Table 1. Key candidate genes involved in regulating alfalfa fall dormancy.

Classification	Number	Tags	Genes	Function [reference]	Expression trend of DM vs. DS	Expression trend of DS vs. NDS
Genes involved in carbohydrate metabolism and transport	1	comp1260_c0	MGDG synthase 3	Synthesis of photosynthetic membranes and chloroplast envelope [19]		Downregulated(-3.53)
	2	comp59094_c0	Beta-D-glucosidase	Catalyzes the hydrolysis of terminal non-reducing residues in beta-D-glucosides with a release of glucose[20]	Downregulated(-2.10)	Upregulated(3.05)
	3	comp25768_c0	UDP-sugar pyrophosphorylase	Catalyzes the conversion of various monosaccharide 1-phosphates to respective UDP-sugars in the salvage pathway[21]	Upregulated(2.14)	Downregulated(-3.19)
	4	comp53413_c0	Ribulose bisphosphate carboxylase/oxygenase (Rubisco) activase	Activates Rubisco	Downregulated(-2.87)	Upregulated(1.01)
Genes regulated by photoperiod and light	5	comp46970_c0	Cryptochrome-2(CRY-2)	Inhibits hypocotyl elongation [22] and stem and root growth[23]	Upregulated(3.50)
	6	comp1262167_c0	Protein FAR-RED IMPAIRED RESPONSE 1(FAR1)	Positively regulates chlorophyll biosynthesis via the activation of HEMB1 gene expression[24]; activates transcription; elongates hypocotyls and reduces expansion of cotyledons[25]		Upregulated(2.23)
	7	comp38709_c0	GATA transcription factor 12(GATA12)	Activates transcription, regulates some light-responsive genes and circadian rhythm[26–28]	Upregulated(2.40)	Downregulated(-2.41)
	8	comp12163_c0	Serine protease SPPA, chloroplastic	the light-dependent degradation of antenna and photosystem II in chloroplasts[29, 30];	Downregulated(-2.22)	Upregulated(2.23)
	9	comp46405_c0	Protein HEADING DATE 3A	Regulates dormancy [31]	Downregulated(-1.72)	Upregulated(4.38)
	10	comp56985_c0	Granule-bound starch synthase 1(GBSS1)	Regulated by photoperiod, may be accompanied by abolition of expression of starch synthesis genes [32]	Downregulated(-2.69)	Upregulated(5.74)
Phytohormone	11	comp36708_c0	Probable indole-3-pyruvate monooxygenase YUCCA3	Participates in indoleacetic acid (IAA) synthesis[33]	Upregulated(3.40)	Downregulated(-1.35)
	12	comp343499_c0	Methylesterase17	Hydrolyzes conjugates of IAA	Downregulated(-1.72)	Upregulated(3.38)
	13	comp522282_c0	IAA-amino acid hydrolase ILR1-like 1	Hydrolyzes conjugates of IAA[34]		Upregulated(2.36)
	14	comp15714_c0	Auxin response factor 6(ARF6)	Activates transcription, participates in transcriptional regulation of a variety of biological processes related to growth and development[35, 36]		Downregulated(-2.74)
	15	comp57456_c0	ABA receptor PYL8	Positively regulates abscisic acid (ABA) signaling pathway[37–40]	Upregulated(2.66)
	16	comp61323_c0	Protein early responsive to dehydration 15	Negatively regulates ABA responses and mediates stress-related ABA signaling[41, 42]	Upregulated(2.05)
Transportation	17	comp46282_c0	ATP-binding cassette (ABC) transporter C family member 7	Involved in the response to biotic stress		Upregulated(2.36)
	18	comp10285_c0	ABC transporter B family member 11	Essential regulator of plant growth	Upregulated(2.55)
	19	comp70285_c0	Monosaccharide-sensing protein 3	Involved in direct growth and differentiation or flexible response to changing environmental conditions (UniProt: Q9SD00)	Upregulated(2.13)
	20	comp40098_c0	Probable ion channel SYM8	A calcium channel[43]	Upregulated(3.15)
	21	comp343967_c0	Putative phospholipid-transporting ATPase 7	Transports phospholipids (UniProt: Q9LVK9)	Upregulated(3.15)	Downregulated(-3.32)
	22	comp928260_c0	Ras-related protein RABH1d	Involved in protein transport(UniProt: Q9SID8)	Downregulated(-0.83)	Upregulated(2.23)
	23	comp1120261_c0	Oligopeptide transporter 6	Translocates tetra- and pentapeptides[44, 45]	Upregulated(2.40)	Downregulated(-2.41)
Cell cycle, division, and growth	24	comp33056_c0	Cyclin-D5-2	Mediates the linking of extracellular and developmental signals to the cell cycle[46]		Downregulated(-3.60)
	25	comp67791_c1	Anaphase-promoting complex (APC)subunit 1	Marks target cell cycle proteins for degradation by 26s proteasome; involved in eukaryotic cell reproduction[47–49]	Downregulated(-1.27)	Upregulated(5.11)
	26	comp686013_c0	Protein S-acyltransferase 24 (PAT24)	Involved in cell growth regulation [50]; affects root hair formation and growth [51, 52]	Upregulated(2.20)
	27	comp32326_c0	Monocopper oxidase-like protein SKU5	Possibly involved in directional growth processes and cell wall expansion[53]	Upregulated(2.20)
	28	comp672512_c0	Prohibitin-3, mitochondrial	Loss of function of the homologs AtPHB3 causes mitochondrial welling, decreases meristematic cell production, increases cell division time, and reduces cell expansion rates, leading to severe growth retardation[54]	Downregulated(-0.83)	Upregulated(2.36)
	29	comp887354_c0	Kinesin-4	Involved in cell cycle[55] and cell division[56–61].	Downregulated(-2.92)	Upregulated(2.23)
	30	comp37666_c0	Structural maintenance of chromosomes protein 3(SMC3)	Essential protein for plant viability, required for cell division during embryogenesis, increased expression accelerates cell cycle [62, 63]		Upregulated(2.23)
Genes regulating transcription	31	comp424089_c0	Probable histone H2A.2	Plays a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. Involved in gene regulation[64]		Upregulated(2.36)
	32	comp57595_c0	Histone H3.3		Upregulated(6.23)	Downregulated(-4.08)
	33	comp391402_c0	MADS-box transcription factor PHERES 1	Regulates dormancy[31, 65]	Downregulated(-3.20)	Upregulated(3.12)
	34	comp50413_c1	Squamosa promoter-binding protein 1(SBP1)	Activates transcription, and involved in leaf development, vegetative phase change, etc. [66, 67]	Upregulated(3.97)
Ubiquitination	35	comp53272_c0	Probable mediator of RNA polymerase II transcription subunit 37c	Coactivator regulates transcription of nearly all RNA polymerase II-dependent genes [UniProt: Q9LHA8—MD37C_ARATH]		Downregulated(-6.76)
	36	comp538610_c0	BTB/POZ domain-containing protein At1g67900	Mediates transcriptional repression [UniProt: Q9C9V6—Y1790_ARATH]	Upregulated(2.40)
	37	comp933338_c0	BTB/POZ domain-containing protein At3g19850	Mediates transcriptional repression [UniProt: Q9LT24—Y3985_ARATH]	Upregulated(2.40)
	38	comp29926_c0	F-box only protein 6	Substrate-recognition component of some SCF-type E3ubiquitin-ligase complexes, participates in regulation of auxin-mediated signaling pathway, leaf vascular tissue pattern formation, and simple leaf morphogenesis[68, 69]		Upregulated(5.50)
	39	comp655910_c0	UBX domain-containing protein 7	Acts in many cellular events such as ubiquitin-dependent degradation and membrane fusion[70]	Upregulated(2.87)	Downregulated(-3.00)
	40	comp909276_c0	Putative E3 ubiquitin-protein ligase LIN	Catalyzes polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro, involved in plant C/N response and early steps of the plant defense signaling pathway[71]	Upregulated(2.40)
	41	comp395328_c0	E3 ubiquitin-protein ligase UPL6	Mediates ubiquitination and subsequent proteasomal degradation of target proteins [UniProt:Q8RWB8—UPL6_ARATH]	Downregulated(-2.96)	Upregulated(1.68)
Receptor kinases	42	comp70176_c0	Wall-associated receptor kinase(WAK)5; Wall-associated receptor kinase-like (WAKL)2	Involved in cell expansion, elongation[72, 73]	Upregulated(2.36)
	43	comp41596_c0	WAK3			Downregulated(-3.00)
	44	comp403595_c0	Serine/threonine-protein kinase Nek1	Involved in sensing and repair of DNA strand breaks at the G1-S and G2-M transitions[74]	Upregulated(2.40)	Downregulated(-2.41)

DM and DS: Leaf samples of the fall-dormant alfalfa variety collected in May and September, respectively; NDS: leaf samples of the non-dormant alfalfa variety collected in September.