Sorghum bicolor Tx2783

Sorghum bicolor (L.) Moench subsp. bicolor, Tx2783 is a widely utilized pollinator parent with sugarcane aphid (SCA)-resistance (Armstrong et al, 2015; Tetreault et al, 2019).

Tx2783 has a complex pedigree (IS12610C/((((ROK Y8/Tx 2536)/SC110 -9)/SC599)/SC110 -14 E)) and was first released by Texas A&M AgriLife Research (Peterson et al, 1984). It was first bred for resistance to sorghum greenbug (Schizaphis graminum Rondani) biotypes C and E; and later on, shown to be highly resistant to the sugarcane aphid (Armstrong et al, 2015; Tetreault et al, 2019).

 

Germplasm

Plant Introduction (PI) number for Sorghum bicolor (L.) Moench subsp. bicolor, ‘Tx2783’ in the U.S. National Plant Germplasm System (GRIN – Global): PI 656001.

This accession is part of the following population panels:

Pedigree

Derived from Capbam.

 

Image

There are no images for this accession in the GRIN database.

 

Statistics (Source: NCBI, April 2021)

Sorghum line   Tx2783
Assembly information
Assembly name Sorghum_bicolor-Tx2783-Reference-CSHL-USDA-1.0
Assembly date
Assembly accession ERZ1345851
WGS accession
Assembly provider
Sequencing description Sequencing technologies: PacBio CLR
  Sequencing method Illumina HiSeq2500 system
  Genome coverage: 76x
Assembly description Assembly methods:
  Construction of pseudomolecules
Finishing strategy
NCBI submission
Publication: Wang et al (2021)
 
Assembly statistics
Number of contigs 447
Total assembly length (Mb) 733
Contig N50 (Mb) 26
 
Annotations stats
Total number of genes 29,612
Total number of transcripts 35,998
Average gene length 3,833
Exons per transcript 5

 

Assembly

The genome assembly of Sorghum Tx2783 has been submitted for publication by (Wang et al, 2021). Sequencing was done by the Ware Lab (USDA at CSHL) in collaboration with Corteva Agriscience using PacBio CLR technology to achieve 76X (reads N50=23.1 kb) coverage. The assembly effort generated contigs with N50 length of 25.6 Mb. In addition, BioNano molecules for Tx2783 yielded a genome map of 721.504 Mb with N50 length of 36.987 Mb. The chromosomes of the genome were constructed with hybrid scaffolds generated from BioNano genome maps. Most of the chromosomes were composed of two scaffolds.

 

Annotation

Gene calling was performed using a hybrid approach with de novo gene predictors and evidence-based methods (Wang et al, 2021), and then filtered based on annotation evidence distance (AED) scores, and homology to maize, brachypodium, rice, and Arabidopsis protein sequences. Ultimately, this approach generated a total of 29,612 protein-coding genes and 4,205 non-coding genes.

 

Literature References

Armstrong, J. Scott, William L. Rooney, Gary C. Peterson, Raul T. Villenueva, Michael J. Brewer, and Danielle Sekula-Ortiz. 2015. “Sugarcane Aphid (Hemiptera: Aphididae): Host Range and Sorghum Resistance Including Cross-Resistance From Greenbug Sources.” Journal of Economic Entomology 108 (2): 576–82. PMID: 26470168. https://doi.org/10.1093/jee/tou065.

Casa, Alexandra M., Gael Pressoir, Patrick J. Brown, Sharon E. Mitchell, William L. Rooney, Mitchell R. Tuinstra, Cleve D. Franks, and Stephen Kresovich. 2008. “Community Resources and Strategies for Association Mapping in Sorghum.” Crop Science 48 (1): 30–40. https://doi.org/10.2135/cropsci2007.02.0080.

Peterson, G. C., J. W. Johnson, G. L. Teetes, and D. T. Rosenow. 1984. “Registration of Tx2783 Greenbug Resistant Sorghum Germplasm Line.” Crop Science 24 (2): 390. https://doi.org/10.2135/cropsci1984.0011183X002400020062x.

Tetreault, Hannah M., Sajjan Grover, Erin D. Scully, Tammy Gries, Nathan A. Palmer, Gautam Sarath, Joe Louis, and Scott E. Sattler. 2019. “Global Responses of Resistant and Susceptible Sorghum (Sorghum Bicolor) to Sugarcane Aphid (Melanaphis Sacchari).” Frontiers in Plant Science 10 (February): 145. PMID: 30853964. https://doi.org/10.3389/fpls.2019.00145.

Wang, Bo, Yinping Jiao, Kapeel Chougule, Andrew Olson, Jian Huang, Victor Llaca, Kevin Fengler, et al. 2021. “Pan-Genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes.” Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.01.03.424980.


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