Sb bicolor PI561071 Tx436 Assembly and Gene Annotation

About Sorghum bicolor RTx436

Sorghum bicolor (L.) Moench subsp. bicolor, inbred line RTx436 is a widely adapted pollinator (male) parent used in the development of high-yielding hybrids. RTx436 is also commonly used in the development of traditional food-grade sorghum hybrids with white grain color and tan glumes, which are suitable traits for the food processing industry.

Germplasm & Population Panels

S. bicolor ‘RTx436’ (GRIN: PI 561071) with pedigree ((SC120-6*Tx7000)Tx7000)-10-4-6-1-1-1-bk, and is part of the following population panels: * Sorghum Association Panel (SAP) - 407 accessions (Casa et al, 2008)

IPR

Crop Science Registration. PL-236, SORGHUM. Issued: 01 Nov 1992. * Miller, F. R., T. F. Dusek, K. L. Prihoda, & L. W. Rooney. 1992. RTx436 Sorghum Parental Line. Crop Sci. (Madison) 32(6):1518. Note: PL-236

Assembly

The genome assembly of sorghum Tx436 has been submitted for publication (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 lengths 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

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.

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

This species currently has no variation database. However you can process your own variants using the Variant Effect Predictor (VEP) with S. bicolor BTx623 in Gramene.

Image

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

Links

U.S. National Plant Germplasm System (GRIN - Global): PI 561071.