Characterization of Two Growth Period QTLs Reveals Modification of PRR3 Genes During Soybean Domestication Man-Wah Li 1 , Wei Liu 1 , Hon-Ming Lam 2 and Joshua M. Gendron 1, * 1 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA 2 Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR *Corresponding author: E-mail, joshua.gendron@yale.edu; Fax, 1-203-432-6161. Subject areas (1) growth and development & (2) environmental and stress responses (Received June 19, 2018; Accepted November 1, 2018) Soybean yield is largely dependent on growth period. We characterized two growth period quantitative trait loci, Gp11 and Gp12, from a recombinant inbred population gen- erated from a cross of wild (W05) and cultivated (C08) soy- bean. Lines carrying Gp11 C08 and Gp12 C08 tend to have a shorter growth period and higher expression of GmFT2a and GmFT5a. Furthermore, multiple interval mapping sug- gests that Gp11 and Gp12 may be genetically interacting with the E2 locus. This is consistent with the observation that GmFT2a and GmFT5a are activated by Gp11 C08 and Gp12 C08 at ZT4 in the recessive e2 but not the dominant E2 background. Gp11 and Gp12 are duplicated genomic regions each containing a copy of the soybean ortholog of PSEUDO RESPONSE REGULATOR 3 (GmPRR3A and GmPRR3B). GmPRR3A and GmPRR3B from C08 carry mutations that delete the CCT domain in the encoded proteins. These mu- tations were selected during soybean improvement and they alter the subcellular localization of GmPRR3A and GmPRR3B. Furthermore, GmPRR3A and GmPRR3B can interact with TOPLESS-related transcription factors, suggesting that they function in a transcription repressor complex. This study addresses previously unexplored components of the genetic network that probably controls the growth period of soybean and puts these loci into context with the well-characterized growth period-regulating E loci. Keywords: Domestication  Flowering  Growth period  Pseudo-response regulator  Soybean. Footnotes: Coding sequences of GmPRR3 genes, confirmed by sequencing, were deposited in GenBank with accession numbers: GmPRR3A C08 , MG586783, GmPRR3A W05 , MG586784, GmPRR3B C08 , MG586785; and GmPRR3B W05 , MG586786. Introduction Soybean flowering time is largely determined by photoperiod. Flowering time determines the length of vegetative growth and number of auxiliary nodes produced by the plant. A longer vegetative growth period results in more auxiliary nodes, in turn increasing the numbers of flowers, pods and finally seeds (Patterson et al. 1977). A 16 d delay in flowering initiation can increase total seed weight by >80% under experimental con- ditions (Patterson et al. 1977). However, long vegetative growth reduces the number of possible harvests per year and increases the chance of damage from biotic or abiotic stress. Soybean flowering is exquisitely sensitive to day length, with just a 0.5 h difference in photoperiod being sufficient to induce flowering in some soybean varieties (Board and Hall 1984). Therefore, changes in latitude are sufficient to induce or suppress flower- ing and affect yield. For effective production of soybean at dif- ferent latitudinal zones, soybean varieties have been categorized into about 10–13 major maturity groups based on productivity potential in different latitudinal clines (Jia et al. 2014). The causative genetic changes allowing these ma- turity groups to maintain productivity at various latitudes are largely determined by the combination of different E loci alleles (Jia et al. 2014, Langewisch et al. 2017). Climate change has mobilized crop cultivation due to changes in growth season temperature, availability of water, soil fertility and market demand. A predictive model of land use in 2100 suggested that soybean cultivation will continue to spread further away from current cultivation zones (Fodor et al. 2017). Maintaining productivity of soybean in the varying photoperiods of new latitudinal cultivation zones will require the generation of new soybean varieties with altered sensitivity to day length. In the past few decades, effort has been made to study the molecular mechanisms controlling flowering and maturation time of soybean. Roughly 10 major loci, named E1–E10, were identified. In brief, E1 encodes a legume specific B3-like domain containing a nuclear protein that suppresses the expression of two florigen genes, GmFT2a and GmFT5a, resulting in delayed flowering (Xia et al. 2012). The majority of natural E1 alleles cluster in four groups, E1, e1-as, e1-fs and e1-nl. E1 most strongly suppresses the expression of GmFT2a and GmFT5a (Xia et al. 2012). e1-as contains a non-synonymous mutation that lead to mislocalization of the E1 protein and reduces its functional potential. e1-fs contains a 1 bp deletion that leads to a trunca- tion of the C-terminal portion of the protein, and e1-nl is a deletion of the entire E1 gene. Both e1-fs and e1-nl are non- functional (Xia et al. 2012). E2 encodes the ortholog of Arabidopsis GIGANTEA (GmGIa) that plays a variety of roles in environmental sensing and development (Watanabe et al. Plant Cell Physiol. 60(2): 407–420 (2019) doi:10.1093/pcp/pcy215, Advance Access publication on 9 November 2018, available online at www.pcp.oxfordjournals.org ! The Author(s) 2018. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com Regular Paper Downloaded from https://academic.oup.com/pcp/article/60/2/407/5168116 by guest on 10 June 2022