Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

Abstract

Photosensitivity plays an essential role in the response of plants to their changing environments throughout their life cycle. In soybean [Glycine max (L.) Merrill], several associations between photosensitivity and maturity loci are known, but only limited information at the molecular level is available. The FT3 locus is one of the quantitative trait loci (QTL) for flowering time that corresponds to the maturity locus E3. To identify the gene responsible for this QTL, a map-based cloning strategy was undertaken. One phytochrome A gene (GmPhyA3) was considered a strong candidate for the FT3 locus. Allelism tests and gene sequence comparisons showed that alleles of Misuzudaizu (FT3/FT3; JP28856) and Harosoy (E3/E3; PI548573) were identical. The GmPhyA3 alleles of Moshidou Gong 503 (ft3/ft3; JP27603) and L62-667 (e3/e3; PI547716) showed weak or complete loss of function, respectively. High red/far-red (R/FR) long-day conditions enhanced the effects of the E3/FT3 alleles in various genetic backgrounds. Moreover, a mutant line harboring the nonfunctional GmPhyA3 flowered earlier than the original Bay (E3/E3; PI553043) under similar conditions. These results suggest that the variation in phytochrome A may contribute to the complex systems of soybean flowering response and geographic adaptation.

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

“…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.…”

“…Approximately 75% of the genes are present as multiple copies, some of which have diverged in their functions, as suggested by different expression patterns between homoeologs [28,29]. phyA is one such example, and consists of 2 sets of homoeologous partners, GmphyA1/GmphyA2(E4) and GmphyA3(E3)/GmphyA4 [16][17][18]. The presence of multiple copies of soybean phyA contrasts sharply with other legume species such as pea (Pisum sativum), Medicago truncatula, and Lotus japonicus, which all possess a single phyA gene [30].…”

“…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.…”

Functional genomics to study stress responses in crop legumes: progress and prospects

“…Thanks to advances in sequencing and the genomewide identification of sequence polymorphisms (e.g. SNPs), MBC became more accessible, and has been conducted in a range of crop species such as rice (Vij and Tyagi 2007) as well as in some legumes including soybean (Watanabe et al 2009). …”

“…The majority of the MBC projects in crop legumes have been applied in soybean. For example, the soybean phytochrome A gene (GmPhyA3) which modulates flowering time has been cloned using an MBC approach (Watanabe et al 2009). In a different study, a candidate gene Ln controlling leaflet and seed number per pod was cloned with a combination of MBC and association study (Fang et al 2013).…”