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Metabolite and transcript markers for the prediction of potato drought tolerance.

ABSTRACT: Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.

SUBMITTER: Sprenger H

PROVIDER: S-EPMC5866952 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Climate models predict an increased likelihood of drought, demanding efficient selection for drought tolerance to maintain yield stability. Classic tolerance breeding relies on selection for yield in arid environments, which depends on yield trials and takes decades. Breeding could be accelerated by marker-assisted selection (MAS). As an alternative to genomic markers, transcript and metabolite markers have been suggested for important crops but also for orphan corps. For potato, we suggested a random-forest-based model that predicts tolerance from leaf metabolite and transcript levels with a precision of more than 90% independent of the agro-environment. To find out how the model based selection compares to yield-based selection in arid environments, we applied this approach to a population of 200 tetraploid Solanum tuberosum ssp. tuberosum lines segregating for drought tolerance. Twenty-four lines were selected into a phenotypic subpopulation (PPt) for superior tolerance based on relative tuber starch yield data from three drought stress trials. Two subpopulations with superior (MPt) and inferior (MPs) tolerance were selected based on drought tolerance predictions based on leaf metabolite and transcript levels from two sites. The 60 selected lines were phenotyped for yield and drought tolerance in 10 multi-environment drought stress trials representing typical Central European drought scenarios. Neither selection affected development or yield potential. Lines with superior drought tolerance and high yields under stress were over-represented in both populations selected for superior tolerance, with a higher number in PPt compared to MPt. However, selection based on leaf metabolites may still be an alternative to yield-based selection in arid environments as it works on leaves sampled in breeder's fields independent of drought trials. As the selection against low tolerance was ineffective, the method is best used in combination with tools that select against sensitive genotypes. Thus, metabolic and transcript marker-based selection for drought tolerance is a viable alternative to the selection on yield in arid environments.

Project description:Drought is a limiting factor for N(2) fixation in soybean [Glycine max (L.) Merr.] thereby resulting in reduced biomass accumulation and yield. Drought-sensitive genotypes accumulate ureides, a product of N(2) fixation, during drought stress; however, drought-tolerant genotypes have lower shoot ureide concentrations, which appear to alleviate drought stress on N(2) fixation. A key enzyme involved in ureide breakdown in shoots is allantoate amidohydrolase (AAH). It is hypothesized that AAH gene expression in soybean determines shoot ureide concentrations during water-deficit stress and is responsible for the differential sensitivities of the N(2)-fixation response to drought among soybean genotypes. The objectives were to examine the relationship between AAH transcript levels and shoot ureide concentration and drought tolerance. Drought-tolerant (Jackson) and drought-sensitive (Williams) genotypes were subjected to three water-availability treatments: well-watered control, moderate water-deficit stress, and severe water-deficit stress. Shoot ureide concentrations were examined, in addition to gene expression of AAH and DREB2, a gene expressed during water-deficit stress. As expected, DREB2 expression was detected only during severe water-deficit stress, and shoot ureide concentrations were greatest in the drought-sensitive genotype relative to the drought-tolerant genotype during water-deficit stress. However, expression of AAH transcripts was similar among water treatments and genotypes, indicating that AAH mRNA was not closely associated with drought tolerance. Ureide concentrations in shoots were weakly associated with AAH mRNA levels. These results indicate that AAH expression is probably not associated with the increased ureide catabolism observed in drought-tolerant genotypes, such as Jackson. Further study of AAH at the post-translational and enzymatic levels is warranted in order to dissect the potential role of this gene in drought tolerance.

Project description:Survival and mortality of plants in response to severe drought may be related to carbon starvation, but little is known about how plasma membrane intrinsic proteins may help alleviate the drought-induced damage. Here, we determined the roles of plasmalemma aquaporin gene in improving plant water status, maintaining carbon accumulation, and thereby enhancing drought tolerance. Seven StPIP1 transformed potato (Solanum tuberosum L.) lines (namely T1, T2…T7) were compared with non-transgenic control plant at molecule and whole-plant levels. The relative expression of StPIP1 gene was found in leaves, stems and roots, with the most abundant expression being in the roots. The transgenic lines T6 and T7 had the highest StPIP1 expression, averaging 7.2 times that of the control and the greatest differences occurred 48 h after mannitol osmotic stress treatment. Using an evaluation index to quantifying the degree of drought tolerance, we found that the StPIP1 transgenic lines T6 and T7 had the highest drought tolerance, averaging 8.5 times that of the control. Measured at 30 days in drought stress treatment, the control plant decreased net photosynthetic rate by 33 and 56%, respectively, under moderate and severe stresses; also decreased stomatal conductance by 39 and 65%; and lowered transpiration rate by 49 and 69%, compared to the no-stress treatment, whereas the transgenic lines T6 and T7 maintained a relatively stable level with slight decreases in these properties. The constitutive overexpression of StPIP1 in potato improved plant water use efficiency and increased nonstructural carbohydrate concentration, which helped alleviate carbon starvation and minimized the loss of biomass and tuber yield due to drought stress. We conclude that the expression of StPIPs improves overall water relations in the plant and helps maintain photosynthesis and stomatal conductance; these help minimize carbon starvation and enhance the whole plant tolerance to drought stress.

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Metabolite and transcript markers for the prediction of potato drought tolerance.

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