Posts by Collection

publications

A digital image-based phenotyping platform for analyzing root shape attributes in carrot

Brainard S.H., Bustamante J.A., Dawson J.C., Spalding E.P., and Goldman I.L. A Digital Image-Based Phenotyping Platform for Analyzing Root Shape Attributes in Carrot. Front Plant Sci (2021)

Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values

Brainard S.H., Ellison S.L., Simon P.W., Dawson J.C., and Goldman I.L. Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values. Theor Appl Genet (2022)

Novel QTL Associated with Rhizoctonia solani Kühn Resistance Identified in Two Table Beet x Sugar Beet F_2:3 Populations Using a New Table Beet Reference Genome

Wigg K.S., Brainard S.H., Metz N., Dorn, K.M., and Goldman I.L. Novel QTL Associated with Rhizoctonia solani Kühn Resistance Identified in Two Table Beet x Sugar Beet F_2:3 Populations Using a New Table Beet Reference Genome. Crop Sci (2023)

QTL mapping utilizing F_2:3 linkage mapping populations reveals regions of chromosomes 2 and 6 are significantly associated with root width in carrot

Vega-Alfaro, A., Brainard, S.H., Goldman, I.L. QTL mapping utilizing F_2:3 link- age mapping populations reveals regions of chromosomes 2 and 6 are significantly associated with root width in carrot. Acta Hort Under review (2023)

Form and contour: Breeding and genetics of organ shape from wild relatives to modern vegetable crops

Goldman, I.L., Vega-Alfaro, A., Brainard, S.H., McGregor, C., Oravec, M., van der Knaap, E., Wan, Y. Form and contour: Breeding and genetics of organ shape from wild relatives to modern vegetable crops. Front Plant Sci (2023)

Improving selection efficiency in C. americana × C. avellana interspecific hybrids through the development of an indel-based genetic map

Brainard, S.H., Fischbach, J.A., Braun, L.C., Dawson, J.C. Improving selection efficiency in C. americana × C. avellana interspecific hybrids through the development of an indel-based genetic map. Acta Hort (2023)

The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Brainard, S.H., Sanders, D.M., Bruna, T., Shengqiang, S., Dawson, J.C. The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus. Plant Biotechnol J (2024)

Linkage mapping of root shape traits associated with market class in two carrot populations

Vega, A., Brainard, S.H., Goldman, I.L. Linkage mapping of root shape traits associated with market class in two carrot populations. G3 (2024)

software

Next-generation sequencing software

Java applications for working with Illumina data and high-density molecular marker datasets

High-throughput phenotyping tools

Python software for high-throughput digital image acquisition, pre-processing, and phenotyping of plant organs.

teaching

bcftools tutorial

Graduate course, HORT615: Genetic Mapping, 2021

A tutorial on how to use bcftools to filter VCF files prior to genetic mapping.

OneMap tutorial