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

Abstract

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.

Functional diversification of Flowering Locus T homologs in soybean: GmFT1a and GmFT2a/5a have opposite roles in controlling flowering and maturation

“…Among the soybean FTs of unknown function, GmFT4 has been noted to be strongly induced by LD conditions, and was reported to function in delaying flowering when ectopically expressed in Arabidopsis (Zhai et al, 2014;Cao et al, 2016a). Recently, it was reported that GmFT4 appears to be the most likely candidate gene at a newly identified maturity locus, E10 (Samanfar et al, 2017). Although the function of GmFT4 still needs to be characterized, for example via overexpression in transgenic soybean, the fact that it delays flowering in Arabidopsis strongly suggests that the soybean FT-like genes might have undergone functional divergence.…”

Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions

“…Soybean flowering time is regulated by both genetic and environmental factors [6, 7]. At least 11 major loci control flowering time and maturity in soybean, including E1 – E10 [8–17] and J [18]. Among them, six genes ( E1 , E2 , E3 , E4 E9 and J ) have been cloned or identified.…”

Evaluation of genetic and morphological distances between soybean (Glycine max L.) cultivars

“…The issue of the relationship between morphological traits and DNA markers has been studied for over 30 years (Burstin, Charcosset, 1997;Geng et al, 2016;Valliyodan et al, 2016). To explore the effect of heterosis, the studies were carried out to determine the correlations between genetic distances of morphological traits and SSR, inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) markers in sunflower and corn (Burstin, Charcosset, 1997;Hudcovicova, Kraic, 2003;Tantasawat et al, 2011;Darvishzadeh, 2012;Abugalieva, 2013;Akond et al, 2013;Goncharov et al, 2016;Samanfar et al, 2017). Leading European plant expertise institutes, such as GEVES (France) and Naktuinbouw (The Netherlands), use the correlation between genetic distances based on SSR marker and morphological trait polymorphism to evaluate new cultivars and to compose their collections for DUS-test (Riday et al, 2003;Karuri et al, 2010;Valliyodan et al, 2016;Shen et al, 2017;Sun et al, 2018).…”