Sb verticilliflorum AusTRCF317961 Assembly and Gene Annotation

About Sorghum AusTRCF317961

AusTRCF317961 is a wild Sorghum bicolor subsp. verticilliflorum accession which was collected when naturalised in an urban setting in South-East Queensland. It has been used as a CWR donor in multiple pre-breeding BCNAM populations – both within the core Australian program and in introgression funded by the Global Crop Diversity Trust. In the core pre-breeding program significant CWR haplotype has persisted in subsequent pedigree breeding and selection for agronomic and trait performance.

The BCNAM populations from AusTRCF317961 have been used to study genetic architecture of grain weight, rust resistance and tillering.

Assembly

The genome assembly of Sorghum AusTRCF317961 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 183X and 35X coverage, respectively. The assembly effort generated a genome of 643.4Mb with contigs N50 of 87.1kb.

Annotation

Gene prediction was performed using a hybrid approach combining de novo gene predictors and evidence-based methods, which led to the identification of 32,392 genes in the genome

References

1. Tao Y, Luo H, Xu J, Cruickshank A, Zhao X, Teng F, Hathorn A. Wu X. Liu Y. Shatte T et al. 2021. Extensive variation within the pan-genome of cultivated and wild sorghum. Nat. Plants 7:766–773. doi: 10.1038/s41477-021-00925-x.
2. Tao Y, Mace E, George-Jaeggli B, Hunt C, Cruickshank A, Henzell R, Jordan D. 2018. Novel grain weight loci revealed in a cross between cultivated and wild sorghum. Plant Genome. 11: 170089. doi: 10.3835/plantgenome2017.10.0089.
3. Alam MM, Mace ES, van Oosterom EJ, Cruickshank A, Hunt CH, Hammer GL, Jordan DR. 2014. QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering. Theor. Appl. Genet. 127: 2253-2266. doi: 10.1007/s00122-014-2377-9.
4. Wang X, Mace ES, Hunt C, Cruickshank A, Henzell R, Parkes H, Jordan DR. 2014. Two distinct classes of QTL determine rust resistance in sorghum. BMC Plant Biol. 14:366. doi: 10.1186/s12870-014-0366-4.
5. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature. 457:551-556. doi: http://doi.org/10.1038/nature07723.
6. McCormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, McKinley B et al. 2018. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. Plant J. 93:338-354. doi: 10.1111/tpj.13781.
7. Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE et al. 2013. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc. Natl. Acad. Sci. U.S.A. 110:453-458. doi: 10.1073/pnas.1215985110.
8. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X et al. 2013. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Nat Commun. 4:2320. doi: 10.1038/ncomms3320.
9. Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z. 2016. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Plant Cell. 28:1551-1562. doi: 10.1105/tpc.16.00373.
10. Xin Z, Wang ML, Barkley NA, Burow G, Franks C, Pederson G, Burke J. 2008. Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biol 2008, 8:103. doi: 10.1186/1471-2229-8-103.
11. Addo-Quaye C, Buescher E, Best N, Chaikam V, Baxter I and Dilkes BP. 2017. Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines. G3: Genes, Genomes, Genetics. 7(2):413-425. doi: 10.1534/g3.116.029660.

Links

• GENESYS: https://www.genesys-pgr.org/a/3035497b-8869-4077-8918-00dff1a9a80c

  More information

General information about this species can be found in Wikipedia.

More information

General information about this species can be found in Wikipedia.