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

Plant Introduction (PI) number for Sorghum bicolor (L.) Moench subsp. bicolor, ‘RTx436’ in the U.S. National Plant Germplasm System (GRIN – Global): PI 561071.

This accession is part of the following population panels:

 

Pedigree

((SC120-6*Tx7000)Tx7000)-10-4-6-1-1-1-bk.

 

Image

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

 

Statistics (Source: NCBI, April 2021)

Sorghum line   Tx436
Assembly information
Assembly name Sorghum_bicolor-Tx436-Reference-CSHL-USDA-1.0
Assembly date
Assembly accession ERZ1345852
WGS accession
Assembly provider
Sequencing description Sequencing technologies: PacBio CLR
  Sequencing method PacBio Sequel v6.0 system
  Genome coverage: 61x
Assembly description Assembly methods:
  Construction of pseudomolecules
Finishing strategy
NCBI submission
Publication: Wang et al (2021)
 
Assembly statistics
Number of contigs 464
Total assembly length (Mb) 725
Contig N50 (Mb) 20
 
Annotations stats
Total number of genes 29,265
Total number of transcripts 41,713
Average gene length 3,900
Exons per transcript 5

 

Assembly

The genome assembly of sorghum Tx436 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 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 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

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.


Author