation in eav1-eav61 early flowering mutants, two temporal indicators were analysed, the time to bolting (DtB) and the number of leaves (TLN). It was found that DtB and TLN are differentially affected in different environmental and genetic contexts, and some factors of dynamic convergence were identified. The quantitative response to photoperiod is markedly contingent on the phototrophic input for DtB, but less so for TLN. To discriminate the light quantity and period components in DtB, two novel temporal indicators were determined, LtB (photosynthetic time to bolting) and PChron (DtB h(-1) of photoperiod), respectively. The use of PChron results in a coincidence of the variation profiles across stPhP and exPhP, interpreted as a buffering of the trophic response. Unlike natural accessions and later flowering mutants, the variation profiles across stPhP and eav mutants are significantly divergent, pointing to differences in environmental and genetic variation in flowering time. Yet, phenocopy effects and dynamic convergence between wild-type and mutant profiles are detected by using exPhP and the LtB indicator. Additional analyses of the cauline leaf number (CLN) show that the apical and basal boundaries of the primary inflorescence vary co-ordinately. The finding that the correlativity between CLN and TLN changes across photoperiods suggests that different states of intra-connectedness are involved in ontogenetic specification of flowering time and embodied in the primary inflorescence.

Use of field observations to characterise genotypic flowering responses to photoperiod and temperature: a soyabean exemplar

Thirty-nine accessions of soyabean [Glycine max (L.) Merrill] and 1 of wild annual soyabean (Glycine soja L.) were sown at two sites in Taiwan in 1989 and 1990 and on six occasions during 1990 at one site in Queensland, Australia. On two of the occasions in Australia additional treatments extended natural daylengths by 0.5 h and 2 h. The number of days from sowing for the first flower to appear on 50% of the plants in each treatment was recorded (f), and from these values the rate of progress towards flowering (1/f) was related to temperature and photoperiod. In photoperiod-insensitive accessions it was confirmed that the rate is linearly related to temperature at least up to about 29°C. In photoperiod-sensitive genotypes this is also the case in shorter daylengths but when the critical photoperiod (P c) is exceeded flowering is delayed. This delay increases with photoperiod until a ceiling photoperiod (P ce) is reached. Between P c and P ce, 1/f is linearly related to both temperature (positive) and photoperiod (negative), but in photoperiods longer than P ce there is no further response to either factor. The resulting triple-intersecting-plane response surface can be defined by six genetically-determined coefficients, the values of which are environment-independent but predict time to flower in any environment, and thus quantify the genotype x environment interaction. By this means the field data were used to characterise the photothermal responses of all 40 accessions. The outcome of this characterisation in conjunction with an analysis of the world-wide range of photothermal environments in which soyabean crops are grown lead to the following conclusions: (1) photoperiod-insensitivity is essential in soyabean crops in temperate latitudes, but such genotypes flower too rapidly for satisfactory yields in the tropics; (2) photoperiod-sensitivity appears to be essential to delay flowering sufficiently to allow adequate biomass accumulation in the warm climates of the tropics; (3) contrary to a widely held view, some degree of photoperiod-sensitivity is also needed in the tropics if crop-duration homeostasis is required where there is variation in sowing dates (this is achieved through a photoperiod-controlled delay in flowering which counteracts the seasonal increase in temperature that is correlated with increase in day-length); and (4) a greater degree of photoperiod-sensitivity is necessary to provide maturity-date homeostasis for variable sowing dates - a valuable attribute in regions of uncertain rainfall. Since the triple-intersecting-plane response model used here also applies to other species, the use of field data to characterise the photothermal responses of other crops is discussed briefly.