Jana Kholova

Stay-green quantitative trait loci’s effects on water extraction, transpiration efficiency and seed yield depend on recipient parent background

A stay-green phenotype enhances the adaptation of sorghum (Sorghum bicolor (L.) Moench) to terminal drought, although the mechanisms leading to its expression remain unclear. Differences in tillering and leaf area at anthesis, transpiration efficiency (TE), water extraction, harvest index (HI) and yield under terminal drought and fully irrigated conditions were assessed in 29 introgression lines (IL) targeting stay-green quantitative trait loci (QTLs) Stg1, Stg2, Stg3, Stg4, StgA and StgB in an S35 background, and 16 IL targeting Stg1, Stg3, Stg4 and StgB in an R16 background. TE was increased by StgB in the R16 background, whereas there was no effect in the S35 background. Water extraction was increased by Stg1 in the S35 background but not in R16. StgB modified the proportion of water extracted before and after anthesis in the S35 background. While tillering and leaf area at anthesis were decreased by Stg1 and Stg3 in S35, there was no effect in R16. Yield data under fully irrigated conditions showed higher tiller grain yield in Stg1, Stg2 and Stg3 ILs. Although yield differences were mostly explained by HI variation, the yield variation unexplained by HI was closely related to TE in S35 (R2=0.29) and R16 (R2=0.72), and was closely related to total water extracted in S35 (R2=0.41) but not in R16. These data indicate the potential for several stay-green QTLs to affect traits related to plant water use. However, these effects depend on the interaction between the genetic background and individual QTLs.

LeasyScan: a novel concept combining 3D imaging and lysimetry for high-throughput phenotyping of traits controlling plant water budget

Highlight We present a new concept combining novel 3D scanning of the plant canopy with seamless assessment of plant water use to measure plant traits influencing the water budget.

II.1.5 Phenotyping pearl millet for adaptation to drought

Pearl millet is highly resilient to some of the driest areas of the world, like the Sahel area or fringes of the Thar desert in India. Despite this, there is a wealth of variation in pearl millet genotypes for their adaptation to drought and the object of this paper was to review some related work in the past 25 years to harness these capacities toward the breeding of better adapted cultivars. Work on short duration cultivars has been a major effort. Pearl millet has also some development plasticity thanks to a high tillering ability, which allows compensating for possible drought-related failure of the main culm under intermittent drought. The development of molecular tools for breeding has made great progress in the last 10–15 years and markers, maps, EST libraries, BACs are now available and a number of quantitative trait loci (QTLs) for different traits, including drought, have been identified. Most of the work on drought has focused on the drought tolerance index (DTI), an index that reflect the genetic differences in drought adaptation that are independent of flowering time and yield potential. The DTI is closely associated to the panicle harvest index (PNHI), a trait that relates to a better grain setting and grain filling capacity. Initial work on the DTI involved empirical breeding and selection based on PNHI. A QTL for PNHI has then been identified and introgressed by marker-assisted backcrossing. More recently, a thorough dissection of that QTL has been carried out and shows that high PNHI is related to the constitutive ability of tolerant lines to save water (lower leaf conductance and sensitivity of transpiration to high vapor pressure deficit) at a vegetative stage and use it for the grain filling period. However, there is no contribution of root traits in this QTL. Current work is taking place to map these water saving traits, understand their genetic interactions, and design ideotypes having specific genetic make-up toward adaptation to specific rainfall environments.

Quantitative trait loci associated with constitutive traits control water use in pearl millet [Pennisetum glaucum (L.) R. Br.]

There is substantial genetic variation for drought adaption in pearl millet in terms of traits controlling plant water use. It is important to understand genomic regions responsible for these traits. Here, F7 recombinant inbred lines were used to identify quantitative trait loci (QTL) and allelic interactions for traits affecting plant water use, and their relevance is discussed for crop productivity in water-limited environments. Four QTL contributed to increased transpiration rate under high vapour pressure deficit (VPD) conditions, all with alleles from drought-sensitive parent ICMB 841. Of these four QTL, a major QTL (35.7%) was mapped on linkage group (LG) 6. The alleles for 863B at this QTL decreased transpiration rate and this QTL co-mapped to a previously detected LG 6 QTL, with alleles from 863B for grain weight and panicle harvest index across severe terminal drought stress environments. This provided additional support for a link between water saving from a lower transpiration rate under high VPD and drought tolerance. 863B alleles in this same genomic region also increased shoot weight, leaf area and total transpiration under well-watered conditions. One unexpected outcome was reduced transpiration under high VPD (15%) from the interaction of two alleles for high VPD transpiration (LG 6 (B), 40.7) and specific leaf mass and biomass (LG 7 (A), 35.3), (A, allele from ICMB 841, B, allele from 863B, marker position). The LG 6 QTL appears to combine alleles for growth potential, beneficial for non-stress conditions, and for saving water under high evaporative demand, beneficial under stressful conditions. Mapping QTL for water-use traits, and assessing their interactions offers considerable potential for improving pearl millet adaptation to specific stress conditions through physiology-informed marker-assisted selection.

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.Domestication reduces genetic diversity and constrains crop improvement. Here the authors identify factors that shaped species diversity in the wild progenitors of chickpea, and produce wild introgression populations that increase diversity for breeding by ~100-fold, including traits of agronomic relevance.

Chickpea Genotypes Contrasting for Vigor and Canopy Conductance Also Differ in Their Dependence on Different Water Transport Pathways

Lower plant transpiration rate (TR) under high vapor pressure deficit (VPD) conditions and early plant vigor are proposed as major traits influencing the rate of crop water use and possibly the fitness of chickpea lines to specific terminal drought conditions—this being the major constraint limiting chickpea productivity. The physiological mechanisms underlying difference in TR under high VPD and vigor are still unresolved, and so is the link between vigor and TR. Lower TR is hypothesized to relate to hydraulic conductance differences. Experiments were conducted in both soil (Vertisol) and hydroponic culture. The assessment of the TR response to increasing VPD showed that high vigor genotypes had TR restriction under high VPD, and this was confirmed in the early vigor parent and progeny genotype (ICC 4958 and RIL 211) having lower TR than the late vigor parent and progeny genotype (ICC 1882 and RIL 022). Inhibition of water transport pathways [apoplast and symplast (aquaporins)] in intact plants led to a lower transpiration inhibition in the early vigor/low TR genotypes than in the late vigor/high TR genotypes. De-rooted shoot treatment with an aquaporin inhibitor led to a lower transpiration inhibition in the early vigor/low TR genotypes than in the late vigor/high TR genotypes. Early vigor genotypes had lower root hydraulic conductivity than late vigor/high TR genotypes. Under inhibited conditions (apoplast, symplast), root hydraulic conductivity was reduced more in the late vigor/high TR genotypes than in the early vigor/low TR genotypes. We interpret that early vigor/low TR genotypes have a lower involvement of aquaporins in water transport pathways and may also have a smaller apoplastic pathway than high TR genotypes, which could explain the transpiration restriction under high VPD and would be helpful to conserve soil water under high evaporative demand. These findings open an opportunity for breeding to tailor genotypes with different “dosage” of these traits toward adaptation to varying drought-prone environments.

Quantitative trait loci (QTLs) for water use and crop production traits co-locate with major QTL for tolerance to water deficit in a fine-mapping population of pearl millet (Pennisetum glaucum L. R.Br.)

Key messageFour genetic regions associated with water use traits, measured at different levels of plant organization, and with agronomic traits were identified within a previously reported region for terminal water deficit adaptation on linkage group 2. Close linkages between these traits showed the value of phenotyping both for agronomic and secondary traits to better understand plant productive processes.AbstractWater saving traits are critical for water stress adaptation of pearl millet, whereas maximizing water use is key to the absence of stress. This research aimed at demonstrating the close relationship between traits measured at different levels of plant organization, some putatively involved in water stress adaptation, and those responsible for agronomic performance. A fine-mapping population of pearl millet, segregating for a previously identified quantitative trait locus (QTL) for adaptation to terminal drought stress on LG02, was phenotyped for traits at different levels of plant organization in different experimental environments (pot culture, high-throughput phenotyping platform, lysimeters, and field). The linkages among traits across the experimental systems were analysed using principal component analysis and QTL co-localization approach. Four regions within the LG02-QTL were found and revealed substantial co-mapping of water use and agronomic traits. These regions, identified across experimental systems, provided genetic evidence of the tight linkages between traits phenotyped at a lower level of plant organization and agronomic traits assessed in the field, therefore deepening our understanding of complex traits and then benefiting both geneticists and breeders. In short: (1) under no/mild stress conditions, increasing biomass and tiller production increased water use and eventually yield; (2) under severe stress conditions, water savings at vegetative stage, from lower plant vigour and fewer tillers in that population, led to more water available during grain filling, expression of stay-green phenotypes, and higher yield.

Molecular cloning and expression analysis of Aquaporin genes in pearl millet [Pennisetum glaucum (L) R. Br.] genotypes contrasting in their transpiration response to high vapour pressure deficits

Pearl millet is a crop of the semi-arid tropics having high degree of genetic diversity and variable tolerance to drought stress. To investigate drought tolerance mechanism that possibly accounts for differences in drought tolerance, four recombinant inbred lines from a high resolution cross (HRC) were selected for variability in their transpiration rate (Tr) response to vapour pressure deficit (VPD) conditions. The differential Tr response of the genotypes to increased VPD conditions was used to classify the genotypes as sensitive or insensitive to high VPD. Aquaporin (AQP) genes PgPIP1;1, PgPIP1;2, PgPIP2;1, PgPIP2;3, PgPIP2;6, PgTIP1;1 and PgTIP2;2 were cloned. Phylogenetic analysis revealed that the cloned PgAQPs were evolutionarily closer to maize AQPs than to rice. PgAQP genes, including PgPIP1;1 and PgPIP2;6 in root tissue showed a significant expression pattern with higher expression in VPD-insensitive genotypes than VPD-sensitive genotypes under low VPD conditions (1.2kPa) i.e when there is no high evaporative demand from the atmosphere. PgAQP genes (PgPIP2;1 in leaf and root tissues; PgPIP1;2 and PgTIP2;2 in leaf and PgPIP2;6 in root) followed a diurnal rhythm in leaves and roots that have either higher or lower expression levels at different time intervals. Under high VPD conditions (4.21kPa), PgPIP2;3 showed higher transcript abundance in VPD-insensitive genotypes, and PgPIP2;1 in VPD-sensitive genotypes, while rest of the PgAQPs showed differential expression. Our current hypothesis is that these differences in the expression of AQP genes under different VPDs suggests a role of the AQPs in tuning the water transport pathways with variation between genotypes.