J. C. Nelson lab

J. C. Nelson lab, KSU Plant Pathology

Long-range aim

The main long-range aim of the group is practical genetic improvement of crops by DNA-marker-assisted selection for alleles influencing quantitative traits. The work we do toward that end is development of bioinformatics resources, in the form of software, databases, and methods.

People

Postdocs

Lecong Zhou
Shichen Wang

Current projects

Linkage-mapping methods (Nelson)
RiceCAP data analysis (Nelson) USDA
Sorghum Translational Genomics Program: mining genomic diversity for sorghum improvement (Nelson, Zhou, Wang)

Recent publications

Nelson JC. 2005. Methods and software for genetic mapping. In Meksem K, Kahl G, eds.: Handbook of Plant Genome Mapping: Genetic and Physical Mapping. Wiley-VCH. ISBN: 3-527-31116-5
Zwart RS, Thompson JP, Sheedy JG, Nelson JC. 2006. Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population. Austr J Agric Res 57: 525-530.
Narasimhamoorthy B, Gill BS, Fritz AK, Nelson JC, Brown-Guedira G. 2006. Advanced backcross QTL analysis of a hard winter wheat X synthetic wheat population. Theor Appl Genet 112: 787-796.
See DR, Brooks S, Nelson JC, Brown-Guedira G, Friebe B, Gill BS. 2006. Gene evolution at the ends of wheat chromosomes. Proc Natl Acad Sci USA 103: 4162-4167.
Nelson JC, Andreescu C, Breseghello F, Finney PL, Gualberto DG, Bergman CG, Peña RJ, Perretant MR, Leroy P, Qualset CO, Sorrells ME. 2006. Quantitative trait locus analysis of wheat quality traits. Euphytica 149: 145-159.
Venu RC, Jia Y, Gowda M, Jia MH, Jantasuriyarat C, Stahlberg E, Li H, Rhineheart A, Boddhireddy P, Singh P, Rutger N, Kudrna D, Wing R, Nelson JC, Wang G-L. 2007. RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Mol Genet Genomics 278: 421-431.
Sukhwinder-Singh, Sharma I, Sehgal SK, Bains NS, Guo Z, Nelson JC, Bowden RL. 2007. Molecular mapping of QTLs for Karnal bunt resistance in two recombinant inbred populations of bread wheat. Theor Appl Genet 116: 147-154.
Joehanes R, Nelson JC. 2008. QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics 24: 2788-2789.
Guo Z, Nelson JC. 2008. Multiple-trait quantitative trait locus mapping with incomplete phenotypic data. BMC Genetics 9: 82.
Boddhireddy P, Jannink J-L, Nelson JC. 2009. Selective advance for accelerated development of recombinant inbred QTL-mapping populations. Crop Sci 49: 1284-1294.
Huang L, Brooks S, Li W, Fellers J, Nelson JC, Gill BS. 2009. Evolution of new disease specificity at a simple resistance locus in a crop–weed complex: reconstitution of the Lr21 gene in wheat. Genetics 182: 595-602.

Software

QGene 4.0, for QTL analysis and data exploration.
tAUDPC, for computing and viewing truncated AUDPC plots. Sample tAUDPC data file
QRMap, for drawing unrolled restriction maps of circular genomes. Sample QRMap data file
MatLink, MATLAB program for computing linkage in exotic line-cross mating designs
PrimerDB, a database and WWW interface for managing PCR primers, especially for mapped wheat ESTs. Details

I have extended CarthaGène, an open-source multipoint linkage-mapping software package developed by Thomas Schiex and colleagues, to handle mating designs consisting of arbitrary series of backcrossing, selfing, and random-intercrossing steps. A 32-bit Linux but not yet a Windows version is available as v1.1 on the CarthaGène site. We can supply a 64-bit version.

Teaching

Bioinformatics Applications
Introduction to Perl for Biologists

Positions available

None open at present.