Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize
Zhou Fanga, Tanja Pyhäjärvib c, Allison Weberd e, R. Kelly Dawef, Jeffrey C. Glaubitzg, José de Jesús Sánchez Gonzálezh, Claudia Ross-Ibarrab c, John Doebleyd, Peter Laurent Morrella, Jeffrey Ross‐Ibarrab i
- aDepartment of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108
- bDepartment of Plant Sciences and
- cUniversity of California at Davis
- dDepartment of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- eNorth Carolina State University
- fDepartment of Plant Biology, University of Georgia, Athens, Georgia 30602
- gInstitute for Genome Diversity, Cornell University, Ithaca, New York 14853
- hCentro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico CP45110
- iCenter for Population Biology and the Genome Center, University of California, Davis, California 95616
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Abstract
Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an ∼50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures >700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.