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

Abstract

Soybean (Glycine max) cultivars adapted to high latitudes have a weakened or absent sensitivity to photoperiod. The purposes of this study were to determine the molecular basis for photoperiod insensitivity in various soybean accessions, focusing on the sequence diversity of the E4 (GmphyA2) gene, which encodes a phytochrome A (phyA) protein, and OPEN ACCESSAgronomy 2013, 3 118 its homoeolog (GmphyA1), and to disclose the evolutionary consequences of two phyA homoeologs after gene duplication. We detected four new single-base deletions in the exons of E4, all of which result in prematurely truncated proteins. A survey of 191 cultivated accessions sourced from various regions of East Asia with allele-specific molecular markers reliably determined that the accessions with dysfunctional alleles were limited to small geographical regions, suggesting the alleles' recent and independent origins from functional E4 alleles. Comparison of nucleotide diversity values revealed lower nucleotide diversity at non-synonymous sites in GmphyA1 than in E4, although both have accumulated mutations at almost the same rate in synonymous and non-coding regions. Natural mutations have repeatedly generated loss-of-function alleles at the E4 locus, and these have accumulated in local populations. The E4 locus is a key player in the adaptation of soybean to high-latitude environments under diverse cropping systems.

Role of Nitrogen on Growth and Seed Yield of Soybean and a New Fertilization Technique to Promote Nitrogen Fixation and Seed Yield

“…Soybean is a short-day plant, and flowering is induced when the day length is shorter than a critical length. This sensitivity to photoperiod is weak or absent in soybean cultivars adapted to high latitudes, which should initiate flowering in early summer to mature in frost-free seasons [2].…”

“…In addition, soybean is a major oilseed crop in the world providing 58% of world oil seed production [1]. Soybean is cultivated over a wide range of latitudes, from the equator to high latitudes of at least 50 o N [2], although each cultivar adapts to the narrow range of latitudes. Soybean is a short-day plant, and flowering is induced when the day length is shorter than a critical length.…”

Current Status and Future Prospects of Soybean Production in Kazakhstan

“…Maturity is one such trait that has substantial significance in the development of cultivars suitable for the environmental conditions in Kazakhstan. Molecular markers linked to genes/alleles for maturity traits have been developed for soybeans (Watanabe et al 2009;Watanabe et al 2011;Xia et al 2012;Tsubokura et al 2013). Such markers are of substantial value in the selection and can be utilized to screen different accessions/landraces to reveal the corresponding alleles.…”

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

“…At recessive E4 locus, a Ty1/copia -like retrotransposon was inserted in the exon 1 of the GmphyA2 gene, which resulted in dysfunction of this gene (Liu et al, 2008). At least five dysfunctional alleles are known in GmphyA2 gene (Tsubokura et al, 2013). Loss-of-function alleles at GmPhyA3 and GmphyA2 can result in some degree of suppression of E1 transcription and correspondingly elevate GmFT expression, leading to relatively early flowering (Xia et al, 2012).…”

“…The maturity genes B3 DNA binding protein gene ( E1 ), GIGANTEA ( E2 ), GmPhyA3 ( E3 ), and GmPhyA2 ( E4 ) down regulate expression of GmFT2a ( E9 ) and GmFT5a to delay flowering and maturation under the long day condition, suggesting that GmFT2a and GmFT5a are the major targets in the control of flowering in soybean (Kong et al, 2010; Thakare et al, 2011; Watanabe et al, 2011; Xia et al, 2012; Zhao et al, 2016). The genes and alleles identified for flowering and maturity traits in soybean have been validated in several studies using germplasm from many countries (Tsubokura et al, 2013, 2014; Jiang et al, 2014; Langewisch et al, 2014; Zhai et al, 2014; Gupta et al, 2016). A lot of information has been generated on flowering and maturity genes in soybean which also reveals the presence of legume specific unique genes in soybean i.e., B3 DNA binding protein gene of E1 loci.…”