Sb bicolor IS8525 Assembly and Gene Annotation

About Sorghum IS8525

IS8525 is a landrace of Sorghum bicolor collected in Ethiopia. Its name is Butha and it is also designated by PI563092 and DL 63/550. The accession has shown variability, notably for the white-dry/juicy midrib trait. It is recognized as a source of resistance to sorghum ergot. Both GRIN and the ICRISAT genebank database describe IS8525 as belonging to the caudatum race.

The accession held in Australia and the subject of sequencing studies has white -dry midrib and is clearly in the kafir race in any molecular genetic classification. This accession IS8525 has been used to construct a mapping population to study grain number, rust resistance, ergot resistance and tillering.

Assembly

The genome assembly of Sorghum IS8525 was reported in Tao et al. 2021. Sequencing was conducted by the Australia Sorghum breeding team in collaboration with BGI-Shenzhen using Illumina HiSeq 4000 platform and the PacBio Sequel platform to achieve 176X and 39X coverage, respectively. The assembly effort generated a genome of 569Mb with contigs N50 of 402.3kb.

Annotation

Gene prediction was performed using a hybrid approach combining de novo gene predictors and evidence-based methods (Tao et al, 2021), which led to the identification of 36,237 genes in the genome.

References

1. QTL analysis of ergot resistance in sorghum. Parh D, Jordan DR, Aitken E, Mace ES, Junai P, McIntyre C, Godwin I, 2008. Theor. Appl. Genet. 117 (3): 369-382.
2. Genetic Components of Variance and the Role of Pollen Traits in Sorghum Ergot Resistance Jordan, D. R., Aitken, E. A. B., Gogel, B. J., McIntyre, L. C., and Godwin, I. D. 2006.. Crop science. 46 (6) 2387-2395
3. [Extensive variation within the pan-genome of cultivated and wild sorghum.] (https://doi.org/10.1038/s41477-021-00925-x)Tao Y, Luo H, Xu J, Cruickshank A, Zhao X, Teng F, Hathorn A. Wu X. Liu Y. Shatte T et al. Nat. Plants.
4. The Sorghum bicolor genome and the diversification of grasses. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. 2009. Nature. 457:551-556.
5. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. McCormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, McKinley B et al. 2018. Plant J. 93:338-354.
6. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE et al. 2013. Proc. Natl. Acad. Sci. U.S.A.. 110:453-458.
7. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X et al. 2013. Nat Commun. 4:2320.
8. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z. 2016. Plant Cell. 28:1551-1562.
9. Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. Xin Z, Wang ML, Barkley NA, Burow G, Franks C, Pederson G, Burke J. 2008. BMC Plant Biol 2008, 8:103.
10. Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines. Addo-Quaye C, Buescher E, Best N, Chaikam V, Baxter I and Dilkes BP. 2017. G3: Genes, Genomes, Genetics. 7(2):413-425.

Links

1. USDA https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1458063
2. ICRISAT http://genebank.icrisat.org/IND/PassportSummary?ID=IS%208525
3. FAO https://doi.org/10.18730/N8KHD

   More information

General information about this species can be found in Wikipedia.

More information

General information about this species can be found in Wikipedia.