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Full-Text Articles in Life Sciences

Analysis Of Bulked And Redundant Accessions Of Brassica Germplasm Using Assignment Tests Of Microsatellite Markers, Von Mark V. Cruz, John D. Nason, Richard Luhman, Laura F. Marek, Randy C. Shoemaker, E. Charles Brummer, Candice A. C. Gardner Dec 2006

Analysis Of Bulked And Redundant Accessions Of Brassica Germplasm Using Assignment Tests Of Microsatellite Markers, Von Mark V. Cruz, John D. Nason, Richard Luhman, Laura F. Marek, Randy C. Shoemaker, E. Charles Brummer, Candice A. C. Gardner

Ecology, Evolution and Organismal Biology Publications

This study was conducted to determine if Brassica germplasm bulks created and maintained by the USDA-ARS North Central Plant Introduction Station (NCRPIS) were made with genetically indistinguishable component accessions and to examine newly identified putative duplicate accessions to determine if they can be bulked. Using ten microsatellite primer pairs, we genotyped two bulks of B. rapa L. ssp. dichotoma (Roxb.) Hanelt comprising four accessions and three bulks of B. rapa L. ssp. trilocularis (Roxb.) Hanelt comprising fourteen accessions, as well as four pairs of putatively duplicate accessions of B.␣napus L. Assignment tests on ten individual plants per accession were ...


Differential Lineage-Specific Amplification Of Transposable Elements Is Responsible For Genome Size Variation In Gossypium, Jennifer S. Hawkins, Hyeran Kim, John D. Nason, Rod A. Wing, Jonathan F. Wendel Oct 2006

Differential Lineage-Specific Amplification Of Transposable Elements Is Responsible For Genome Size Variation In Gossypium, Jennifer S. Hawkins, Hyeran Kim, John D. Nason, Rod A. Wing, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

The DNA content of eukaryotic nuclei (C-value) varies ∼200,000-fold, but there is only a ∼20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the repetitive fraction, although little is known about the evolutionary dynamics of the specific components that lead to genome size variation. To understand the modes and mechanisms that underlie variation in genome composition, we generated sequence data from whole genome shotgun (WGS) libraries for three representative diploid (n = 13) members of Gossypium that vary in genome size from 880 to 2460 Mb (1C) and from a phylogenetic outgroup, Gossypioides kirkii ...


A Global Assembly Of Cotton Ests, Joshua A. Udall, Jordan M. Swanson, Karl Haller, Ryan A. Rapp, Michael Edward Sparks, Jamie Hatfield, Yeisoo Yu, Yingru Wu, Catriona Dowd, Aladdin B. Arpat, Brad A. Sickler, Thea A. Wilkins, Yin Ying Guo, Xiao Ya Chen, Jodi Scheffler, Earl Taliercio, Ricky Turley, Helen Mcfadden, Paxton Payton, Natalya Klueva, Randell Allen, Deshui Zhang, Candace Haigler, Curtis Wilkerson, Jinfeng Suo, Stefan R. Schulze, Margaret L. Pierce, Margaret Essenberg, Hyeran Kim, Danny J. Llewellyn, Elizabeth S. Dennis, Rod Wing, Andrew H. Paterson, Cari Soderlund, Jonathan F. Wendel Feb 2006

A Global Assembly Of Cotton Ests, Joshua A. Udall, Jordan M. Swanson, Karl Haller, Ryan A. Rapp, Michael Edward Sparks, Jamie Hatfield, Yeisoo Yu, Yingru Wu, Catriona Dowd, Aladdin B. Arpat, Brad A. Sickler, Thea A. Wilkins, Yin Ying Guo, Xiao Ya Chen, Jodi Scheffler, Earl Taliercio, Ricky Turley, Helen Mcfadden, Paxton Payton, Natalya Klueva, Randell Allen, Deshui Zhang, Candace Haigler, Curtis Wilkerson, Jinfeng Suo, Stefan R. Schulze, Margaret L. Pierce, Margaret Essenberg, Hyeran Kim, Danny J. Llewellyn, Elizabeth S. Dennis, Rod Wing, Andrew H. Paterson, Cari Soderlund, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; AT and DT genomes) as well as its two diploid progenitors,Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to ...


Mitigating Scoring Errors In Microsatellite Data From Wild Populations, Jennifer Dewoody, John D. Nason, Valerie D. Hipkins Jan 2006

Mitigating Scoring Errors In Microsatellite Data From Wild Populations, Jennifer Dewoody, John D. Nason, Valerie D. Hipkins

Ecology, Evolution and Organismal Biology Publications

Microsatellite data are widely used to test ecological and evolutionary hypotheses in wild populations. In this paper, we consider three typical sources of scoring errors capable of biasing biological conclusions: stuttering, large-allele dropout and null alleles. We describe methods to detect errors and propose conventions to mitigate scoring errors and report error rates in studies of wild populations. Finally, we discuss potential bias in ecological or evolutionary conclusions based on data sets containing these scoring errors.