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Genetics, Vol. 165, 367-386, September 2003, Copyright © 2003

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

John E. Bowersa, Colette Abbeyb, Sharon Andersonb, Charlene Changb, Xavier Drayeb, Alison H. Hoppeb, Russell Jessupb, Cornelia Lemkea, Jennifer Lenningtonb, Zhikang Lib, Yann-rong Linb, Sin-chieh Liub, Lijun Luob, Barry S. Marlera, Reiguang Mingb, Sharon E. Mitchellc, Dou Qiangb, Kim Reischmannb, Stefan R. Schulzea, D. Neil Skinnera, Yue-wen Wangb, Stephen Kresovichc, Keith F. Schertzb, and Andrew H. Patersona,b
a Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602,
b Plant Genome Mapping Laboratory, Department of Soil and Crop Science, Texas A&M University, College Station, Texas 77843
c Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850

Corresponding author: Andrew H. Paterson, 111 Riverbend Rd., Rm. 228, University of Georgia, Athens, GA 30602., paterson{at}uga.edu (E-mail)

Communicating editor: J. A. BIRCHLER

We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM (~300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of <=50 cM. Significant variations in DNA marker density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny—in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.




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