Joshua Udall Publications

See THIS webpage for a current list (though it doesn't have links to the PDFs):

1.          Page, J.T., Gingle, A., Udall, J.A. 2013. PolyCat: A Resource for Genome Categorization of Sequencing Reads from Allopolyploid Organisms G3:Genes|Genetics|Genomes (Accepted). (PDF)

2.          Paterson, A. et al. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres Nature 492:423-427. (PDF)

3.           Richardson, B.A., Page, J.T., Bajgain, P., Sanderson, S.C., Udall, J.A. 2012. Deep Sequencing of Amplicons Reveals Widespread Hybridiazation and Polyploidization in Big Sagebrush American Journal of Botany 99:1962-1975.

4.           Flagel, L. E., Wendel, J. F., & Udall, J. A. 2012. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics, 13: 302. (PDF)

5.          Salmon, A., Udall, J.A., Jeddolah, J. Wendel, J.F. 2012.  Targetted capture of homoelogous coding and non-coding sequence in polyploid cotton. GS:Genes|Genetics|Genomes 2:921-930. (PDF)

6.            Parra-Gonzalez, L. B., Aravena-Abarzua, G. A., Navarro-Navarro, C. S., Udall, J. A., Maugham, P. J., Peterson, L. M., Salgo-Garrido, H. E., et al. 2012. Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies. BMC Genomics 13:425 (PDF)

7.             Maughan, P. J., Smith, S. M., Rojas-Beltrán, J. A., & Elzinga, D., Raney, J.A., Jellen, E.N., Bonifacio, A., Udall, J.A., and Fairbanks, D. 2012. Single nucleotide polymorphisms identification, characterization and linkage mapping in Chenopodium quinoa. The Plant Journal 5:1-7.

8.              Byers, R. L., Harker, D. B., Yourstone, S. M., Maughan, P. J., & Udall, J. A. 2012. Development and mapping of SNP assays in allotetraploid cotton. Theoretical and Applied Genetics, 124:1201–1214.

9.              Cronn, R., Knaus, B. J., Liston, A., Maughan, P. J., Parks, M., Syring, J. V., & Udall, J. 2012. Targeted enrichment strategies for next-generation plant biology. American Journal of Botany, 99:291–311.

10.             Bushakra, J. M., Stephens, M. J., Atmadjaja, A. N., Lewers, K. S., Symonds, V. V., Udall, J. A., Chagné, D., et al. (2012). Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theoretical and Applied Genetics, 125:311–327. (PDF)

11.             Bybee, S. M., Bracken-Grisson, H., Haynes, B.D., Hermansen, R. A., Byers, R. L., Clement, M. J., Udall, J. A., et al.  2011.  Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics.  Genome Biology and Evolution 3:1312-1323.

12.              Morales, A. J., Bajgain, P., Garver, Z., Maughan, P. J., and Udall, J. A. 2011. Physiological responses of Chenopodium quinoa to salt stress. International Journal of Plant Physiology and Biochemistry 3:219-232 (PDF)

13.               Bajgain, P., R.A. Richardson, J.C. Price, R.C. Cronn, and J.A. Udall. 2011.
Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics 12:370 (PDF).

14.              Rapp RA, C.H. Haigler, L.E. Flagel, R.H. Hovav, J.A. Udall, and J.F. Wendel. 2010.
Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication BMC Biology 8:139 (PDF)

15.               Maughan, P.J., S.M. Yourstone, R.L. Byers, S.M. Smith, and J.A. Udall. 2010.
Single-Nucleotide Polymorphism Genotyping in Mapping Populations via Genomic Reduction and Next-Generation Sequencing: Proof of Concept. The Plant Genome 3:3:166-178. (PDF)

16.               Maughan, P.J., S.M. Yourstone, E.N. Jellen, and J.A. Udall. 2009.
SNP Discovery via Genomic Reduction, Barcoding, and 454-Pyrosequencing in Amaranth. The Plant Genome 2: 3: 260-270. (PDF)

17.               Maughan. P.J., T. Turner, C. Coleman, D. Elzinga, E. Jellen, A.J. Morales, J.A Udall, D. Fairbanks, and A. Bonifacio 2009.
Characterization of Salt Overly Sensitive (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd). Genome 52:647-657 (PDF)

18.               Chaudhary, B., Flagel L., R. Stupar, J.A. Udall, N. Verma, N. Springer, and J.F. Wendel 2009. Reciprocal silencing, transcriptional bias and functional divergence of homoeologs in polyploid cotton Genetics 182:503-517. (PDF)

19.                Rapp, R., J.A. Udall, and J.F. Wendel. 2009. Genomic expression dominance in allopolyploids BMC Biology 2009, 7:18. (PDF)

20.               Flagel L., J.A. Udall, D. Nettleton, and J.F. Wendel 2008.  Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology 6:16. (PDF)

21.              Chaudhary, B., R. Hovav, R. Rapp, N. Verma, J.A. Udall, and J.F. Wendel. 2008. Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evolution and Development 10:567-582. (PDF)

22.               Hovav R, B. Chaudhary, J.A. Udall, L. Flagel, and J.F. Wendel 2008. Parallel Domestication, Convergent Evolution and Duplicated Gene Recruitment in Allopolyploid Cotton. Genetics 179:1725-1733 (PDF)

23.               Hovav, R., J.A. Udall, B. Chaudhary, L. Flagel, E. Hovav, R. Rapp, and J.F. Wendel. 2008. Partitioned expression of duplicated genes during development of a single cell in a polyploid plant. PNAS 105:6191-6195 (PDF)

24.               Hovav, R., J.A. Udall, B. Chaudhary, E. Hovav, L.E. Flagel, G. Hu, and J.F. Wendel. 2008. The evolution of spinable cotton fiber entailed natural selection for prolonged development and a novel metabolism.  PLOS Genetics 4:25 (PDF)

25.               Hovav, R., J.A. Udall, E. Hovav, R. Rapp, L. Flagel, and J. Wendel. 2008. A majority of cotton genes are expressed in single-celled fiber. Planta 227: 319 – 329 (PDF)

26.                 Udall, J.A., L.E. Flagel, F. Cheung, A. Woodward, R. Hovav, R.A. Rapp, J.M. Swanson, J. Lee, A. Gingle, D. Nettleton, C.D. Town, Z.J. Chen, and J.F. Wendel. 2007. Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics 8:81. (PDF)

27.                Amarasinghe, B. R., E. F. Nitschke, Y. Wu, J.A. Udall, E. S. Dennis, G. Constable, and D. J. Llewellyn. 2007. Genomic approaches to the discovery of promoters for sustained expression in cotton (Gossypium hirsutum L.) under field conditions: expression analysis in transgenic cotton and Arabidopsis of a Rubisco small subunit promoter identified using EST sequence analysis and cDNA microarrays. Plant Biotech 5: 437 – 450. (PDF)

28.                Udall, J.A. and J. F. Wendel, 2006. Polyploidy and crop improvement. The Plant Genome, a supplement to Crop Science 1:S1-S14. (PDF)

29.                Udall, J. A., J. M. Swanson, D. Nettleton, R. J. Percifield, and J. F. Wendel. 2006.  A novel approach for characterizing expression levels of genes duplicated by polyploidy.  Genetics 173: 1823-1827. (PDF)

30.                Udall, J.A., J. Swanson, R.A. Rapp, J. Hatfield, K. Haller, Y. Yu, et al. 2006. A large global assembly of cotton ESTs.  Genome Research 16: 441 - 450. (PDF)