Summary
Resource Type
Organism
Abbreviation
J. nigra
Genus
Juglans
Species
nigra
Common Name
Black Walnut
Organism Image
Description

Order: Fagales
Family: Juglandaceae
Chromosome Number: 2n=32 1

Image used courtesy of Paul Wray, Iowa State University, Bugwood.org
licensed under a Creative Commons Attribution-Noncommercial 3.0 License.

Cross Reference
JBrowse

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

Transcriptome
NameProgramDate Constructed
de novo Black Walnut (Juglans nigra)Trinity; CD-HIT-ESTDec 3rd, 2013
Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
Black Walnut (blastx against TrEMBL)blastxApr 18th, 2016
Interpro Analysis of Black Walnut (Juglans nigra)InterProScanApr 18th, 2016
Black Walnut (blastx against sprot)blastxApr 18th, 2016
de novo Black Walnut (Juglans nigra)Trinity; CD-HIT-ESTDec 3rd, 2013
Black Walnut Ozone TreatmentsHTSeq; RPKMJul 9th, 2014
Biological Samples
NameTissueTreatmentDescription
BW-M-19Not setNot setBlack Walnut-Sparrow-Mother tree
BW-CH10-28DNot setNot setBlack Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-OW-9Not setNot setBlack Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-OW-12Not setNot setBlack Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-M-29Not setNot setBlack Walnut-Sparrow-Mother tree
BW-M-28Not setNot setBlack Walnut-Sparrow-Mother tree
BW-M-22Not setNot setBlack Walnut-Sparrow-Mother tree
BW-M-23Not setNot setBlack Walnut-Sparrow-Mother tree
BW-M-24Not setNot setBlack Walnut-Sparrow-Mother tree
BW-M-21Not setNot setBlack Walnut-Sparrow-Mother tree

Pages

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)

Publication: Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, Cronn R, Arumuganathan AK, Coggeshall M, Gailing O. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PloS one. 2015 Dec 23;10(12):e0145031.

In order to develop SSR resources for ten important North American hardwood tree species, we individually barcoded and multiplex sequenced DNA from ten hardwood forest tree species using short reads produced from an Illumina HiSeq. Raw reads can be downloaded from the NCBI short read archive, project SRP021923. Bioinformatic processing included trimming, assembly, SSR identification and primer design, processing details including scripts are available.

Statistics:

Untrimmed Pairs 17,205,517
Untrimmed Bases 3,475,514,434
Reconstructed Fragments 7,033,939
Reconstructed Fragments - Bases 1,191,496,671
Dinucleotide repeats with primers 11,859
Trinucleotide repeats with primers 753
Tetranucleotide repeats with primers 139

Download Files:

Libraries
NameTypeStatus
BAC Library JNC_Babac_librarycurrent
BAC Library JNC_Bbbac_librarycurrent