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ARS Home » Midwest Area » Ames, Iowa » Plant Introduction Research » Research » Research Project #437142

Research Project: Digital Root Phenotyping and Genotyping of the USDA-NPGS Carrot Collection

Location: Plant Introduction Research

Project Number: 5030-21000-064-007-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2019
End Date: Jul 31, 2020

Carrot production is driven by market class and market type is largely determined by root shape, size, color, and end-use. Available, genetically diverse, unencumbered germplasm for variety improvement is limited, and evaluation of root shape and size has eluded researchers because of the difficulty of obtaining these data. Evaluate root phenotypic traits of available, USDA-NPGS (National Plant Germplasm Collection) cultivated Daucus germplasm using Cooperator's digital phenotyping platform to produce accurate quantitive measurements. Genomic data is as important to germplasm characterization as phenotypic data, and SNP (single nucleotide polymorphism) data will be collected for the same accessions for use in association analyses with the phenotypic data, and to generate predicted breeding values of different accessions in the context of specific market-class breeding programs.

Production of the crop in a soil where it can be easily harvested and cleaned, and then phenotyped in a reliable and time efficient manner has proved very difficult. Carrot accessions will be grown in Cooperator's carrot nursery at a farm in Randolph, Wisconsin. Accessions will be planted in paired 3.7 m rows on raised beds that have 1.2 m alleys between ranges. Accessions will be planted using a planter fitted with a cone seeder attachment. Plants will be thinned to approximately 30 plants per meter to allow for the fullest expansion of roots shape for each accession. Immediately after harvesting plots after approximately 110 days of growth, carrots will be packed in paper bags with wood shavings and stored at 4C in the dark until the time of digital phenotyping. After four weeks of growth in the field, leaf tissue from a single plant of each accession will be harvested into plates for DNA extraction and quantified using PicoGreen. Sequencing 6 with 150 bp paired-end reads will be conducted at the University of Wisconsin-Madison Biotechnology Center on each sample using adapters. SNPs will be called on the GBS dataset, and after accounting for population structure, associations between phenotypic and genotypic variation investigated. By using the digital phenotyping platform described above, multiple roots per accession can be assayed, and thereby GWAS analysis limited to those accessions that show low intra accession variability for specific root shape traits (e.g., length, width, aspect ratio, tip curvature, degree of shouldering, and principal components of the contour). GBS data obtained on this collection could be used in future studies attempting to characterize the USDA-NPGS collection on the basis of other agronomic traits. Cooperators will use their high-throughput digital phenotyping platform for efficient and reliable phenotypic characterization of root traits.