Community Resources and Strategies for Association Mapping in Sorghum

Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic and phenotypic diversity of a sorghum (Sorghum bicolor (L.) Moench) panel suitable for association mapping, comprised of 377 acces- sions representing all major cultivated races (tropical lines from diverse geographic and cli- matic regions), and important U.S. breeding lines and their progenitors. Accessions were pheno- typed for eight traits, and levels of population structure and familial relatedness were assessed with 47 simple sequence repeat (SSR) loci. The panel exhibited substantial morphological variation and little genotypic differentiation was observed between the converted tropical and breeding lines. The phenotypic and genotypic data were used to evaluate the performance of several association models in controlling for spurious associations. Our analysis indicated that association models that accounted for both population structure and kinship performed bet- ter than those that did not. In addition, we found that the optimal number of subpopulations used to correct for population structure was trait dependent. Although augmentation of the geno- typic data with additional SSR loci may be nec- essary, the association models, genotypic data, and germplasm panel described here provide a starting point for sorghum researchers to begin association studies of traits and markers or can- didate genes of interest.

[1]  N. Rosenberg.  distruct: a program for the graphical display of population structure , 2003 .

[2]  J. Harlan,et al.  A Simplified Classification of Cultivated Sorghum 1 , 1972 .

[3]  Ncbi.  National Center for Biotechnology Information , 2008 .

[4]  B. Gaut,et al.  Molecular population genetics and the search for adaptive evolution in plants. , 2005, Molecular biology and evolution.

[5]  M. Sorrells,et al.  Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) Cultivars , 2006, Genetics.

[6]  M. Lynch,et al.  Estimation of pairwise relatedness with molecular markers. , 1999, Genetics.

[7]  M. McMullen,et al.  A unified mixed-model method for association mapping that accounts for multiple levels of relatedness , 2006, Nature Genetics.

[8]  John Doebley,et al.  Maize association population: a high-resolution platform for quantitative trait locus dissection. , 2005, The Plant journal : for cell and molecular biology.

[9]  Rajeev K. Varshney,et al.  Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties , 2006, Proceedings of the National Academy of Sciences.

[10]  A. Paterson,et al.  Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population. , 1995, Genetics.

[11]  Edward S. Buckler,et al.  Dwarf8 polymorphisms associate with variation in flowering time , 2001, Nature Genetics.

[12]  Bette A. Loiselle,et al.  Spatial genetic structure of a tropical understory shrub, PSYCHOTRIA OFFICINALIS (RuBIACEAE) , 1995 .

[13]  A. Paterson,et al.  Challenges of Detecting Directional Selection After a Bottleneck: Lessons From Sorghum bicolor , 2006, Genetics.

[14]  C. W. Smith,et al.  Sorghum: origin, history, technology and production. , 2000 .

[15]  A. Paterson,et al.  Equilibrium Processes Cannot Explain High Levels of Short- and Medium-Range Linkage Disequilibrium in the Domesticated Grass Sorghum bicolor , 2005, Genetics.

[16]  T. Rocheford,et al.  Dissection of Maize Kernel Composition and Starch Production by Candidate Gene Association , 2004, The Plant Cell Online.

[17]  A. Paterson,et al.  Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats , 2005, Theoretical and Applied Genetics.

[18]  M. McMullen,et al.  Genetic Design and Statistical Power of Nested Association Mapping in Maize , 2008, Genetics.

[19]  P. Klein,et al.  Comprehensive Molecular Cytogenetic Analysis of Sorghum Genome Architecture: Distribution of Euchromatin, Heterochromatin, Genes and Recombination in Comparison to Rice , 2005, Genetics.

[20]  F. Miller,et al.  Conversion of Alien Sorghums to Early Combine Genotypes1 , 1967 .

[21]  E. Buckler,et al.  Structure of linkage disequilibrium in plants. , 2003, Annual review of plant biology.

[22]  Kermit Ritland,et al.  Estimators for pairwise relatedness and individual inbreeding coefficients , 1996 .

[23]  S. Muthukrishnan,et al.  Agrobacterium tumefaciens-mediated sorghum transformation using a mannose selection system. , 2005, Plant biotechnology journal.

[24]  A. Paterson,et al.  Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  L A Tatum,et al.  The Southern Corn Leaf Blight Epidemic , 1971, Science.

[26]  A. Paterson,et al.  Evidence for a Selective Sweep on Chromosome 1 of Cultivated Sorghum , 2006 .

[27]  P. Klein,et al.  A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP®, RFLP and SSR markers , 2002, Plant Molecular Biology.

[28]  Markus Schuelke,et al.  An economic method for the fluorescent labeling of PCR fragments , 2000, Nature Biotechnology.

[29]  C. Royo,et al.  A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies , 2006, Plant Genetic Resources.

[30]  J. Bennetzen,et al.  A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[31]  B. Gaut,et al.  Genetic diversity and selection in the maize starch pathway , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[32]  A. Paterson,et al.  Comparative Population Genetics of the Panicoid Grasses: Sequence Polymorphism, Linkage Disequilibrium and Selection in a Diverse Sample of Sorghum bicolor , 2004, Genetics.

[33]  K. Gabriel.  A study of heterotic relationships in sorghum , 2006 .

[34]  S. Tanksley,et al.  Seed banks and molecular maps: unlocking genetic potential from the wild. , 1997, Science.

[35]  Stefan R. Schulze,et al.  A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. , 2003, Genetics.

[36]  M. Morgante,et al.  Contrasting Effects of Selection on Sequence Diversity and Linkage Disequilibrium at Two Phytoene Synthase Loci Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012526. , 2003, The Plant Cell Online.

[37]  G. Schwarz.  Estimating the Dimension of a Model , 1978 .

[38]  E. Pahlich,et al.  A rapid DNA isolation procedure for small quantities of fresh leaf tissue , 1980 .

[39]  F. Rousset,et al.  Inbreeding and relatedness coefficients: what do they measure? , 2002, Heredity.

[40]  Kejun Liu,et al.  PowerMarker: an integrated analysis environment for genetic marker analysis , 2005, Bioinform..

[41]  Randall L. Nelson,et al.  Impacts of genetic bottlenecks on soybean genome diversity , 2006, Proceedings of the National Academy of Sciences.

[42]  W. Richard McCombie,et al.  Sorghum Genome Sequencing by Methylation Filtration , 2005, PLoS biology.

[43]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[44]  O. Hardy,et al.  spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels , 2002 .