Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome

Background Terminal drought stress leads to substantial annual yield losses in chickpea (Cicer arietinum L.). Adaptation to water limitation is a matter of matching water supply to water demand by the crop. Therefore, harnessing the genetics of traits contributing to plant water use, i.e. transpiration rate and canopy development dynamics, is important to design crop ideotypes suited to a varying range of water limited environments. With an aim of identifying genomic regions for plant vigour (growth and canopy size) and canopy conductance traits, 232 recombinant inbred lines derived from a cross between ICC 4958 and ICC 1882, were phenotyped at vegetative stage under well-watered conditions using a high throughput phenotyping platform (LeasyScan). Results Twenty one major quantitative trait loci (M-QTLs) were identified for plant vigour and canopy conductance traits using an ultra-high density bin map. Plant vigour traits had 13 M-QTLs on CaLG04, with favourable alleles from high vigour parent ICC 4958. Most of them co-mapped with a previously fine mapped major drought tolerance “QTL-hotspot” region on CaLG04. One M-QTL was found for canopy conductance on CaLG03 with the ultra-high density bin map. Comparative analysis of the QTLs found across different density genetic maps revealed that QTL size reduced considerably and % of phenotypic variation increased as marker density increased. Conclusion Earlier reported drought tolerance hotspot is a vigour locus. The fact that canopy conductance traits, i.e. the other important determinant of plant water use, mapped on CaLG03 provides an opportunity to manipulate these loci to tailor recombinants having low/high transpiration rate and plant vigour, fitted to specific drought stress scenarios in chickpea

High throughput phenotyping and advanced genotyping reveals QTLs for plant vigor and water saving traits in a “QTL-hotspot”: New opportunities for enhancing drought tolerance in chickpea

Terminal drought stress leads to substantial yield losses in chickpea (Cicer arietinum L.). Water conservation at vegetative growth (canopy conductivity and canopy size and development) allow plants to increase soil water extraction during grain filling and are hypothesised to help chickpea adaptation to water limited environments. Plant vigour and water saving traits were phenotyped in 232 recombinant inbred lines (RILs), derived from a cross between ICC4958 and ICC1882, at 28 days after sowing under well water conditions using a high throughput phenotyping platform. Different density genetic maps (241-SSRLow density, 1007-SSR+SNPs-High density and 1557-SNPs-Ultra high density) were used for QTLs identification. Several major QTLs (M-QTLs) for plant vigour traits (3D-leaf area, shoot biomass, plant height and growth related traits) were identified on CaLG04, and co-mapped with previously identified and fine mapped major drought tolerance QTL-hotspot region on CaLG04 (~300Kb).The canopy conductance trait (e.g Transpiration rate) had a M-QTL mapped on CaLG03 using ultra-high density bin markers. Plant vigour traits on CaLG04 and canopy conductance related traits on CaLG03 provide opportunity to manipulate these loci to tailor recombinants having lower transpiration rate and high plant vigour. This ideotype might be enhancing the water stress adaptation in chickpea. To test this hypothesis, a subset of 40 RILs contrasting for vigour and water use traits was tested in lysimeters and field under different water stress treatments. High vigour low water use lines had higher seed yield under severe water stress treatments than high vigour and high water use lines, validating the hypothesis