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A cost-effective and customizable automated irrigation system for precise high-throughput phenotyping in drought stress studies.

ABSTRACT: The development of high-yielding crops with drought tolerance is necessary to increase food, feed, fiber and fuel production. Methods that create similar environmental conditions for a large number of genotypes are essential to investigate plant responses to drought in gene discovery studies. Modern facilities that control water availability for each plant remain cost-prohibited to some sections of the research community. We present an alternative cost-effective automated irrigation system scalable for a high-throughput and controlled dry-down treatment of plants. This system was tested in sorghum using two experiments. First, four genotypes were subjected to ten days of dry-down to achieve three final Volumetric Water Content (VWC) levels: drought (0.10 and 0.20 m3 m-3) and control (0.30 m3 m-3). The final average VWC was 0.11, 0.22, and 0.31 m3 m-3, respectively, and significant differences in biomass accumulation were observed between control and drought treatments. Second, 42 diverse sorghum genotypes were subjected to a seven-day dry-down treatment for a final drought stress of 0.15 m3 m-3 VWC. The final average VWC was 0.17 m3 m-3, and plants presented significant differences in photosynthetic rate during the drought period. These results demonstrate that cost-effective automation systems can successfully control substrate water content for each plant, to accurately compare their phenotypic responses to drought, and be scaled up for high-throughput phenotyping studies.

SUBMITTER: Ortiz D

PROVIDER: S-EPMC5988304 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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A cost-effective and customizable automated irrigation system for precise high-throughput phenotyping in drought stress studies.

Ortiz Diego D Litvin Alexander G AG Salas Fernandez Maria G MG

PloS one 20180605 6

The development of high-yielding crops with drought tolerance is necessary to increase food, feed, fiber and fuel production. Methods that create similar environmental conditions for a large number of genotypes are essential to investigate plant responses to drought in gene discovery studies. Modern facilities that control water availability for each plant remain cost-prohibited to some sections of the research community. We present an alternative cost-effective automated irrigation system scala ...[more]

PMID: 29870560

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Project description:Background: Genetic and genomic selection programs require large numbers of phenotypes observed for animals in shared environments. Direct measurements of phenotypes like meat quality, methane emission, and disease susceptibility are difficult and expensive to measure at scale but are critically important to livestock production. Our work leans on our understanding of the “Central Dogma” of molecular genetics to leverage molecular intermediates as cheaply-measured proxies of organism-level phenotypes. The rapidly declining cost of next-generation sequencing presents opportunities for population-level molecular phenotyping. While the cost of whole transcriptome sequencing has declined recently, its required sequencing depth still makes it an expensive choice for wide-scale molecular phenotyping. We aim to optimize 3′ mRNA sequencing (3′ mRNA-Seq) approaches for collecting cost-effective proxy molecular phenotypes for cattle from easy-to-collect tissue samples (i.e., whole blood). We used matched 3′ mRNA-Seq samples for 15 Holstein male calves in a heat stress trail to identify the 1) best library preparation kit (Takara SMART-Seq v4 3′ DE and Lexogen QuantSeq) and 2) optimal sequencing depth (0.5 to 20 million reads/sample) to capture gene expression phenotypes most cost-effectively. Results: Takara SMART-Seq v4 3′ DE outperformed Lexogen QuantSeq libraries across all metrics: number of quality reads, expressed genes, informative genes, differentially expressed genes, and 3′ biased intragenic variants. Serial downsampling analyses identified that as few as 8.0 million reads per sample could effectively capture most of the between-sample variation in gene expression. However, progressively more reads did provide marginal increases in recall across metrics. These 3′ mRNA-Seq reads can also capture animal genotypes that could be used as the basis for downstream imputation. The 10 million read downsampled groups called an average of 104,386 SNPs and 20,131 INDELs, many of which segregate at moderate minor allele frequencies in the population. Conclusion: This work demonstrates that 3′ mRNA-Seq with Takara SMART-Seq v4 3′ DE can provide an incredibly cost-effective (<$25/sample) approach to quantifying molecular phenotypes (gene expression) while discovering sufficient variation for use in genotype imputation. Ongoing work is evaluating the accuracy of imputation and the ability of much larger datasets to predict individual animal phenotypes.

Dataset Information

A cost-effective and customizable automated irrigation system for precise high-throughput phenotyping in drought stress studies.

Publications

A cost-effective and customizable automated irrigation system for precise high-throughput phenotyping in drought stress studies.

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