TABLE 4.

Exhaustive list of various DEG and candidate genes contributing to FW resistance in grain legumes.

Crop	Genotype name	Differentially expressed genes/candidate gene	Function	Platform used	References
Chickpea	JG62 and WR315	6272 ESTs related to cell signaling and transcription and RNA processing and modification, cellular transport and homeostasis, hormone responses, cellular redox and energy metabolism, defense, and stress responsive genes	Defense mechanism, cellular metabolism and hormone signaling	RNA blot analysis	Ashraf et al., 2009
Chickpea	JG62 and WR315	Redox signaling genes such as redox regulatory respiratory burst oxidase homolog F (RBOHF), thioredoxin 3 (TRX3), cationic peroxidase 3 (OCP3), flavodoxin-like quinone reductase 1 (FQR1), iron superoxide dismutase 1, NADH cytochrome b5 reductase (CBR), Fe (II) oxidoreductase 7 (FRO7), Genes related to intracellular transportation ABC transporter like gene, polyol transporter gene, translocase, heavy metal transporter (detoxifying protein) (FRS6), bZIP, homeodomain leucine zipper, MYB, helix loop helix, zinc finger (CCHC type), and heat shock family protein, sucrose synthase (SUS4), β-amylase (BAM1), serine threonine kinase (CDKB1.1), and vacuolar ATPase (TUF)	Defense activity, ROS activity, and sugar transportation, sugar metabolism	qPCR	Gupta et al., 2013a
Chickpea	ICC4958	car-miRNA008 targets the chalcone synthase miR2118 and car-miR5213 targeting defense gene encoding Toll/Interleukin-1 receptor-nucleotide binding site-leucine-rich repeats miR2111 targets a Kelch repeat-containing F-box protein	Flavonoid biosynthesis involved in defense mechanism	Illumina (NGS) qPCR	Kohli et al., 2014
Chickpea	Digvijay and JG62	Glutamate dehydrogenase-GDH, glutamate synthase Glutamine synthase and asparagine synthase Methionine synthase and AdoMet synthetase CCoAMT, CHS, CHI, iso-flavone 40-O-methyltransferase, IFS, and IFR	Nitrogen mobilization and methionine metabolism, lignin and phytoalexin biosynthetic pathways	qPCR	Kumar et al., 2016
Chickpea	Digvijay and JG62	Chitin synthase VII (Chs7) G protein β subunit gene Mitochondrial carrier protein (Fow1) Xylanases gene, pectate lyases gene, polygalacturonases gene	Involved in establishment of pathogen in the host plant	qPCR	Upasani et al., 2016
Chickpea	Digvijay and JG62	3816 DEGs	Lignification, hormonal homeostasis, plant defense signaling, ROS homeostasis, R-gene mediated defense	LongSAGE	Upasani et al., 2017
Chickpea	NILs—RIP8-94-5 resistant R/RIP8-94-11 susceptible (S)	Upregulation of LOC101509359, LOC101495941, LOC101510206 genes in resistant NILs and upregulation of LOC101503802, LOC101505941, LOC101506693, LOC101507659, LOC101509037, LOC101510206, LOC101510544, LOC101501552, and LOC101502928 candidate genes in susceptible NILs	Encodes MADS-box transcription factor, encodes protein related to multidrug and toxic compound extrusion (MATE) family, encodes for a serine hydroxymethyl- transferase	qPCR	Caballo et al., 2019a
Chickpea	JG62 and WR315	PR10, pectinesterase, Aquaporin, ATP synthase, mtr3, exosome, immunity associated differentially expressed genes, cystatin and DnaJ, pectinesterase and xyloglucosyl transferase, actin and profilin-like genes, cytochrome P450, cytochrome P450 monooxygenase, and peroxidase	Immunity, ATP, ROS activity, cell wall remodelers, cytoskeleton related function	qPCR, Microarray analysis	Ashraf et al., 2018
Common bean	BRB130 and CAAS260205	122 transcript-derived fragments (redox-related genes, hormone response genes, transport-related genes, defense and stress response-related, signal transduction genes development and cytoskeletal organization). Upregulation of candidate genes viz., CBFi28,CBFi43,CBFi45,CBFi76,CBFi56, CBFi63, and CBFi122 CBFi54, CBFi58, CBFi83 and CBFi171 in resistant genotype	Signal transduction, hormonal response, defense and cellular metabolism, etc.	qPCR, cDNA-AFLP analysis	Xue et al., 2015
Common bean	Liyun No. 2	8269 downregulated genes, 13,771 upregulated genes Upregulated candidate genes PHAVU_007G070400g, PHAVU_004G134300g, PHAVU_011G042100g, PHAVU_008G232600g, PHAVU_007G185300g. Downregulated candidate genes PHAVU_003G141800g, PHAVU_007G0495001g, and PHAVU_007G236300g down regulation of UDP-glucuronic acid decarboxylase and cellulose synthases high accumulation of pectate lyases, pectin methylesterase inhibitors (PMEI), pectin methylesterases (PME), and Polygalacturonases genes, genes responsive to hormone signaling	Structural defense Defense related proteins Hormones signaling pathways Energy metabolism and nitrogen mobilization Flavonoid biosynthesis pathway	Illumina (NGS)	Chen et al., 2009