Maize HapMap2 identifies extant variation from a genome in flux
Jer-Ming Chiaa b, Chi Songc, Peter J. Bradburyd e f, Denise E. Costichd e f, Natalia de Leóng h i j, John Doebleyk l, Robert J. Elshired f, Brandon S. Gautm n, Laura Gellera b, Jeffrey C. Glaubitzd f, Michael A. Goree o, Kate E Guille p q, James Brendan Hollande r s, Matthew B. Huffordt u, Jinsheng Laiv w x, Meng Lid f, Xin Liuc, Yanli Luy z, William Richard McCombiea b, Rebecca Nelsonaa ab, Jesse Polande ac, Boddupalli Maruthi Prasannaad ae, Tanja Pyhäjärvit u, Tingzhao Rongy z, Rajandeep S. Sekhong h i j, Qi Sund f, Maud Irène Tenaillonm af ag, Feng Tiand f, Jun Wangc, Xun Xuc and 8 others
- aCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- bCold Spring Harbor Laboratory Cold Spring Harbor USA
- cBGI-Shenzhen, Shenzhen, China
- dInstitute for Genomic Diversity, Cornell University, Ithaca, New York, USA
- eUS Department of Agriculture–Agriculture Research Service (USDA-ARS)
- fInstitute for Genomic Diversity, Cornell University, Ithaca, USA
- gDepartment of Agronomy, University of Wisconsin, Madison, Wisconsin, USA
- hUS Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- iDepartment of Agronomy, University of Wisconsin, Madison, USA
- jUS Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, USA
- kDepartment of Genetics, University of Wisconsin, Madison, Wisconsin, USA
- l
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Abstract
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.
TL;DRIt is found that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits and the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. (Semantic Scholar)