Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering

Abstract

The complex and coordinated regulation of flowering has high ecological and agricultural significance. The maturity locus E1 has a large impact on flowering time in soybean, but the molecular basis for the E1 locus is largely unknown. Through positional cloning, we delimited the E1 locus to a 17.4-kb region containing an intron-free gene (E1). The E1 protein contains a putative bipartite nuclear localization signal and a region distantly related to B3 domain. In the recessive allele, a nonsynonymous substitution occurred in the putative nuclear localization signal, leading to the loss of localization specificity of the E1 protein and earlier flowering. The early-flowering phenotype was consistently observed in three ethylmethanesulfonate-induced mutants and two natural mutations that harbored a premature stop codon or a deletion of the entire E1 gene. E1 expression was significantly suppressed under short-day conditions and showed a bimodal diurnal pattern under long-day conditions, suggesting its response to photoperiod and its dominant effect induced by long day length. When a functional E1 gene was transformed into the early-flowering cultivar Kariyutaka with low E1 expression, transgenic plants carrying exogenous E1 displayed late flowering. Furthermore, the transcript abundance of E1 was negatively correlated with that of GmFT2a and GmFT5a, homologues of FLOWERING LOCUS T that promote flowering. These findings demonstrated the key role of E1 in repressing flowering and delaying maturity in soybean. The molecular identification of the maturity locus E1 will contribute to our understanding of the molecular mechanisms by which a short-day plant regulates flowering time and maturity. photoperiodism | quantitative trait locus | photoperiodic insensibility

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…We identified some local differentiation signals that have not been detected previously in the screening of domestication and improvement selection, such as the E1 gene, which is responsible for the major flowering time (FT) QTL 29,30 . Typically, soybeans in northern regions have shorter maturity periods, whereas those in southern regions have longer maturity periods 31 .…”

Genetic Variation in Soybean at the Maturity Locus E4 Is Involved in Adaptation to Long Days at High Latitudes

“…The dysfunction of e4 allele in Miharudaizu is caused by an insertion of a Ty1/copia-like retrotransposon, SORE-1, in exon 1 [17]. An analysis with allele-specific Aomori L145 (6) Sakamotowase (15) Kosodefuri (9) Yoshiokachuryu (11) Pando (14) Aomori L146 (19) (27) GL1738 (13) GL2216 (12) Keshuang (25) 0.05 markers, which detect the presence or absence of the insertion, however, revealed that Kamaishi-17 did not have the e4 allele in which SORE-1 had been inserted [22]. This prompted us to analyze the E4 (GmphyA2) sequences of Kamaishi-17 and the other photoperiod-insensitive accessions.…”

“…Group II consisted of landraces that are grown as a short-season crop across Japan and the Korean peninsula (9-15), including Sakamotowase, which has the genotype e3e3E4E4 and a dysfunctional allele (e1-fs) at the E1 locus [19][20][21]. Group III consisted of landraces collected in northern Honshu, Japan (16)(17)(18)(19)(20)(21). Tsukue-4 (group IV, accession 22) and Otomewase (group V, accession 23) together formed a loose clade.…”

“…One of these cultivars, Sakamotowase, has the e3e3E4E4 genotype [20,21] and an allele at or a gene tightly linked to the E1 locus that controls the insensitivity in the presence of E4 [21]. Xia et al [19] analyzed the E1 sequence of Sakamotowase, and found that it possessed a dysfunctional allele, e1-fs, that produced a truncated protein that was unable to suppress the function of GmFTs owing to a premature stop codon due to a frame shift caused by a single-base deletion. The photoperiod insensitivity of Sakamotowase is thus most likely controlled by a dysfunctional allele at the E1 locus under the genetic background of the e3e3E4E4 genotype.…”

“…Four major maturity loci-E1, E3, E4, and E7-have so far been reported to be involved in the control of this insensitivity [9-15, reviewed in 16]. Recent molecular analyses have revealed that E3 and E4 encode the phytochrome A (phyA) proteins GmphyA3 and GmphyA2, respectively [17,18]; and that E1 encodes a protein that contains a putative bipartite nuclear localization signal and a region distantly related to a B3 domain, and controls time to flowering by suppressing the expression of two soybean orthologs of FT, GmFT2a and GmFT5a, under the regulation of E3 and E4 [19]. A phyA-regulated E1-GmFT pathway is thus a key determinant of the adaptation of soybean to long-daylength environments.…”