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Letter

Gene Loss and Movement in the Maize Genome

Jinsheng Lai¹, Jianxin Ma^2,3, Zuzana Swigoová¹, Wusirika Ramakrishna^2,4, Eric Linton^1,5, Victor Llaca^1,6, Bahattin Tanyolac^1,7, Yong-Jin Park^2,8, O-Young Jeong^2,9, Jeffrey L. Bennetzen^2,3 and Joachim Messing^1,10

¹ Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020, USA ² Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA

Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compared corresponding regions from sorghum and rice, two important crops that have largely collinear maps with maize. The split of sorghum and maize progenitors was recently estimated to be 11.9 Mya, whereas rice diverged from the common ancestor of maize and sorghum 50 Mya. A data set of roughly 4 Mb yielded 206 predicted genes from the three species, excluding any transposon-related genes, but including eight gene remnants. On average, 14% of the genes within the aligned regions are noncollinear between any two species. However, scoring each maize region separately, the set of noncollinear genes between all four regions jumps to 68%. This is largely because at least 50% of the duplicated genes from the two progenitors of maize have been lost over a very short period of time, possibly as short as 5 million years. Using the nearly completed rice sequence, we found noncollinear genes in other chromosomal positions, frequently in more than one. This demonstrates that many genes in these species have moved to new chromosomal locations in the last 50 million years or less, most as single gene events that did not dramatically alter gene structure.

⁴ Present address: Department of Biological Sciences, 740 DOW, Michigan Tech University, Houghton, MI 49931, USA

⁵ Present address: Plant Biology Labs, Michigan State University, East Lansing, MI 48824, USA

⁶ Present address: Analytical and Genomic Technologies, Crop Genetics R&D, DuPont Agriculture & Nutrition, Wilmington, DE 19880-0353, USA

⁷ Present address: Department of Bioengineering, Ege University, Izmir, 35100 Turkey

⁸ Present address: National Institute of Agricultural Biotechnology, Suwon 441-707, Republic of Korea

⁹ Present address: National Institute of Crop Science, Suwon 441-857, Republic of Korea.

¹⁰ Corresponding author.
E-MAIL messing{at}waksman.rutgers.edu; FAX (732) 445-0072.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2701104.

[The sequence data from this study have been submitted to GenBank under accession nos. AY555142, AY555143, AY560576-AY560578, AF466202, AF466203, AY542310, AY530950-AY530952, AF464738, AY325816, AF466646, AY542797, AY542798, AF466200, AF466201, AY542311, AF466199, and AF466204.]

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