Computer aided data acquisition tool for high-throughput phenotyping of plant populations

Abstract

BackgroundThe data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and analysis of such large datasets often becomes tedious for biologists and lab technicians. Most of the current phenotype data acquisition management systems do not cater to the specialized needs of large-scale data analysis. The successful application of genomic tools/strategies to introduce desired traits in plants requires extensive and precise phenotyping of plant populations or gene bank material, thus necessitating an efficient data acquisition system.ResultsHere we describe newly developed software "PHENOME" for high-throughput phenotyping, which allows researchers to accumulate, categorize, and manage large volume of phenotypic data. In this study, a large number of individual tomato plants were phenotyped with the "PHENOME" application using a Personal Digital Assistant (PDA) with built-in barcode scanner in concert with customized database specific for handling large populations.ConclusionThe phenotyping of large population of plants both in the laboratory and in the field is very efficiently managed using PDA. The data is transferred to a specialized database(s) where it can be further analyzed and catalogued. The "PHENOME" aids collection and analysis of data obtained in large-scale mutagenesis, assessing quantitative trait loci (QTLs), raising mapping population, sampling of several individuals in one or more ecological niches etc.

Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity

“…Each accession was tagged with a unique plant-ID barcode label as described earlier in [ 23 ]. At different developmental stages of the plant, 16 major phenotype categories [ 25 ] were recorded using a hand-held Personal Digital Assistant (PDA) equipped with barcode scanner and customized software, PHENOME, for large-scale phenotypic data collection [ 23 ]. The phenotypic variations were recorded using a digital camera.…”

“…In the present study, we phenotyped a large number of tomato accessions with special emphasis on fruit morphological and biochemical parameters. The phenotypic diversity of the population was assessed utilizing high throughput digital data collection tools such as PDA [ 23 ] and Tomato Analyzer [ 24 ] in combination with the assessment of SNPs by a reverse genetic screen, EcoTILLING. Statistical analysis of the morphometric data by TA showed fruit shape to be a complex trait.…”

Field Phenotyping and Long-Term Platforms to Characterise How Crop Genotypes Interact with Soil Processes and the Environment

“…While phenotyping data output from these systems will give us better understanding of the overall growth and stability of phenotypes in field it is necessary to keep accurate records of climate data, and also acquire environmental data relating to the management effects, such as tillage on soil structure, such that these can be linked back to crop phenotypic changes. Further, systems need to be put in place that allow the integration of the phenotyping data and environmental data across different platforms [119].…”

Informational Support of the Breeding Experiment in Wheat in the WheatPGE System

“…Однако наряду с этими методами необходимо внедрение технологий, которые бы позволяли повысить эффективность традиционных способов измерения параметров фенотипа, в особенности в полевых условиях. Такие технологии позволят быстро вносить результаты измерений в компьютерные базы данных (БД), что приведет к ускорению процесса сбора фенотипических данных [8][9][10][11].…”

“…В последнее время все активнее разрабатываются подходы по информационной поддержке самих селекционно-генетических экспериментов, при выполнении которых создаются большие массивы разнородных экспериментальных данных [8,17]. Управление такими массивами с целью получения достоверных, ясных выводов является крайне актуальной задачей.…”