S Table 1 Function and Effect of Altered Expression of Different Genes Involved In

S Table 1 Function and effect of altered expression of different genes involved in transcriptional, epigenetic and phytohormone controlled regulatory mechanisms of seed development identified in Arabidopsis, rice or soybean. ‘LOF’ stands for loss of function and ‘OE’ stands for overexpression

Function / Gene / Encoded protein / Expression alteration / References
Transcriptional Regulation / IKU1 / VQ motif containing protein, expressed in central cell of the embryo sac and endosperm after fertilization. IKU1 functions upstream of MINI3 and IKU2 in the IKU-MINI3-IKU2 pathway / LOF lead to smaller size seeds due to reduced endosperm growth / Wang et al. 2010
IKU2 / IKU2 encodes a leucine-rich repeat transmembrane protein kinase. It regulates endosperm proliferation through in the IKU-MINI3-IKU2 pathway. IKU2 is expressed only in endosperm of developing seed. / iku2 mutant display small seeds due to reduced embryo. OE of IKU2 in Arabidopsis displayed larger and heavier seeds with increased oil up to 35% / Luo et al. 2005
Fatihi et al. 2013
OE of IKU2 with MINI3 promoter enhanced seed mass in B. napus / Xiao et al. 2016
MINI3 / WRKY transcription factor expressed after fertilization in both the endosperm and the embryo. It regulates functioning of IKU2 in the IKU-MINI3-IKU2 pathway / mini3 plants have a similar phenotype as that of the seed mutant iku2 / Luo et al.2005
TTG2 / WRKY transcription factor involved in pigmentation of the seed coat and leaf trichome formation / LOF reduced the seed size seeds in ttg2 mutants due to reduced elongation of integuments which constricts endosperm growth / Garcia et al. 2005
ARF2 / TF regulating expression of auxin response genes by binding to auxin response element / LOF increased seed size and weight due to increased cell division in the integuments / Okushima et al. 2005
GRF1 / Putative transcription factor / OE results in larger leaves and seeds due to increased storage of photosynthates / Kim et al. 2003
CYP78A98 / Cytochrome P450 gene from Jatropha curcas / OE ofCYP78A98 from Jatropha curcasL. increases seed size of transgenic tobacco / Tian et al. 2016
KLUH / Cytochrome P450 monooxygenase acting locally in developing ovules promotes cell proliferation in inner integuments / OE in ovule-specific manner increased seed size and oil content due to increased embryo to seed volume ratio / Adamski et al.2009
SHB1 / SYG1 family TF regulating cell size and cell number in endosperm through IKU-MINI3 pathway and in embryo through an IKU independent pathway / OE increases seed size / Zhou et al. 2009
OE of SHB1 enhanced seed mass in B. napus / Xiao et al. 2016
AP2 / Floral homeotic gene limiting cell elongation in the two outer integuments / LOF increases seed size / Jofuku et al. 2005
DA1 / Ubiquitin receptor in limiting integument elongation in synergy with DA2 and EOD1, and antagonistically with SOD3 acting in independent ubiquitin pathways / LOF increases seed size and organ growth / Li et al. 2008
EOD1 / Enhancer of da1-1 negatively regulate integument elongation in synergy with DA1 / LOF increases seed and organ size / Li et al. 2008
DA2 / RING-type protein with E3 ubiquitin ligase activity and negatively integument elongation in synergy with DA1 / LOF increases seed and organ size / Xia et al. 2013
EOD3 / Cytochrome P450/CYP78A6 component of DA1 pathway controlling seed size / OE of EOD3 increases seed size / Fang et al. 2012
TaGW2-6A / RING E3 ubiquitin-ligase that negatively regulates grain size / Allelic variant increases seed size / Geng et al. 2017
Epigenetic Regulators / FIS2,FIS3
FIS1/MEA
MSI1,SWN / Polycomb Group (PcG) proteins form repressive complexes that suppress the expressions of genes involved in regulation of developmental processes through the methylation of chromatin histones / LOF of FIS2,FIS3,MEA reduces seed size due to the reduced endosperm cellularisation / Kang et al. 2008; Kohler et al. 2003; Grossniklaus et al.1998
MET1, PHE1, DDM1, DME / Enzymes involved in methylation and demethylation of genes involved in endosperm development / met1mutation increases in the seed size / Xiao et al.2006
Hormonal regulation / ABP1 / Auxin Binding Protein1 / LOF of ABP1 results in abnormal embryogenesis due to the failure of cell elongation and in cell division / Chen et al. 2001
YUC1,4,10, 11 / Auxin biosynthesis rate limiting enzymes / LOF results in defective seed phenotype / Bernardi et al. 2012
AtCUL1 / F-box protein functioning in response to auxins during embryogenesis / LOF of AtCUL1 gene result in small seed size / Shen et al. 2002
ARF2 / Auxin responsive TF acts as a repressor of cell division in integuments and the embryo / LOF of ARF2 produces larger and heavier seeds / Schruff et al. 2006
ARF8 / Auxin responsive TF andnegatively regulates fruit initiation / LOF of ARF8 produces larger seeds / Goetz et al. 2006
AHKs
AHPs
ARR / Proteins involved in cytokinins mediated expression of genes. AHKs, cytokininreceptorsactivate histidine phosphotransfer proteins (AHPs) which phosphorylate and activate the TF Arabidopsis response regulators (ARRs) / LOF of AHKs, AHPs and ARRs produce larger seeds / Day et al. 2008
IPT / Cytokinin biosynthesis / Endosperm specific expression increases seed weight / Song et al. 2015
CKI1 / Histidine kinase lacking the cytokinin perception domain involved in cytokinin signal transduction / LOF of CKI1 has larger seeds / Deng et al.2010
CKX2 / Cytokinin oxidase controls the growth of endosperm by regulating cytokinin levels. Its expression is regulated by IKU2 and H3K27m3 / LOF of CKX2 produce larger seeds / Li et al. 2013
Seed Dormancy1-2 / OsGA20ox2 / GA biosynthesis gene / LOF in OsGA20ox2 resulted in lower GA levels and delayed seed morphogenesis, ABA accumulation and seed maturation / Ye et al. 2015
GA-2-OX / GA-inactivating enzyme / OE results in smaller seeds / Singh et al. 2002
GASA4 / Gibberellic acid signaling component possibly governing embryogenesis / OE of GASA4 increased seed size / Roxrud et al. 2007
CYP72C1 / A protein similar to BAS1/ CYP734A1 inactivates Brassinosteroids by hydroxylation. Its expression pattern suggests a possible role in embryo, endosperm and seed coat growth. / OE produces short siliques and seeds with reduced elongation / Takahashi et al. 2005
CYP24B1 / Cytochrome P450 having homology to enzymes involved in brassinosteroid (BR) biosynthesis / LOF reduces seed length / Tanabe et al. 2005
brd2 / Homolog of Arabidopsis DIMINUTO/ DWARF1involved in brassinosteroids signaling and has a possible role in embryo endosperm and seed coat growth. / LOF produces smaller and shorter seeds / Hong et al. 2005
SG1 SGL / Restricts elongation of organs such as seeds by reducing brassinosteroid hormones / LOF produce longer grains and rachis / Nakagawa et al. 2012
BZR1 / BR signaling protein,activate positive regulators of seed size: SHB1,MINI3, and HAIKU2, but repress the expression of negative regulators of seed size: AP2 and ARF2 in response to Brassinosteroids / LOF produce smaller and less elongated seeds / Jiang et al. 2013
ABI4,ABI2, ABI5 / ABA receptors, whichrestrict the seed size by negatively regulating SHB1 in response to ABA / LOF produce larger and heavier seeds / Cheng et al. 2014
ACC deaminase / An enzyme involved in ethylene metabolism / LOF results in lower levels of ethylene and produces smaller seeds and siliques / Walton et al. 2012
Peptide and Sugar signaling mediated regulation / CLE8 / A small signaling peptide that is expressed in developing embryos and endosperm / LOF results in reduced seed size / Fiume and Fletcher 2012
ESF1 / Small peptide expressed in central cell gametes andembryo surrounding endosperm cells / Involved in early embryonic patterning / Costa et al. 2014
RALF-like peptides / Expressed in the integuments and nucellus of ovules / Probable role in seed development / Chevalier et al. 2013
GhCWIN1 / A cell wall invertase enzymeexpressed in embryo sac in the asymmetric spatial manner / Regulatory role in the sequential proliferation of endosperm and embryo / Wang and Ruan 2012
TPS1 / Trehalose-6-phosphate synthase/phosphatase / LOF results in slower embryo proliferation and embryos are halted at torpedo stage / Gómez et al. 2010
AN3 / AN3 protein along with YDA, which is a mitogen-activated protein kinase kinase kinase regulate sucrose and glucose contents in developing seeds / LOF results in disrupting normal sucrose and glucose contents and cause altered seed size / Meng et al. 2017