The DOI matches its Crossref record; 77 of the 77 references it cites were found in a registry or an index.
Insights into the Maize Pan-Genome and Pan-Transcriptome
Open accessAbstract
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
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Self-citationMcCormick, R. F., Truong, S. K., Sreedasyam, A., Jenkins, J., Shu, S., Sims, D., Kennedy, M., Amirebrahimi, M., Weers, B. D., McKinley, B., et al. (2018) · The Plant Journal · doi:10.1111/tpj.13781 · Cited by 586
Atta, K., Mondal, S., Gorai, S., Singh, A. P., Kumari, A., Ghosh, T., Roy, A., Hembram, S., Gaikwad, D. J., Mondal, S., et al. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1241736 · Cited by 523
Salt stress under the scalpel – dissecting the genetics of salt tolerance
Morton, M. J. L., Awlia, M., Al‐Tamimi, N., Saade, S., Pailles, Y., Negrão, S., & Tester, M. (2019) · The Plant Journal · doi:10.1111/tpj.14189 · Cited by 373
Pan-genomics in the human genome era
Sherman, R. M., & Salzberg, S. L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0210-7 · Cited by 359
Metadata
- Authors
- Hirsch, C. N., Foerster, J. M., Johnson, J. M., Sekhon, R. S., Muttoni, G., Vaillancourt, B., Peñagaricano, F., Lindquist, E., Pedraza, M. A., Barry, K., de Leon, N., Kaeppler, S. M., & Buell, C. R.
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-01-01
- Volume
- 26
- Issue
- 1
- Pages
- 121-135
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- OpenAlex
- W2145928478
- Cited by
- 572
- References
- 77
- FWCI
- 20.01
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Hirsch, C. N., Foerster, J. M., Johnson, J. M., Sekhon, R. S., Muttoni, G., Vaillancourt, B., Peñagaricano, F., Lindquist, E., Pedraza, M. A., Barry, K., de Leon, N., Kaeppler, S. M., & Buell, C. R. (2014). Insights into the Maize Pan-Genome and Pan-Transcriptome. The Plant Cell. https://doi.org/10.1105/tpc.113.119982
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