A Domestication-Associated Gene GmPRR3b Regulates the Circadian Clock and Flowering Time in Soybean

Abstract

Improved soybean cultivars have been adapted to grow at a wide range of latitudes, enabling expansion of cultivation worldwide. However, the genetic basis of this broad adaptation is still not clear. Here, we report the identification of GmPRR3b as a major flowering time regulatory gene that has been selected during domestication and genetic improvement for geographic expansion. Through a genome-wide association study of a diverse soybean landrace panel consisting of 279 accessions, we identified 16 candidate quantitative loci associated with flowering time and maturity time. The strongest signal resides in the known flowering gene E2, verifying the effectiveness of our approach. We detected strong signals associated with both flowering and maturity time in a genomic region containing GmPRR3b. Haplotype analysis revealed that GmPRR3b H6 is the major form of GmPRR3b that has been utilized during recent breeding of modern cultivars. mRNA profiling analysis showed that GmPRR3b H6 displays rhythmic and photoperioddependent expression and is preferentially induced under long-day conditions. Overexpression of GmPRR3b H6 increased main stem node number and yield, while knockout of GmPRR3b H6 using CRISPR/ Cas9 technology delayed growth and the floral transition. GmPRR3b H6 appears to act as a transcriptional repressor of multiple predicted circadian clock genes, including GmCCA1a, which directly upregulates J/GmELF3a to modulate flowering time. The causal SNP (Chr12:5520945) likely endows GmPRR3b H6 a moderate but appropriate level of activity, leading to early flowering and vigorous growth traits preferentially selected during broad adaptation of landraces and improvement of cultivars.

High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

“…Recent study suggested two homologous PRR3 genes controlling flowering and maturity were sequentially selected during soybean domestication (Lu et al 2020). Another research group also reported that GmPRR3b H6 may have a pleiotropic role favorited for domestication and genetic improvement (Li et al 2020). In our results, SiPRR37 has been shown to contribute to local adaptation of foxtail millet.…”

Agricultural productivity convergence in China

“…LHY proteins bind to the promoter of E1 to suppress its transcription, and in turn release its transcriptional suppression of the two key soybean FT homologs, ultimately resulting in promotion of flowering and earlier maturity (Figure 1). The Tof12 locus and its causative gene PRR3b were also characterized in other recent studies, highlighting the functional significance of this locus in soybean flowering and adaptation (Li et al 2019a(Li et al , 2019bLi et al 2020;Wang et al 2020).…”

Flowering phenology as a core domestication trait in soybean

“…LHY proteins bind to the promoter of E1 to suppress its transcription, and in turn release its transcriptional suppression of the two key soybean FT homologs, ultimately resulting in promotion of flowering and earlier maturity (Figure 1). The Tof12 locus and its causative gene PRR3b were also characterized in other recent studies, highlighting the functional significance of this locus in soybean flowering and adaptation (Li et al 2019a, 2019b; Li et al 2020; Wang et al 2020).…”