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The Genomic Signatures of Highland Adaptation in Maize Matthew Hufford Iowa State University Overview of Talk 1) Background on Landrace Adaptations 2) Highland Adaptation through Introgression 3) Parallel Adaptation to the Highlands Overview of Talk 1) Background on Landrace Adaptations 2) Highland Adaptation through Introgression 3) Parallel Adaptation to the Highlands Improved Landraces Teosinte Vigouroux et al. 2008 Mark Miller Highland Adaptation in Maize Landraces Southwestern US Highlands Adaptations to: ✦ Cooler temperature ✦ Lower partial pressure of atmospheric gases ✦ Higher Mexican Central Plateau Guatemalan Highlands Andes UV radiation 6 Highland Phenotypes mexicana ✦ Highland mexicana and lowland parviglumis distinguished by pigment and macrohairs ✦ Both traits are thought to be adaptations to highland conditions ✦ Highland maize landraces share these traits parviglumis Lauter et al. (2004) Genetics Highland Maize Lowland Maize Are Highland Traits Adaptive? Barthakur (1974) Int. J Biomet Overview of Talk 1) Background on Landrace Adaptations 2) Highland Adaptation through Introgression 3) Parallel Adaptation to the Highlands Local Adaptation through Introgression mexicana parviglumis altitude (m) * altitude (m) 0 - 500 0 - 500 500 - 1,000 500 - 1,000 1,000 - 1,500 - 2,000 1,0001,500 - 1,500 2,000 - 2,500 1,5002,500 - 2,000 - 3,000 2,000 - 2,500 2,500 - 3,000 Hufford et al. (2013) PLoS Genetics ± ± 0 125 250 0 500 Kilometers 125 250 500 Kilometers Background: Evidence for Hybridization ✦ mexicana maize ✦ is sympatric to hybrids are frequently found Maize mexicana Photo by Pesach Lubinsky ✦ 20% admixture of highland maize with mexicana Wilkes (1977) Economic Botany van Heerwaarden et al. (2011) PNAS Photo by John Doebley Ixtlan Puruandiro El Porvenir Santa Clara Opopeo Tenango del Aire Nabogame Sample: ✦ ✦ ✦ ✦ ✦ 9 sympatric population pairs 2 allopatric references 120 mexicana 95 maize 40,000 SNPs Hufford et al. (2013) PLoS Genetics Xochimilco San Pedro Amatlan Genome-wide Introgression: HAPMIX ✦ Utilizes a Hidden Markov Model (HMM) ✦ Admixed chromosomes modeled as mosaics of ancestral haplotypes Price et al. (2009) PLoS Genetics Genome-wide Introgression: STRUCTURE ✦ Site-by-site assignment using the linkage model Chromosome 4: maize ✦ Loci created from SNPs separated by < 5kb (~20,000 loci) Chromosome 4: mexicana ✦ Considers all populations Falush et al. (2003) Genetics Hufford et al. (2013) PLoS Genetics Mb Identifying Introgressed Regions Chromosome 4: maize (STRUCTURE) Chromosome 4: maize (HapMix) 0 50 100 150 Mb Characterized by: Low FST Many shared variants Few fixed differences Long shared haplotypes Hufford et al. (2013) PLoS Genetics 200 250 Common Introgression: Chromosome 4 Hufford et al. (2013) PLoS Genetics El Porvenir El Porvenir Opopeo Opopeo Santa Clara Santa Clara Nabogame Nabogame Puruandiro Puruandiro Xochimilco Xochimilco Tenango del Aire Tenango del Aire San Pedro San Pedro Ixtlan Ixtlan Allopatric Allopatric * * * Common Introgression: Chromosome 9 El Porvenir Opopeo Santa Clara Nabogame * Puruandiro Xochimilco Tenango del Aire San Pedro * Ixtlan * Allopatric Hufford et al. (2013) PLoS Genetics * * Pairwise FST: Populations with and without Introgression Introgression No Introgression Hufford et al. (2013) PLoS Genetics Overlap with QTL in Teosinte Lauter et al. (2004) Genetics Barthakur (1974) Int. J. Biometeor. Greenblatt (1968) Maize Genet. Coop. ✦ 9 common mexicana introgression regions into maize ✦ 6 overlap with 5 QTL for pigment and macrohairs in teosinte ✦ mhl1 locus on chromosome 9 fine-mapped Moose et al. (2004) Genetics Phenotypes under Highland Conditions No Introgression Introgression Hufford et al. (2013) PLoS Genetics Signature of Local Adaptation Hufford et al. (2013) PLoS Genetics Overview of Talk 1) Background on Landrace Adaptations 2) Highland Adaptation through Introgression 3) Parallel Adaptation to the Highlands Two Independent Highland Adaptations in Maize 1. Adaptation to the highlands of the Central Plateau in Mexico 1 2 2. Adaptation to the highlands of the Andes in South America Independent Highland Adaptation 24 Samples Each: -Lowland Mexico -Highland Mexico -Lowland SA -Highland SA ~40,000 SNPs, 55K chip ~90,000 SNPs, GBS Takuno et al. (In Prep) Fitting a Demographic Model Without Introgression With Introgression Model IA Model IB Mode tmex NA tD tE tF NA NB NC N1 N2 tD tE tF Nmex NB NC N1 N2 N2P Lowland NC Highland NA tD tE tF N1 tG N2P Mexico Mexico Lowland Highland NC NA mexicana Mexico Lowlan Takuno et al. (In Prep) NC Evidence for Parallel Adaptation? ✦ More adaptation in parallel than expected by chance ✦ Predominantly independent adaptation Takuno et al. (In Prep) Parallel Highland Adaptation in Maize ✦ 6 landraces per region (n = 36) ✦ Illumina HiSeq to 30X Depth ✦ High-density, genomewide analysis of parallel adaptation Acknowledgements Jeffrey Ross-Ibarra Shohei Takuno Tanja Pyhäjärvi Norm Ellstrand Pesach Lubinski Michael Devengenzo Thanks!! Questions? email: [email protected] Next Steps: Developing Near Isogenic Lines Photos by Brian Gervais
