Translational Genomics in Agriculture: Some Examples in Grain Legumes

Figures & data

FIG. 1. A snapshot on sequencing status of key model plant/ crop genomes. This figure shows sequencing status of some key model plant as well as crop species including legumes. Initiation of the sequencing project has been shown by dotted lines with the year and % genome assembled has been showed as filled circles.

TABLE 1 Some candidate genes identified in five legume crops

Crop	Candidate gene(s)	Stress/trait(s)	Approach	Reference
Chickpea	CarNAC3	Drought and developmental processes	cDNA library	(Peng et al., 2009)
	CarF -box1	Drought, salinity and developmental processes	Molecular cloning	(Jia et al., 2012)
Common bean	αAI-Pv	Bruchid beetles	Overexpression	(Shade et al., 1994)
Groundnut	AhLPAT	Triacylglycerol biosynthesis	Homology based	(Chen et al., 2009)
Pigeonpea	CcHyPRP	Drought	Overexpression	(Priyanka et al., 2010)
	CcCYP	Drought, salinity and extreme temperatures	Overexpression	(Sekhar et al., 2010)
	CcMT1	Heavy metal stress	Overexpression	(Sekhar et al., 2010)
Soybean	GmRPS1, GmRPS6, GmRPL37	Cold stress	SuppressionSubtractiveHybridization	(Kim et al., 2004)
	P5CR	Drought and heat	Overexpression	(de Ronde et al., 2004)
	GmDREBa, GmDREBb, GmDREBc	Salinity, drought and cold	Expression analysis	(Li et al., 2005a)
	GmMIPS1	Seed development	RNAi-mediated silencing	(Nunes et al., 2006)
	GmNAC	Cold and developmental processes	Molecular cloning	(Meng et al., 2007)
	GmEREBP1	Defense response	Overexpression	(Mazarei et al., 2007)
	GmbZIP44, GmbZIP62 or GmbZIP78	Salt and freezing tolerance	Overexpression	(Liao et al., 2008)
	GS52	Nodulation	RNAi-mediated silencing	(Govindarajulu et al., 2009)
	Rpp4C4	Asian soybean rust	virus-induced gene silencing	(Meyer et al., 2009)
	GmDREB3	Cold, drought and salt	Overexpression	(Chen et al., 2009)
	GmOLPb, P21e	Salinity, methyl jasmonate and salicylic acid	Expression analysis	(Tachi et al., 2009)
	Glyma14g38510, 38560 and 38580	Soybean mosaic virus	Homology based	(Wang et al., 2011)
	Glyma03g28610/ Glyma03g 28630	Iron deficiency chlorosis	Transcriptome sequencing	(Pieffer et al., 2012)
	Glyma07g05410/ Glyma16g01980	Flowering time/maturation	Homology based	(Kim et al., 2012)
	GmDGAT2C/ GmDGAR1B	Seed yield	Homology based	(Eskandari et al., 2013)

TABLE 2 NGS-based transcriptome assemblies and genomic resources

Crops	Platform	Unigenes/ transcripts	SSRs	SNPs	Reference
Chickpea	Illumina	53,409	4,816	-	(Garg et al., 2011a)
	454FLX	34,760	4,111	495	(Garg et al., 2011b)
	454FLX and Illumina	1,03,215	26,252	26,082	(Hiremath et al., 2011)
	454FLX	1,60,883	-	1,022	(Gaur et al., 2012a)
	454FLX and Illumina	-	-	14,454	(Hiremath et al., 2012)
	454FLX	37,265	4,072	36,446	(Jhanwar et al., 2012)
	454FLX and Illumina	43,389	5,409	39,940	(Agarwal et al., 2012)
Common bean	454FLX and Illumina	1,60,036	-	3,487	(Hyten et al., 2010)
	454FLX	59,295	1,516	-	(Kalavacharla et al., 2011)
Groundnut	454FLX	7,43,232	2,884	-	(Guimarães et al., 2012)
	Illumina	59,077	5,883	-	(Zhang et al., 2012)
Pigeonpea	454FLX	43,324	3,771	-	(Dutta et al., 2011)
	454FLX and Illumina	127,754	50,566	12,141	(Dubey et al., 2011)
	Illumina	-	-	17,113	(Saxena et al., 2012)
Soybean	Illumina	5,02,020	-	1,682	(Deschamps et al., 2010)
	Illumina	-	-	205,614	(Lam et al., 2010)

TABLE 3 List of some comprehensive genetic maps for selected legumes

Name of population	Type	Number of loci	References
Chickpea
ICC 4958 × PI 489777	RIL	406	(Choudhary et al., 2012)
ICC 4958 × PI 489777	RIL	1,063	(Gaur et al., 2012b)
ICC 4958 × PI 489777	RIL	1,328	(Hiremath et al., 2012)
ICC 4958 × PI 489777	RIL	1,291	(Thudi et al., 2011)
ICC 4958 × PI 489777	RIL	300	(Gujaria et al., 2011)
ICC 4958 × PI 489777	RIL	521	(Nayak et al., 2010)
Common Bean
DOR3646 × BAT477	RIL	291	(Galeano et al., 2011)
BAT93 × Jalo EEP558	RIL	275	(McConnell et al., 2010)
BAT93 × Jalo EEP558	RIL	413	(Hanai et al., 2010)
BAT93 × Jalo EEP558	RIL	275	(McConnell et al., 2010)
DOR364 × G19833	RIL	215	(Córdoba et al., 2010)
Xana × Cornell 49242	RIL	294	(Pérez-Vega et al., 2010)
Faba bean
Vf 6 × Vf 136	RIL	277	(Díaz-Ruiz et al., 2009a)
Vf 6 × Vf 27	RIL	258	(Cruz-Izquierdo et al., 2012)
Groundnut
A-genome genetic maps
A. duranensis × A. duranensis	F2	2,319	(Nagy et al., 2010)
A. duranensis × A. stenosperma	F2	369	(Leal-Bertioli et al., 2009)
B-genome genetic maps
A. batizocoi PI 298639 × A. batizocoi PI 468327	F2	449	(Guo et al., 2010)
AB genome genetic maps
Tifrunner × GT-C20	F2	381	(Wang et al., 2013; 2012)
Satonoka × Kintoki	F2	516	(Shirasawa et al., 2013; 2012)
Nakateyutaka × YI-0311	F2	293	(Shirasawa et al., 2013; 2012)
Tifrunner × GT-C20	RIL	239	(Qin et al., 2012)
A. duranensis × (A. ipäensis × A. duranensis)	BC1F1	298	(Foncéka et al., 2009)
ICP 28 × ICPW 94	F2	239	(Bohra et al., 2011)
ICP 28 × ICPW 94	F2	910	(Saxena et al., 2012)
Pusa Dwarf × HDM04-1	F2	296	(Kumawat et al., 2012)
Lentil
ILL 5588 × L 692-16-1(s)	RIL	283	(Hamwieh et al., 2005)
Eston × PI 320937	RIL	207	(Tullu et al. 2006; 2008)
Digger (ILL 5722) × NorthWeld (ILL 5588)	RIL	211	(Gupta et al., 2012a)
CDC Robin × 964a-46	RIL	543	(Sharpe et al., 2013)
CDC Robin × 964a-46	RIL	577	(Fedoruk et al., 2013)
Pea
Puget × 90-2079	RIL	324	(Pilet-Nayel et al., 2002)
Wt 10245 × Wt 11238	F2	204	(Irzykowska and Wolko, 2004)
Carneval × MP 1401	RIL	207	(Tar’an et al., 2003a; 2004)
DP × JI 296	RIL	206	(Prioul et al., 2004)
Shawnee × Bohatyr	RIL	302	(Loridon et al., 2005)
Orb × CDC Striker	RIL	224	(Ubayasena et al., 2010)
P665 × Messire	RIL	246	(Fondevilla et al., 2008; 2010)
Orb × CDC Striker	RIL	255	(Sindhu et al., 2013)
Soybean
Essex × Forrest	RIL	959	(Xia et al., 2007)
Essex × Forrest	RIL	237	(Kassem et al., 2006)

TABLE 4 Summary of some trait mapping studies in select legumes

Trait	Gene/ QTL	*PVE (%)	Reference
Chickpea
Resistance to biotic stresss
Fusarium wilt	foc-0, foc-1, foc-2, foc-3, foc-4, foc-5	15	(Cobos et al., 2005; Iruela et al., 2007)
	QTL		(Gowda et al., 2009)
Ascochyta blight	QTL	14–56	(Anbessa et al., 2009; Cobos et al., 2006; Irula et al., 2006; Kottapalli et al., 2009; Lichtenzveig et al., 2006; Tar’an et al., 2007)
	BSA	-	(Rajesh et al., 2002)
	AR2, ar1, ar1a, ar1b, ar2a, ar2b, Ar19	28	(Cho et al., 200)
Botrytis gray mold	QTL	44	(Anuradha et al., 2011)
Rust	QTL	31	(Madrid et al., 2008)
Agronomic and yield related traits
Agronomic and yield related traits	QTL	19	(Gowda et al., 201)
Days to flower	QTL	26–56	(Cobos et al., 2007; 2009; Lichtenzveig et al., 2006)
Double podding	QTL	-	(Cobos et al., 2005; Cho et al., 2002; Rajesh et al., 2002)
100-seed weight	QTL	52	(Cho et al., 2002)
Flower colour	B/b		(Gowda et al., 2009)
Seed coat colour, thickness, size weight	QTL	49–73	(Cobos et al., 2005; 2009; 2007; Gowda et al., 2011; Hossain et al., 2011; Lichtenzveig et al., 2006)
Common bean
Resistance to biotic stresses
Angular leaf spot	QTL	22–64	(López et al., 2003; Oblessuc et al., 2012; Teixeira et al., 2005)
Anthracnose	Co-genes	-	(Rodriguez-Suarez et al., 2007)
Ashy stem blight	QTL	16–29	(Miklas et al., 2006b)
Bean common mosaic necrosis virus	BSA	-	Strausbaugh et al., 1999)
	bc-3; I	4	(Johnson et al., 1997)
Bean golden yellow mosaic virus	QTL	15	(Miklas et al., 2006)
	bgm	1	(Blair et al., 2007)
Bean pod weevil	QTL	22	(Blair et al., 2006)
Bruchids	Arc gene		(Blair et al., 2010)
Bean rust resistance	BSA	-	(Correa et al., 2000; Johnson et al., 1995; Mienie et al., 2005; Miklas et al., 1993; Park et al., 2008)
Bacterial brown spot	QTL		(Jung et al., 2003)
Beet curly top virus	BSA	-	(Larsen and Miklas, 2004)
Climbing ability and component traits	QTL	25	(Checa and Blair, 2008)
Common bacterial blight (CBB) resistance	QTL	30–73	(Liu et al., 2005; Miklas et al., 2006; Vandemark et al., 2008)
Charcoal rot	QTL	1	(Hernandez-Delgado et al., 2009)
Fusarium wilt	QTL	63	(Fall et al., 2001)
	PvPR2, PvPR1	3	(Schneider et al., 2001)
Halo blight	QTL	-	(Miklas et al., 2011)
	Pse	1	(Miklas et al., 2009)
Thrips	Tpr6.1		(Frei et al., 2005)
White mold	QTL	39–52	(Park et al., 2001; Soule et al., 2011)
Phosphorus uptake	Pup4.1, 10.1 and 2.1		(Beebe et al., 2006)
Rust	UR-6, UR-13	19	(Mienie et al., 2005)
Seed chemical content	QTL	51	(Casanas et al., 2013)
Faba Bean
Ascochyta blight	QTL	24–45	(Avila et al., 2004; Díaz-Ruiz et al., 2009b; Roman et al., 2003)
Broomrape resistance	QTL	33–43	(Díaz-Ruiz et al., 2009a; Gutiérrez et al., 2013; Román et al., 2002)
Rust	Uvf1		(Avila et al., 2003)
Floral characters	QTL	20	(Avila et al., 2005)
Days to flowering	QTL	28	(Cruz-Izquierdo et al., 2012)
Flowering length	QTL	31	(Cruz-Izquierdo et al., 2012)
Pod length	QTL	25	(Cruz-Izquierdo et al., 2012)
Number of ovules per pod	QTL	27	(Cruz-Izquierdo et al., 2012)
Number of seeds per pod	QTL	26	(Cruz-Izquierdo et al., 2012)
Yield characters	QTL	58	(Avila et al., 2005)
Frost tolerance	QTL	40	(Arbaoui et al., 2008)
Fatty acid content	QTL	63	(Arbaoui et al., 2008)
Groundnut
Resistance to biotic stresses
Late leaf spot, Leaf rust, Aspergillus flavus invasion, groundnut rosette disease, Tomato Spotted Wilt Virus	QTL	1.70–82.96	(Khedikar et al., 2010; Liang et al., 2009a; Qin et al., 2012; Sujay et al., 2012; Wang et al., 2013)
Drought tolerance related traits
Transpiration,Transpiration efficiency, Specific leaf area, Leaf area, SPAD chlorophyll meter reading (SCMR), Biomass, Canopy conductance, Total dry matter	QTL	3.48–22.39	(Gautami et al., 2012b; Ravi et al., 2011; Varshney et al., 2009b)
Morphological and yield related traits
Shoot dry weight, Pod weight, Seed weight, Haulm weight, Harvest index, Pod mass/plant, Mature pods/plant, Number of branches, Height of main axis, Stem diameter, Leaf length, width and length /width ratio, Length of main stem, Length of the longest branch, Number of branches, Weight of plant, Weight of mature pod per plant, Thickness of pod, Width of pod, Shape of tip of pods, Number of seeds per a plant, Yield parameters	QTL	3.78–40.10	(Gautami et al., 2012a; Liang et al., 2009; Ravi et al., 2011; Selvaraj et al., 2009; Shirasawa et al., 2012; Varshney et al., 2009b)
Seed and oil quality
Oil content, Oil quality, Protein content, High oleate trait	QTL	1.4–74.03	(Liang et al., 2009; Pandey et al., 2012c; Sarvamangala et al., 2011; Selvaraj et al., 2009; Shirasawa et al., 2012)
Pea
Plant height	QTL	19–65	(Tullu et al., 2008; Tar’an et al., 2003b; Dirlewanger et al., 1994)
Days to 50% flowering	QTL	35	(Fedoruk et al., 2013)
Days to maturity (DM)	QTL	34	(Tar’an et al., 2004)
Plant Maturity	QTL	27	(Timmerman-Vaughan et al., 2004)
Earliness	QTL	46	(Tullu et al., 2008)
Powdery mildew	genes		(Fondevilla et al., 2011)
Fusarium wilt (FW) resistance	QTL	-	(Hamwieh et al., 2005)
Stemphylium blight (SB) resistance	QTL	46	(Saha et al., 2010)
Rust	QTL	63	(Barilli et al., 2010)
Aphanomyces root rot	QTL	21–60	(Hamon et al., 2011, 2013; Pilet-Nayel et al., 2002)
Ascochyta blight (AB) resistance	QTL	35–75	(Fondevilla et al., 2008; Gupta et al., 2012b; Prioul et al., 2004; Rubeena et al., 2006; 2003; Tar’an et al., 2003b; Timmerman-Vaughan et al., 2002; Tullu et al., 2006)
Orobanche	QTL	8–36	(Fondevilla et al., 2010)
Frost resistance/damage	QTL	61	(Dumont et al., 2009; Klein et al., 2014)
Winter hardiness	QTL	43	(Kahraman et al., 2010)
Seed thickness	QTL	38	(Fedoruk et al., 2013)
Seed plumpness	QTL	40	(Fedoruk et al., 2013)
Grain yield	QTL	38	(Tar’an et al., 2004)
Lodging resistance	QTL	58	(Tar’an et al., 2003b)
Seed protein concentration/content	QTL	59	(Tar’an et al., 2004; Burstin et al., 2007)
Yield component and developmental traits	QTL	62	(Timmerman-Vaughan et al., 2005)
Yield-related traits and seed protein content	QTL	56	(Irzykowska and Wolko, 2004)
Pigeonpea
Fertility restoration	QTL	15–24	(Bohra et al., 2012)
Fusarium wilt	BSA		(Kotresh et al., 2006)
Number of pods per plant	QTL	19	(Kumawat et al., 2012)
Plant height	QTL	28	(Kumawat et al., 2012)
Plant type	BSA		(Dhanasekar et al., 2010)
Primary branches per plant	QTL	20	(Kumawat et al., 2012)
SMD resistance	QTL	25	(Gnanesh et al., 2011)
	BSA		(Ganapathy et al., 2009)
Soybean
Resistance to biotic stresses
Cyst nematode, Corn earworm, Brown stem rot, Sclerotinia stem rot, Phytophora root rot, Sclerotinia stem rot, Soybean mosaic virus, Asian rust, Brown stem rot, Sudden death syndrome	QTL	2–28	(Atibalentja et al., 2005; Guo et al., 2006; Guo et al., 2008; Han et al., 2008; Huynh et al., 2010; Kazi et al., 2008; Li et al., 2010; Ruben et al., 2006; Shi et al., 2008; Silva and Danielle, 2008; Vuong et al., 2008; Wang et al., 2010; Winter et al., 2007)
Soybean mosaic virus	Rsv, Rsv	1 to 3	(Shi et al., 2008)
Cyst nematode	rhg1, Rhg4	5	(Guo et al., 2005; Ruben et al., 2006; Vuong et al., 2010; Winter et al., 2007; Wu et al., 2009)
Agronomic and yield related traits
Seed protein oil content, Water use efficiency, Specific leaf weight and leaf size, Seed weight, Flowering time, Yield, maturity, Sprout yield, Seed isoflavone, Seed size, viability of seed, germination rate of seed, water absorbability of seed, ability, frequency, and efficiency of somatic embryogenesis, Vitamin E content, Chlorophyll a fluorescence parameter, Developmental behavior, Browning in soybean seed coats, Domestication, Seed composition, Seed shape, Photoperiod insensitivity, Net-like cracking in seed coats, Cleistogamy, Nodule number and nodule dry weight, Water logging, Oligosaccharide and sucrose	QTL	3–63	(Choi et al., 2010; Funatsuki et al., 2005; Githiri et al., 2006; Githiri et al., 2007; Khan et al., 2008; Kim et al., 2006; Lee et al., 2009; Li-H. et al., 2010; Liu et al., 2007; Liu and Abe, 2010; Nicolas et al., 2006; Oyoo et al., 2010; Panthee et al., 2006; Qi et al., 2008; Reinprecht et al., 2009; Salas et al., 2006; Song et al., 2010; Sun et al., 2006; Tuyen et al., 2010; Yin et al., 2010)
Early maturity	E8	8	(Cober et al., 2010)
Phosphorus deficiency	fsw1, fsw2, rp1, fsw3, rp2, lp1, lp2	12	(Li et al., 2005)

FIG. 2. Integrative genomics for accelerated crop improvement. The figure depicts the use of genomic resources for identification of marker /candidate gene. Subsequently the markers/genes identified may be used to detect gene-trait associations thus by enhancing molecular breeding program by deploying different approaches like MABC, MARS and GS. Ultimately integrating genomic resources through translational genomics would result in improved lines or developed cultivars.

TABLE 5 Key success stories of TGA in legume crops

Crop	Trait	Progenies developed/ cultivars released	Reference/source
Chickpea	Fusarium wilt resistance	Back cross progenies from (C 214 × WR 315)	(Varshney et al., 2013c)
	Aschochyta blight resistance	Back cross progenies from (C 214 × ILC 3279)	(Varshney et al., 2013c)
	Drought tolerance	Back cross progenies from (JG 11 × ICC 4958)	(Varshney et al., 2013b)
		Back cross progenies from (Chefe × ICC 8261), (KAK2 × ICC 8261), (ICCV 10 × ICC 4958)	(ICRISAT, India)
		Back cross progenies from (Ejere × ICC 4958), (Arerti × ICC 4958)	(EIAR, Ethiopia)
		Back cross progenies from (ICCV 97105 × ICC 4958), (ICCV 95423 × ICC 4958)	(EU, Kenya)
Common bean	Disease resistance	USPT-ANT-1, ABCP-8, ABC-Weihing	(Miklas et al., 2003; Mutlu et al., 2005, 2008)
	Resistance to white mold	Back cross lines	(Carneiro et al., 2010)
Groundnut	Nematode resistance	COAN cultivar, NemaTam	(Simpson et al., 2003)
	Nematode resistance and High O/L ratio	Tifguard High O/L	(Chu et al., 2011)
	Rust resistance	Back cross progenies from (JL 24 × GPBD 4), (TAG24 × GPBD 4), (ICGV 91114 × GPBD 4)	(Varshney et al., 2014)
	High O/L ratio	Back cross lines	(Koilkonda et al., 2012)
Soybean	Disease resistance	JTN-5503, JTN-5303	(Arelli et al., 2006; 2007)
	Soybean mosic virus	F4:5 lines, Near Isogenic Line (NILs)	(Saghai-Maroof et al., 2008; Shi et al., 2008)
	Low phytate	Back cross lines	(Landau-Ellis and Pantalone, 2009)
	Soybean cyst nematode resistance	JTN-5109, DS-880	(Smith et al., 2010)
	Rust resistance	Back cross lines	(Khanh et al., 2013)

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