Sb bicolor PI656001 Tx2783 Assembly and Gene Annotation

About 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 in 1984 (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 & Population Panels

S. bicolor ‘Tx2783' (GRIN: PI 656001) is derived from Capbam, and part of the following population panels: * Sorghum Association Panel (SAP) - 407 accessions (Casa et al, 2008)

IPR

Crop Science Registration. GP-137, SORGHUM. Issued: 01 Mar 1984. * 1984. Crop Sci. (Madison) 24(2):390. Note: GP-137

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 75X (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 annotations were built by the Ware Lab in CSHL using a pan-gene index from reference gene models and propagated to representative assemblies using the Liftoff tool and further updating their structure using PASA tool.

Gene calling was performed using a hybrid approach with de novo gene predictors and evidence-based methods (Wang et al, submitted), 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.

Source: NCBI, April 2021.

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.

Variation

About 32.5 million SNPs were called in 400 SAP lines by Rod Wing's group with the HPC-based AFW-GVC/GATK4 pipeline [Yong Zhou, Nagarajan Kathiresan and Rod A. Wing (2023), manuscript in preparation], and are now available from the Tx2783 genome browser. See for example 4_6047465_C_T, a SNP predicted to introduce a STOP codon and result in a truncated SbiRTX2783.04G076100 protein product.

Image

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

Links

U.S. National Plant Germplasm System (GRIN - Global): PI 656001.