A new resource for plant research

The plant research community has a valuable and practical new resource available: a rapid-cycling Brassica oleracea population that can be used to map the genetics of many traits simply by phenotyping. The population and related resources are described in a recent publication led by Zach Stansell in Thomas Björkman’s lab at Cornell University.

  • The map and reference genome are complete
  • Bioinformatic-analysis pipeline is available
  • Seed is available for free
  • Researchers only need to phenotype and analyze

The BolTBDH population is derived from a from a cross of rapid-cycling Chinese kale with broccoli. It is particularly valuable for studying reproductive development because progeny lines have inflorescences that range from non-heading to fully heading broccoli. Variation is documented for many other traits, such as architecture and glucosinolate content, and variation in many others remains to be explored and documented.

To1000 is a small plant with long inflorescences, Early Big is a normal broccoli
Parents of BolTBDH: the rapid-cycling Chinese kale, TO1000 and the broccoli ‘Early Big’.

The BolTBDH population provides both precise locations because it has enough markers and high detection power because it has enough individuals. Previous mapping populations have had one or the other limitation. The population is fully genotyped at 1881 SNP markers and has 175 segregating individuals, enough that quantitative trait loci (QTL) can be mapped with considerable power. The lines are double haploid, making all seed produced from each fully homozygous individual genetically identical to the parent. Code for identifying QTL is available at GitHub.

The genetic map is dense enough to capture all the crossing-over events within the BolTBDH population. The genotypes of each locus can be assigned to one of the parents unambiguously. Candidate genes can be identified efficiently because the markers are aligned to a fully annotated reference genome derived from the Chinese-kale parent. Experiments and seed increases are easy to plan using the provided descriptors of each line, including such useful information as time to flowering, plant size, and relative seed yield.

Seed will be available from the USDA National Germplasm System so that it can be used by the research and education community. Few other mapping populations have enough seed available for sharing with other researchers. This population will be in excellent hands. Vegetable crop curator Joanne Labate and technician Paul Kisly have begun increasing seed so that samples can be made available quickly. Allocations of five seeds per line will be available to researchers for free.

A man is looking at seedlings in greenhouse trays. They are at the four-leaf stage in mid-October 2019.
Paul Kisly of USDA-ARS Plant Germplasm unit is producing seed of the 175 progeny lines so that they can be distributed to researchers through the plant germplasm system.

Five seeds should be sufficient for phenotyping because most traits are expressed consistently among the genetically identical individuals in each line. The number is also about what one can manage in a single grow out.

Users can produce additional seed through hand-pollinations. Increasing seed for the entire population takes about seven months and uses about 500 square feet of greenhouse bench.

BolTBDH has several other useful qualities.

Ideal for undergraduate research experience.

The population will be a valuable undergraduate teaching tool. The relatively short time from sowing to flowering means that students can complete a research project in a semester. The same set of plants can be used by several teams, each analyzing a different set of traits. For example, evaluation of glucosinolates and leaf morphology could be conducted concurrently using the same plants.

Safe to invest lab resources.

Investment in this population is worthwhile for several reasons. Genotyping is already completed and the genetic map captures the upper limit of crossover-event saturation. This map will not be superseded by a higher density, or more accurate, version. Unlike other mapping populations, BolTBDH seed can be readily regenerated.

Usable by novice genomicists.

The tricky genomics is already done. Mapping QTLs can be done even by relatively inexperienced investigators because the genomics pipeline for this analysis is available on GitHub. The quality-control has been carefully done, and the appropriate parameters selected.

Useful for validating pathways and genetic mechanisms.

Researchers who have identified candidate genes for particular traits can test allelic variation at those loci causes variation in the phenotype. The relevant loci can be identified on the annotated reference genome.

If there is variation in the phenotype of interest, but not in the candidate gene, this population may help identify other genes in the pathway that contribute to the phenotype of interest.

Additionally, this mapping population can be a useful precursor in developing hypotheses testing for subsequent association mapping studies.

Filled with low-hanging fruit.

We have identified QTL for 24 developmental traits, particularly ones associated with inflorescence and flower development. Other traits remain to be assessed, such as secondary metabolites and a more detailed dissection of inflorescence traits.

This population should be particularly valuable for researchers studying flowering. For traits under simple genetic control (e.g.: flower color), we report LOD scores as high as 40.

About the population.

The population was initially developed under Tom Osborne, then at the University of Wisconsin. The double haploids were made by Mark Farnham at USDA-ARS in Charleston, SC. The initial description was by Federico Iniguez, now in Argentina. The BolTBDH population (N = 175) was developed by crossing rapid-cycling Chinese kale ‘TO1000DH3’ DH (B. oleracea var.  alboglabra) with ‘Early Big’ DH broccoli (B. oleracea var. italica). The progeny were maintained by Dr. Farnham, the parents were obtained from the germplasm repository at HRI Warwick and Dr. Osborne.


  • Publication: Stansell, Z., Farnham, M., Björkman T. 2019. Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH mapping population. Frontiers in Plant Science. 10: 1104, doi: 10.3389/fpls.2019.01104
  • Germplasm repository for seed: https://www.ars.usda.gov/northeast-area/geneva-ny/plant-genetic-resources-research/. Joanne Labate, curator.
    Ordering will be available in late 2020. The PI numbers will be listed with the genomics pipeline. Order through the Genetic Resource Information System https://npgsweb.ars-grin.gov/gringlobal/search.aspx?
  • Genomics pipeline: https://github.com/zacharystansell/BolTBDH
  • Reference genome: Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F. 2014. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology 15:R77.https://plants.ensembl.org/Brassica_oleracea/Info/Index
  • Development of population: Iniguez-Luy, F. L., Lukens, L., Farnham, M. W., Amasino, R. M., and Osborn, T. C. 2009. Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and oleracea. Theoretical and Applied Genetics 120: 31–43. https://link.springer.com/article/10.1007/s00122-009-1157-4