Table 3. Functional annotation of twelve differential expression genes supported by previous omics data and qRT-PCR.

Marker	Gene ID#	Tissuea	Associated Traits	R2	AAEb	Description	GO annotation	Enzyme	Pathway
MeESSR36	Manes.02G009300	Leaf, Root	AGFW-2015	7.90	positive	NAD DEPENDENT EPIMERASE/DEHYDRATASE	F:UDP-glucose 4-epimerase activity P:galactose metabolic process	EC:5.1.3.2	map00052,Galactose metabolism; map00520, Amino sugar and nucleotide sugar metabolism
			MDA-R-2014	3.84	negative
EME628	Manes.09G068800	Leaf	SRN-2014	5.28	positive	AQUAPORIN PIP2-1-RELATED	C:integral component of plasma membrane P:water transport C:plasmodesma F:glycerol channel activity P:cellular water homeostasis P:glycerol transport P:ion transmembrane transport F:water channel activity C:vacuole
EME710	Manes.10G078800	Leaf, Root	CAT-L-2014	16.75	positive	Caffeoyl-CoA O-methyltransferase	P:coumarin biosynthetic process F:caffeoyl-CoA O-methyltransferase activity F:metal ion binding P:lignin biosynthetic process P:methylation	EC:2.1.1.104	map00940, Phenylpropanoid biosynthesis; map00360, Phenylalanine metabolism; map00945, Stilbenoid, diarylheptanoid and gingerol biosynthesis; map00941, Flavonoid biosynthesis
			POD-L-2014	5.23	positive
			SRN-2014	5.55	positive
EME425	Manes.12G005000	Leaf, Root	AGFW-2015	16.64	positive	PROTEIN PHOSPHATASE 2C 33-RELATED	F:protein serine/threonine phosphatase activity P:protein dephosphorylation
			SOD-R-2015	12.11	positive
MeESSR74	Manes.12G129800	Leaf, Root	Proline-L-2015	9.13	positive	HOMEOBOX-LEUCINE ZIPPER PROTEIN ATHB-16-RELATED	C:nucleus F:transcription factor activity sequence-specific DNA binding F:transaminase activity P:regulation of transcription DNA-templated F:sequence-specific DNA binding
MeESSR31	Manes.13G127100	Leaf, Root	Proline-L-2014	8.31	positive	CYCLIN-DEPENDENT KINASE INHIBITOR 6	P:cell cycle arrest C:nucleus F:cyclin-dependent protein serine/threonine kinase inhibitor activity P:negative regulation of protein serine/threonine kinase activity
MeSSR38	Manes.02G124800	Leaf, Root	CAT-R-2014	3.37	negative	17.6 KDA CLASS I HEAT SHOCK PROTEIN 1-RELATED	P:response to oxidative stress, response to heat C: cytoplasm F: protein binding, protein self-association		map04141:Protein processing in endoplasmic reticulum
MeSSR44	Manes.03G053400	Leaf, Root	AGFW-2015	6.95	positive	Cation transport ATPase	P:copper ion transport, metal ion transport C: plasma membrane, chloroplast thylakoid membrane, integral component of membrane, integral component of membrane F: nucleotide binding, copper-exporting ATPase activity, copper ion transmembrane transporter activity, ATP binding, ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism, cation-transporting ATPase activity, metal ion binding	EC:3.6.3.4
MeESSR18	Manes.07G029200	Leaf, Root	Proline-L-2015	5.28	negative	GLUTATHIONE S-TRANSFERASE, GST, SUPERFAMILY, GST DOMAIN CONTAINING	P: gluthione metabolic process, toxin catabolic process, response to toxic substance, response to salicylic acid C: cytoplasm, cytosol F: gluathione transferase activity	EC:2.5.1.18	map00480:Glutathione metabolism
EME171	Manes.13G013400	Root	CAT-R-2015	5.34	negative	SMALL HEAT-SHOCK PROTEIN HSP20 FAMILY	P: response to heat, response to high light intensity, response to hydrogen peroxide C: chloroplast		map04141:Protein processing in endoplasmic reticulum
EME212	Manes.02G062400	Root	SOD-L-2015	15.2	positive	Domain of unknown function
			SRFW-2014	6.21	positive
MeESSR71	Manes.06G045100	Leaf, Root	CAT-L-2014	5.77	positive	Inorganic diphosphatase / Pyrophosphate phosphohydrolase	P:response to water deprivation, response to salt stress, auxin polar transport, establishment or maintenance of transmembrane electrochemical gradient, proton transport, leaf development C: Plant-type vacuole, mitochondrion, vacuole, vacuolar membrane, golgi apparatus, cytosol, plasma membrane, chloroplast, plant-type vacuole membrane, chloroplast envelope, endosome membrane, membrane, integral component of membrane F:inorganic diphosphatase activity, hydrogen-translocating pyrophosphatase activity, metal ion binding	EC:3.6.1.1	map00190:Oxidative phosphorylation
			CAT-L-2015	10.47	positive
			SRDW-2014	6.91	positive
			SRFW-2014	10.99	positive

^a was the differential expressed tissue under drought stress.

^b was the AAEs of EST-SSR loci of associated genes for traits which they were associated to.