Table 1.

Twenty-eight seed color-related known/candidate gene orthologs of chickpea selected for genetic association mapping.

Characterized known cloned genes				Kabuli chickpea gene homologs
Crop plants	Gene identity	Gene accession IDs	References	Gene identity	Chromosomes	Sequenced gene amplicon size (bp)	Coding and upstream regulatory SNPs discovered	Average SNP frequency (SNP/kb)
Soybean	AR (Anthocyanidin reductase)	Glyma08g06630	Yang et al., 2010	Ca05336	Ca_Kabuli_Chr06	3793	12	3.16
Soybean	ANS (Leucoanthocyanidin dioxygenase)	Glyma01g42350		Ca02395	Ca_Kabuli_Chr08	2179	6	2.75
Soybean	DFR1 (Dihydroflavonol 4-reductase 1)	Glyma14g07940		Ca10786	Ca_Kabuli_Chr04	5497	15	2.73
Soybean	DFR2 (Dihydroflavonol 4-reductase 2)	Glyma17g37060		Ca10787	Ca_Kabuli_Chr04	4719	13	2.75
Soybean	Myb TF (Myeloblastoma Transcription Factor)	Glyma13g09980		Ca11427	Ca_Kabuli_Chr05	1816	5	2.75
Soybean	F3H1 (Flavanone 3-hydroxylase 1)	Glyma16g23880		Ca09972	Ca_Kabuli_Chr07	3822	13	3.40
Soybean	F3H2 (Flavanone 3-hydroxylase 2)	Glyma02g05450		Ca09973	Ca_Kabuli_Chr07	3872	10	2.58
Arabidopsis	tt3-DFR (Dihydroflavonol 4-reductase)	AT5G42800	Wang et al., 2013	Ca10786	Ca_Kabuli_Chr04	5497	20	3.64
Arabidopsis	tt4-CHS (Chalcone Synthase)	AT5G13930	Wroblewski et al., 2014	Ca08294	Ca_Kabuli_Chr03	3010	11	3.65
Arabidopsis	tt5-CHI (Chalcone isomerase)	AT3G55120	Pourcel et al., 2013	Ca03250	Ca_Kabuli_Chr07	11604	37	3.19
Arabidopsis	tt7-F3‘H (Flavonoid 3′-hydroxylase)	AT5G07990	Routaboul et al., 2012	Ca13196	Ca_Kabuli_Chr07	1443	4	2.77
Arabidopsis	tt10-PPO (Polyphenol oxidase)	AT5G48100	Zhang et al., 2012	Ca23340	Ca_Kabuli_Chr03	3106	10	3.22
Arabidopsis	tt12-MATE secondary transporter (Multi antimicrobial extrusion)	AT3G59030	Debeaujon et al., 2001	Ca10158	Ca_Kabuli_Chr02	3676	9	2.45
Arabidopsis	tt15-GT (Glucosyl transferase)	AT1G43620	Focks et al., 1999	Ca04376	Ca_Kabuli_Chr04	6919	21	3.04
Arabidopsis	tt18-LDOX (Leucoanthocyanidin dioxygenase)	AT4G22880	Liu et al., 2014	Ca02395	Ca_Kabuli_Chr08	2179	4	1.84
Arabidopsis	tt19-GST (Glutathione S-transferase)	AT5G17220	Xu et al., 2014	Ca03442	Ca_Kabuli_Chr04	1903	3	1.58
Arabidopsis	ban-ANR (Anthocyanin reductase)	AT1G61720	Bowerman et al., 2012	Ca05336	Ca_Kabuli_Chr06	3793	9	2.37
Arabidopsis	aha10 (Autoinhibited H+ ATPase isoform 10)	AT1G17260	Baxter et al., 2005	Ca01370	Ca_Kabuli_Chr03	10262	35	3.41
Arabidopsis	tt1-TF WIP (Wiskott-aldrich syndrome protein) type zinc finger	AT1G34790	Sagasser et al., 2002	Ca27078	Ca_Kabuli_Scaffold-2269	2324	5	2.15
Arabidopsis	tt2-TF AtMYB123 (Myeloblastoma transcription factor)	AT5G35550	Chen et al., 2012	Ca12762	Ca_Kabuli_Chr07	2226	5	2.25
Arabidopsis	tt8-TF AtbHLH042 (Basic helix-loop-helix)	AT4G09820	Chen et al., 2014	Ca14089	Ca_Kabuli_Chr01	2283	6	2.63
Arabidopsis	tt16-TF MADS AtAGL32 (Agamous like-32)	AT5G23260	Erdmann et al., 2010	Ca15760	Ca_Kabuli_Chr07	3027	8	2.64
Arabidopsis	ttg1-WD40	AT5G24520	Nguyen et al., 2013	Ca04058	Ca_Kabuli_Chr05	2028	4	1.97
Arabidopsis	ttg2-TF WRKY	AT2G37260	Pesch et al., 2014	Ca17273	Ca_Kabuli_Chr02	4380	16	3.65
Arabidopsis	tt9-Unknown	AT3G28430	Ichino et al., 2014	Ca22116	Ca_Kabuli_Chr01	16647	47	2.82
Medicago	MATE secondary transporter (TRANSPARENT TESTA)	MTR1g108990	Zhao and Dixon, 2009	Ca05556a	Ca_Kabuli_Chr04	3936	10	2.54
Medicago	MATE secondary transporter (TRANSPARENT TESTA)	MTR1g108840		Ca05557a	Ca_Kabuli_Chr04	5315	19	3.57
Medicago	MATE secondary transporter (TRANSPARENT TESTA)	MTR1g108810		Ca05558a	Ca_Kabuli_Chr04	4540	15	3.30

^aTandem array of three seed color candidate co-orthologous tt12-MATE family transporter repeated genes located at the selective sweep target region of kabuli chromosome 4 reported by Varshney et al. (2013).