The College of Life Sciences

Udall, Joshua

Plant & Wildlife Sciences

Email: 1kbvebmmAczv/fev  (Email Form)

Website: http://udall-lab.byu.edu

5133  LSB
Provo, UT 84602
(801) 422-9307

Associate Professor

Curriculum Vitae

 Biography
Grew up in Provo Canyon and Orem
Orem High Class of '88
BYU Class of '95
Master's at University of Idaho ('97), Wheat Breeding
Ph.D. University of Wisconsin ('03), Plant Breeding and Genetics
Post-doc ('06) Iowa State University, Cotton Genome Evolution
 Teaching Interests
Bioinformatics and Genomics
 Research Interests
Cotton Genomics and Genome Evolution
 Memberships
  • American Society of Plant Biologists, 2006-Present
  • Society for the Study of Evolution, 2008-2009
 Courses Taught

Winter 2014
  • BIO 799R: Dissertation Section 012
  • PWS 288: Mentored Lab Techniques Section 001
  • PWS 494R: Mentored Learning Experience Section 017
  • PWS 598R: Adv Topics in PWS Section 007
  • PWS 670: Analysis of Complex Genomes Section 001
  • PWS 699R: Master's Thesis Section 017
Fall 2013
  • BIO 468: Genomics Section 001
  • BIO 799R: Dissertation Section 001
  • MMBIO 468: Genomics Section 001
  • PWS 288: Mentored Lab Techniques Section 001
  • PWS 468: Genomics Section 001
  • PWS 494R: Mentored Learning Experience Section 018
Summer 2013
  • BIO 799R: Dissertation Section 012
Spring 2013
  • PWS 288: Mentored Lab Techniques Section 001
  • PWS 494R: Mentored Learning Experience Section 006
  • PWS 598R: Adv Topics in PWS Section 001

Selected Publications
Journal Articles

Raney JA, Reynolds DJ, Elzinga DB, Page J, Udall JA, Jellen EN, Bonfacio A, Fairbanks D, Maughan PJ. Transcriptome Analysis of Drought Induced Stress in Chenopodium quinoa. American Journal of Plant Sciences. 2014 Feb;5(3):338-357. <website>

Rambani A, Page JT, Udall JA. Polyploidy and the petal transcriptome of Gossypium. BMC Plant Biology. 2014 Jan;14:3. <website>

Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Campbell BT. RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water deficit stress. PLOS One. 2013 Dec;8(12):e82634. <website>

Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 2013 Oct.

Page JT, Huynh MD, Liechty ZS, Grupp K, Stelly D, Hulse AM, Ashrafi H, Van Deynze A, Wendel JF, Udall JA. Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing. 2013 Oct;3(10):1809-1818. <website>

Page JT, Gingle AR, Udall JA. PolyCat: A Resource for Genome Categorization of Sequencing Reads from Allopolyploid Organisms. G3: Genes, Genomes, and Genomics. 2013 Feb.

Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Dianchuan Jin DL, Showmaker KC, Shu S, Byers R, Udall JA, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 2012 Dec;492:423-427. <website>

Richardson BA, Page JT, Bajgain P, Sanderson SC, Udall JA. Deep Sequencing of Amplicons Reveals Widespread Hybridiazation and Polyploidization in Big Sagebrush. American Journal of Botany. 2012 Oct;99(12):1962-1975. <website>

Maughan PJ, Smith SM, Rojas-Beltrán JA, Elzinga D, Raney JA, Jellen EN, Bonifacio A, Udall JA, Fairbanks D. Single nucleotide polymorphisms identification, characterization and linkage mapping in Chenopodium quinoa. The Plant Genome. 2012 Sep;5(3):1-7. <website>

Salmon A, Udall JA, Jeddeloh J, Wendel JF. Targeted capture of homoeologous coding and non-coding sequence in polyploid cotton. G3: Genes, Genomes, and Genetics. 2012 Aug;2:921-930. <website>

Parra-Gonzalez LB, Aravena-Abarzúa GA, Navarro-Navarro CS, Udall JA, Maughan PJ, Peterson LM, Salvo-Garrido HE, Maureira-Butler IJ. Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies. BMC Genomics. 2012 Jul;13:425-440. <website>

Flagel LE, Wendel JF, Udall JA. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics. 2012 Jul;13:302. <website>

Bushakra J, Stephens M, Atmadjaja A, Lewers K, Symonds V, Udall JA, Chagne D, Buck E, Gardiner S. 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. 2012 Apr;125(2):311-327. <website>

Cronn R, Knaus B, Liston A, Maughan PJ, Parks M, Syring J, Udall JA. Targeted enrichment strategies for Next-Generation plant biology. American Journal of Botany. 2012 Feb;99:1-22. <website>

Byers RL, Harker DB, Yourstone SM, Maughan PJ, Udall JA. Development and Mapping of SNP Assays in Allotetraploid Cotton. Theoretical and Applied Genetics. 2012 Feb;124:1201-1214. <website>

Bybee SM, Bracken-Grissom HD, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics. Genome Biology and Evolution. 2011 Nov;3:1312-1323.

Morales AJ, Bajgain P, Garver Z, Maughan PJ, Udall JA. Physiological responses of Chenopodium quinoa to salt stress. International Journal of Plant Physiology and Biochemistry. 2011 Nov;3:219-232. <website>

Bajgian P, Richardson BA, Price JC, Cronn RC, Udall JA. Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics. 2011 Sep;12:370-385. <website>

Udall JA, Maughan PJ, Yourstone SM, Byers RL, Smith SM. Single-Nucleotide Polymorphism Genotyping in Mapping Populations via Genomic Reduction and Next-Generation Sequencing: Proof of Concept. The Plant Genome. 2010 Oct.

Rapp RA, Haigler CH, Hovav RH, Udall JA, Wendel JF. Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biology. 2010 Jul;8:139. <website>

Maughan PJ, Yourstone S, Jellen EN, Udall JA. SNP Discovery via Genomic Reduction, Barcoding, and 454-Pyrosequencing in Amaranth. The Plant Genome. 2009 Nov;2:260-270. <website>

Maughan PJ, Turner TB, Coleman CE, Elzinga DB, Jellen EN, Morales JA, Udall JA, Fairbanks D, Bonifacio A. Characterization of salt overly sensitive (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd). Genome. 2009 Jul;52:647-657. <website>

Rapp RA, Udall JA, Wendel JF. Genomic expression dominance in allopolyploids. BMC Biology. 2009 May;7:18. <website>

Chaudhary B, Hovav R, Rapp R, Verma N, Udall JA, Wendel JF. Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evolution and Development. 2008 Oct;10:567-582. <website>

Flagel L, Udall JA, Nettleton D, Wendel J. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology. 2008 Apr;6:16. <website>

Hovav R, Udall JA, Chaudhary B, Rapp R, Flagel L, Wendel JF. Paritioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. PNAS. 2008 Jan;Accepted.

Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L, Hu G, Wendel JF. The evolution of spinable cotton fiber entailed natural selection for prolonged development and a novel metabolism. PLOS Genetics. 2008 Jan. <website>

Hovav R, Udall JA, Hovav E, Rapp R, Flagel L, Wendel JF. A majority of cotton genes are expressed in single-celled fiber. Planta. 2007 Sep;227:319-329. <website>

Butler IJ, Udall JA, Osborn TC. Analyses of a multi-parent population derived from two diverse alfalfa germplasms: Testcross evaluations and phenotype-DNA associations. Theoretical and Applied Genetics. 2007 Jul;Online First. <website>

Udall JA, Flagel LE, Cheung F, Woodward AW, Hovav R, Rapp R, Swanson JM, Lee JJ, Gingle AR, Nettleton D, et al. Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics. 2007 Mar;8:81. <website>

Udall JA, Wendel JF. Polyploidy and Crop Improvement. The Plant Genome. 2006 Nov;1:1-12. <website>

Udall JA, Swanson JM, Nettleton D, Percifield RJ, Wendel JF. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics. 2006 Jul;173:1823-1827.

Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, et al. A global assembly of cotton ESTs. Genome Research. 2006 Mar;16:441-450. <website>

Conference Proceedings

Soliai MM, Maughan PJ, Espinoza-Herrera PA, Fuentes F, King B, Petty BO, Rainey J, Adhikary D, Leggett A, Coleman CE, et al. Genome relationships in New World Chenopodium species: II. Evidence from DNA sequencing. 2009. <website>

Presentations

Huyhn M, Page JT, Udall JA. Chloroplast Studies in Sagebrush. International Plant and Animal Genome Conference. San Diego, CA, USA. 2014 Jan.

Kuraparthy V, Tyagi P, Gore MA, Campbell BT, Udall JA, Bowman DT. Genetic Diversity and Population Structure in the US Upland Cotton (Gossypium hirsutum L.). International Plant and Animal Genome Conference. San Diego, CA, USA. 2014 Jan.

Page JT, Huynh MD, Liechty ZS, Udall JA. Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Resequencing. International Plant and Animal Genome Conference. San Diego, CA, USA. 2014 Jan.

Todd Campbell B, Bowman MJ, Wonkeun Park PB, Scheffler BE, Udall JA, Jones DC. Using RNA-seq transcriptome profiling in support of field based strategies to improve cotton productivity under water deficit stress. International Plant and Animal Genome Conference. San Diego, CA. 2014 Jan.

Page JT, Huynh MD, Clemons K, Liechty ZS, Udall JA. Whole Genome Resequencing of Cotton Tetraploids (Gossypium barbadense). International Plant and Animal Genome Conference. San Diego, CA, USA. 2014 Jan.

Houston DD, Davis N, Page J, Ridge P, Evans RP, Maughan PJ, Udall JA, Shiozawa DK. Whole transcriptome sequencing facilitates nuclear marker development in salmonid fishes. Evolution 2013. Snowbird, Utah. 2013 Jun.

Richardson BA, Huynh M, Udall JA. Correspondence between phylogenetic relationships and taxonomic characters in big sagebrush: implications for the seed certification. National Native Seed Conference. Santa Fe, New Mexico. 2013 Apr.

Hulse AM, Hoegenauer K, Wang F, Ashrafi H, Van Deynze A, Zhang H, Saski C, Scheffler B, Udall JA, Yu JZ. Localization of Allotetraploid Gossypium SNPs Using Physical Mapping Resources. 2013 Beltwide Cotton Conference. 2013 Jan.

Bowman MJ, Park W, Udall JA, Page JT, Bauer PJ, Campbell BT. Tissue Specific Transcriptome Changes Occurring During Water Deficit Stress in Tetraploid Cotton. Annual Beltwide Cotton Conference. Memphis, TN. 2013 Jan.

Page JT, Huynh MD, Van Deynze A, Udall JA. Genome Resquencing of Select Cotton Diploid Accessions. International Plant and Animal Genome Conference. San Diego, CA. 2013 Jan.

Hulse AM, Hoegenauer KA, Ashrafi H, Wang F, Stelly D, Van Deynze A, Hinze L, Yu JZ, Fang D, Pepper AE, et al. Genome-wide SNP Development and Validation for Intraspecific SNPs in Upland Cotton. International Plant and Animal Genome Conference. San Diego, CA. 2013 Jan.

Wendel JF, Yoo M, Udall JA, Hu G, Gong L, Grupp K, Gore MA. Jeans, genes, and the independent domestications of cotton. International Plant and Animal Genome Conference. San Diego, CA. 2013 Jan.

Udall JA, Rambani A, Page JT, Grupp K, Wendel JF. The Correlation Of DNA Methylation and Homoeologous Gene Expression In Cotton Petals. International Plant and Animal Genome Conference. San Diego, CA. 2013 Jan.

Szadkowski E, Page JT, Udall JA, Jeddeloh JA, Grover CE, Grupp KK, Salmon A, Wendel JF. Unequal Accumulation Of Nucleotide Diversity In The Two Co-Resident Genomes Of Allopolyploid Cotton. International Plant and Animal Genome Conference. San Diego, CA. 2013 Jan.

Udall JA, Page JT, Rambani A, Grupp K. Transcriptome and Methylation Analysis of Gossypium Petal Tissue. Department Seminar. Maricopa, AZ. 2012 Oct.

Ashrafi H, Hulse AM, Hoegenauer K, Wang F, Schmutz J, Udall JA, Stelly DM, Deynze AV. Comparison and evaluation of cotton SNPs developed by transcriptome, genome reduction on restriction site conservation and RAD-based sequencing. International Cotton Genomics Initiative. Cary, NC. 2012 Oct.

Gingle AR, Paterson AH, Udall JA, Wendel JF. Data search and visualization tools at the Comparative Evolutionary Genomics of Cotton Web resource. International Cotton Genomics Initiative. Cary, NC. 2012 Oct.

Hulse AM, Hoegenauer K, Wang F, Stelly DM, Ashrafi H, Van Deynze A, Udall JA, Zhang H, Saski C, Paterson AH, et al. Localization of Allotetraploid Gossypium SNPs Using Physical Mapping Resources. International Cotton Genomics Initiative. Cary, NC. 2012 Oct.

Nah G, Guan X, Udall JA, Stelly DM, Chen ZJ. Transcriptome analysis of extant cotton progenitors and identification of genome-specific-single nucleotide polymorphism (GNP) for allelic discrimination in allotetraploid cotton. International Cotton Genomics Initiative. Cary, NC. 2012 Oct.

Park W, Udall JA, Page JT, Bauer P, Campbell BT. Transcriptomic approaches for the identification of drought-responsive genes in cotton. International Cotton Genomics Initiative. Cary, NC. 2012 Oct.

Udall JA, Rambani A, Page JT, Grupp K, Wendel JF. The Correlation of DNA Methylation and Homeologous Gene Expression in Cotton Petals. Plant Biology 2012. Austin, TX. 2012 Jul.

Udall JA, Page J, Grupp K, Jeddeloh J, Wendel JF. Diversity of duplicated gene pairs in allotetraploid Gossypium hirsutum. 2nd Annual Progress and Applications of Next-Generation Sequencing Workshop. Saskatoon, CA. 2012 May.

Smith S, Jellen EN, Udall JA, Munir H, Maughan PJ. Discovery, Characterization, and Linkage Mapping of Single Nucleotide Polymorphism in Chenopodium quinoa Willd. Utah Plant Genetics Conference. Aspen Grove, Utah. 2012 Feb.

Udall JA, Salmon A, Grupp K, Page J, Jeddeloh J, Wendel JF. Diversity of 534 pairs of duplicated genes in allotetraploid G. hirsutum. Utah Plant Genetics Conference. Aspen Grove. 2012 Feb.

Raney J, Udall JA, Raney JC, Maughan PJ. Drought Tolerance in Chenopodium quinoa. Utah Plant Genetics Conference. Aspen Grove, Utah. 2012 Feb.

Rambani A, Page JT, Grupp K, Wendel JF, Udall JA. Homoeologous gene expression and DNA methylation in cotton petals. International Plant and Animal Genome Conference. San Diego, CA. 2012 Jan.

Gingle A, Udall JA, Wendel J, Paterson A. Data search and visualization tools at the Comparative Evolutionary Genomics of Cotton Web resource. Plant and Animal Genome Conference. San Diego, CA. 2012 Jan.

Hulse AM, Wang F, Hoegenauer KA, Ashrafi H, Van Deynze A, Udall JA, Yu JZ, Chen ZJ, Jones DC. Genome-wide SNP Development and Validation for Allotetraploid Gossypium. Plant and Animal Genome Conference. San Diego, CA. 2012 Jan.

Cronn R, Hayden K, Klopfenstein N, Knaus BJ, Mock KE, Hardeep Rai BR, Ross-Davis A, Wright J, Udall JA. Western Forest Transcriptome Survey: Applying genomic discoveries towards understanding genome responses to climate change. Plant and Animal Genome Conference. San Diego, CA. 2012 Jan.

Jimenez F, Maughan PJ, Alvarez A, Pratt DB, Kietlinski K, Smith S, Udall JA, Patton K, Jellen EN. Application of Markers Developed from Genome Reduction-454 Sequencing in Orphaned Andean Crops. Plant and Animal Genome XIX Conference. San Diego, CA. 2012 Jan.

Smith S, Jellen EN, Udall JA, Munir H, Maughan PJ. Discovery, Characterization, and Linkage Mapping of Single Nucleotide Polymorphism in Chenopodium quinoa Willd. Plant and Animal Genome XIX Conference. San Diego, CA. 2012 Jan.

Raney J, Udall JA, Raney JC, Maughan PJ. Drought Tolerance in Chenopodium quinoa. Plant and Animal Genome XIX Conference. San Diego, CA. 2012 Jan.

Udall JA, Aravena G, Parra LB, Aravena JP, Ribera DB, Espinosa MH, Amiard V, Maughan PJ, Raney J, Maureira IJ. Associative mapping of phytic acid and alpha-galactoside content, two key plant anti-nutritionals, in yellow lupin (L. luteus). 13th International Lupin Conference. Warsaw, Poland. 2011 Jul.

Cronn R, Knaus B, Liston A, Maughan PJ, Parks M, Syring J, Udall JA. Advances in Plant Systematics and Population Genomics: Applications of Next Generation Techniques. Botany 2011. St. Louis, MO. 2011 Jul.

Udall JA, Bajgain P, Richardson B, Page J. Natural Sequence Diversity of Artemesia tridentata in the Western United States. Botany 2011. St. Louis, MO. 2011 Jul.

Udall JA, Baigain P, Richardson B, Price JC. Transcriptome characterization and polymorphism detection between two Artemisia tridentata subspecies via 454-pyrosequencing. Great Basin Native Plant Selection and Increase Project. Salt Lake City. 2011 Mar.

Udall JA, Salmon A, Grupp K, Jeddeloh JA, Wendel JF. Diversity Of 534 Pairs Of Duplicated Genes In Allotetraploid Gossypium hirsutum. Plant and Animal Genome Conference. San Diego, CA. 2011 Jan.

Byers RL, Harker DB, Maughan PJ, Udall JA. Genetic Mapping Of SNPs In Allotetraploid Cotton. Plant and Animal Genome Conference. San Diego, CA. 2011 Jan.

Gingle A, Swanson J, Udall JA. New Transcriptome Data And Tools At The Comparative Evolutionary Genomics Of Cotton Web Resource. Plant and Animal Genome Conference. San Diego, CA. 2011 Jan.

Bajgain P, Price JC, Richardson BA, Udall JA. Transcriptome Characterization And Polymorphism Detection Between Two Artemisia tridentata subspecies via 454-Pyrosequencing. Plant and Animal Genome Conference. San Diego, CA. 2011 Jan.

Price JC, Ward JA, Clement MJ, Weber CA, Lewers KS, Hagan W, Haynes B, Swanson JD, Udall JA. Whole genome sequencing of the highly heterozygous diploid red raspberry, Rubus idaeus cv. Heritage. Plant and Animal Genome Conference. San Diego, CA. 2011 Jan.

Byers RL, Harker DB, Maughan PJ, Udall JA. Genetic Mapping of SNPS in Allotetraploid Cotton. Plant and Animal Genome XIX Conference. San Diego, CA. 2011 Jan.

Jimenez FR, Maughan PJ, Meza G, Probst OS, Ames NC, Patton KC, Udall JA, Jellen EN. SNP Discovery And Validation Using Genome Reduction And Next-Generation Sequencing In The Orphaned Andean Tuber Crop Papalisa, Ullucus tuberosus Caldas (2n=2x=24). Plant and Animal Genome XIX Conference. San Diego, CA. 2011 Jan.

Maughan PJ, Yourstone SM, Byers RL, Smith S, Udall JA. SNP genotyping in mapping populations via genomic reduction and next-generation sequencing: Proof-of-concept. Plant and Animal Genome XIX Conference. San Diego, CA. 2011 Jan.

Udall JA, Wendel JF, Flagel LE. A Cotton Reference Transcriptome. International Cotton Genomics Initiative. Canberra, Australia. 2010 Sep.

Udall JA, Saavedra HU, Trujillo MO, Navarro CN, Gonzalez LP, Abarzua GA, Straub SC, Garrido HS, Butler IM. Analysis Of Genomic Sequences From Lupinus luteus L. Plant and Animal Genome Conference. San Diego, CA. 2010 Jan.

Udall JA, Salmon A, Flagel L, Wendel JF. Detection Of Homoeologous Recombinants From Cotton EST Assemblies. Plant and Animal Genome Conference. San Diego, CA. 2010 Jan.

Udall JA, Flagel LE, Grupp K, Wendel JF, Standage DS. Measuring Gene Expression in Tetraploid Cotton Through Illumina Sequencing. Plant and Animal Genome Conference. San Diego, CA. 2010 Jan.

Udall JA, Maughan PJ, Jellen EN, Yourstone SM. SNP Discovery via Genomic Reduction, Barcoding And 454-Pyrosequencing In Amaranth. Plant and Animal Genome Conference. San Diego, CA. 2010 Jan.

Byers R, Yourstone S, Maughan PJ, Udall JA. Identification of molecular markers in allotetraploid cotton. Plant and Animal Genome XVII Conference. San Diego, CA. 2010 Jan.

Maughan PJ, Yourstone S, Lade E, Jellen EN, Udall JA. SNP Discovery Via Genomic Reduction, Barcoding and 454-Pyrosequencing in Amaranth. Plant and Animal Genome XVII Conference. San Diego, California. 2010 Jan.

Udall JA, Byers R, Wendel J. Evolutionary Genomics of Cotton: Gene and Marker Discovery. Department of Plant Breeding and Department of Cotton. Coimbatore, India. 2009 Dec.