Resource Type
J. nigra
Common Name
Black Walnut
Organism Image
Cross Reference
Order: Fagales Family: Juglandaceae Chromosome Number: 2n=32 1 Juglans nigra, commonly called black walnut, is a large deciduous tree typically growing 75-100’ (less frequently to 125’) tall with and an oval to rounded crown. Mature trees characteristically have long trunks, often with an absence of lower branching. Fissured, sharply ridged, dark gray-black bark forms diamond patterns. Black walnut is native from Massachusetts through southern Ontario to South Dakota south to Florida and Texas. Yellow green monoecious flowers appear in late spring (May-June), the male flowers in drooping hairy catkins and the female flowers in short terminal spikes. Female flowers give way to edible nuts, each being encased in a yellow-green husk. Credits: Missouri Botanical Garden Image used courtesy of Paul Wray, Iowa State University, licensed under a Creative Commons Attribution-Noncommercial 3.0 License.
Reference Genome
NameProgramDate Constructed
Draft reference genomes for six Juglans species and Pterocarya stenopteraTrinity, MUMmer, SamtoolsJun 14th, 2018
Ebrahimi (Purdue) - Reference GenomesN/ASep 3rd, 2019

The Black walnut (Juglans nigra) transcriptome was mapped to the English walnut (Juglans regia) genome assembly using GMAP.

Total J. nigra mrna contigs Contigs mapped to J. regia >90% identity >90% coverage
78,834 74,984 68,235 62,387

Reference: Thomas D. Wu and Colin K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005 21:1859-1875

Go to JBrowse

NameProgramDate Constructed
Juglans nigra - Transcriptome AssemblyTrinity; CD-HIT-ESTDec 3rd, 2013
[Archived] Juglans nigrans - Transcriptome Assembly OzoneTrinityDec 19th, 2012
Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
Biological Samples
BW-M-19dormant twigsnoneBlack Walnut-Sparrow-Mother tree
BW-CH10-28Dleafozone exposure 80ppb for 28 daysBlack Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-OW-9leafcontrol chamber ozone 10ppb+ mecanical wounding on day 28Black Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-OW-12leafozone exposure 225ppb for 29 day + mecanical wounding on day 28Black Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-M-29female flowersnoneBlack Walnut-Sparrow-Mother tree
BW-M-28catkins (male flowers-immature/not shed polen yetnoneBlack Walnut-Sparrow-Mother tree
BW-M-22undamaged twigsnoneBlack Walnut-Sparrow-Mother tree
BW-M-23damaged twigsmechanical woundingBlack Walnut-Sparrow-Mother tree
BW-M-24green twigs/buds-this year growthnoneBlack Walnut-Sparrow-Mother tree
BW-M-21damaged leavesmechanical woundingBlack Walnut-Sparrow-Mother tree


Mapping Population

Location: University of Missouri, Horticulture and Agroforestry Research Center (HARC) in New Franklin, MO

Principal Investigators: Mark Coggeshall, Jeanne Romero-Severson

A full sibling population was created, representing two nut cultivars in the University of Missouri (MU) germplasm repository, 'Sparrow' and "Schlessler'. The population consists of 323 seedling full sibs (all derived from the 2008 seed years), plus both parents. Full sibling status was confirmed via paternity exclusion genetic testing on all individuals. This paternity exclusion (PE) work was initiated in 2009 and primarily funded through the University of Missouri Center for Agroforestry (UMCA), in cooperation with the Romero-Severson (JRS) lab at the University of Notre Dame (ND).

Phenotyping of this of this population will be initiated in the spring 2015 and will include:

  • leafing date
  • bud burst
  • pistillate & staminate bloom
  • season length
  • anthracnose susceptibility

As circumstances permit, standardized nut characteristics will be assessed using standardized descriptor values developed by IPGRI (1990), including:

  • % kernel
  • veination
  • kernel color
  • harvest date
  • shell thickness

Genotyping of this population is ongoing. A set of SSR markers are being used for the entire population, and a subset of trees are also undergoing ddRADTag genotyping.

Please contact us for more information or if you are interested in utilizing this population for research. Genotype and phenotype information will be posted here when publicly available.

A second full-sib population totaling 135 to date, sharing the female parent “Sparrow” with the first population, was started at UM in 2015. The seed parent Sparrow was selected for whole genome resequencing at UC-Davis for a USDA Specialty Crops Research Initiative (SCRI) project headed by David Neale. Data is expected sometime in 2016.

Predicted SSRS (genomic)
There are 939 SSR markers associated with 939 features in this organism.

The complete list of SSR markers, their properties, and primers to amplify then can be found on the corresponding analysis page.

Analysis Name
Simple Sequence Repeats (SSR) prediction ( J. nigra)

You can search for markers below: the form will return the gene features they are associated with.

Search for markers

BAC Library JNC_Banucleic_acid_librarycurrent
BAC Library JNC_Bbnucleic_acid_librarycurrent
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