Feb 2017

High throughput phenotyping and advanced genotyping reveals QTLs for plant vigour and water saving traits co-localize in a “QTL-hotspot”: Progress in understanding the drought adaptations in chickpeaKaliamoorthy Sivasakthi1,2, Mahendar Thudi1, Murugesan Tharanya1,2, Sandeep M Kale1, Jana Kholová1, Mahamat Hissene Halime1, Deepa Jaganathan1, Rekha Baddam1, Thiyagarajan Thirunalasundari2, Pooran M Gaur1, Rajeev K Varshney1, Vincent Vadez1*1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India2Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

About ICRISAT: www.icrisat.orgICRISAT’s scientific information: http://EXPLOREit.icrisat.org

For more details contact v.vadez@cgiar.org

Introduction• Earlier, root traits (depth and density) were hypothesized to improve water extraction and so

contribute to yield increase under water limited environments in chickpea (Varshney et al 2013). • Usually across the crop species, enhanced root growth is functionally linked with enhanced shoot

growth. • Therefore, here we want to investigate whether enhanced root growth also links to enhanced shoot

vigour (e.g. canopy conductivity, canopy size & development) and so functionally explain increased chickpea crop productivity in water limited environments.

Figure 1. Phenotyping facility for lower level traits (Canopy development; High throughput crop phenotyping facility-LeasyScan) to higher level (Crop production; Semi-field (Lysimeter) and field).

Figure 2. a) Dynamics of 3D-leaf area development in parental lines, b) Transpiration rate (TR; mg H2O mm-2 min-1) in population (232 RILs) and parents (ICC 4958 & ICC 1882) at 28 DAS under WW conditions.

Figure 3. Comparison of different density markers in “QTL hotspot” genomic region harbouring QTLs for vigour traits (present study) and drought tolerance / root traits (earlier studies) on CaLG04 using QTL cartographer software.

Figure 4. a) Water extraction at pod filling stage, b) Seed yield for selected 40 RILs contrasting for plant vigour and canopy conductivity [HLA-HTR (High leaf area & high transpiration rate); HLA-LTR (High leaf area & low transpiration rate); LLA-HTR (Low leaf area & high transpiration rate) and LLA-LTR (Low leaf area & low transpiration rate)] characteristics were evaluated in lysimeter (semi-field) and field under different water stress treatments [Well water (WW), mild stress (MS), severe stress (SS)].

Aerial view-LeasyScan-Facility

Pot Scanning & gravimetric measurements

Aerial view-chickpea field evaluation

Lysimeter facility

• In the semi-field (Lysimeter) and field, lines combining high vigour and lower canopy conductivity attained higher water extraction at pod filling stage and also higher seed yield especially compared to lines combining high vigour and higher canopy conductivity lines under severe water stress conditions.

Conclusion• Our study shows that hotspot region on LG4 previously reported to underlies root growth

characteristics and yield under water stress also harbours plant vigour-related traits. • This implies that vigour-related root traits reported earlier (Varshney et al 2014) could be assessed by

vigour-related shoot traits which considerably ease its phenotyping. • We showed that plant vigour traits on CaLG04 combined with lowered canopy conductivity traits

on CaLG03 provide an opportunity to tailor recombinants enhancing the water extraction and crop production in severe water stress situation.

Selected referencesVadez V et al (2015) J. Exp. Bot. (2015) 66 (18): 5581-5593.Varshney et al (2014) Theor. Appl. Genet. 127:445–462.

AcknowledgementsThe authors are greatly thankful for the funding from ICRISAT, USAID (Feed the Future Innovation Lab—Climate Resilient Chickpea) and CGIAR Research Program on Dryland Cereals (CRP-DC) and Grain Legumes (CRP-GL) towards the establishment of LeasyScan facility.

Specific objectives• To identify genomic regions (QTLs) responsible for plant vigour-related traits in recombinant inbred

lines (RILs) material• Comparison of QTLs for vigour-related traits with previously reported QTLs for root-related traits.• Validation of water saving and crop production traits in selected 40 RILs contrasting for vigour and

water use chrecterists.

Refined QTL hotspot region (~15cM) 1007-High density SSR + SNPs (GBS) markers

Sivasakthi et al-Present study

Fine mapped QTL hotspot region (~300 Kb) 1557-Ultra-high density SNPs (Bin) markers

Sivasakthi et al-Present study Kale S.M et al 2015

Materials and methods• Plant materials: 232 recombinant inbred lines (RILs) derived from a cross between ICC 4958 (high

vigour) and ICC 1882 (low vigour).• Genotyping data: Two types of genetic maps; i) “High density map” containing 1007 markers

(SSR+SNPs; Jaganathan et al 2015) and ii) “Ultra high density map” containing 1557 markers (SNPs; Kale S.M et al 2015).

• Software used: QTL Cartographer and ICIM (QTL IciMapping) for high density and Ultra-high density marker analysis

• Phenotyping at LeasyScan: 15 plant vigor-related traits were phenotyped under LeasyScan platform in well-watered conditions at Nov-Dec-2014 and 15 (working principle & more information see Vadez et al 2015).

• Phenotyping at Lysimeter and Field: Dynamics of plant water extraction and crop production traits were assessed under different water stress treatments [mild stress (MS; 85 mm/season), severe stress (SS; 60 mm/ season) and well water (WW; 150 mm/ season)].

Key results• Using both genetic maps, we identified several major-QTLs underlying vigour-related traits on

CaLG04 (~300Kb) where the QTLs for major “drought tolerance” were reported earlier while canopy conductivity traits mapped to locus on CaLG03.

• Plant vigour-related traits were underlied by positive allele from ICC 4958, while canopy conductivity-related traits had allele from ICC 1882.

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