Signatures of local adaptation in lowland and highland teosintes from whole‐genome sequencing of pooled samples

• DOI: 10.1111/mec.14082
• Publication Date: 2017-03-03T08:36:42Z
• Authors: M.‐A. Fustier; J.‐T. Brandenburg; S. Boitard; J. Lapeyronnie; L. E. Eguiarte; Y. Vigouroux; D. Manicacci; M. I. Tenaillon
• Keywords: Local adaptation; Linkage Disequilibrium; Candidate gene; Nucleotide diversity; Selective sweep

Spatially varying selection triggers differential adaptation of local populations. Here, we mined the determinants at genomewide scale in two closest maize wild relatives, teosintes Zea mays ssp parviglumis and ssp. mexicana. We sequenced 120 individuals from six populations: lowland, intermediate highland populations sampled along altitudinal gradients. detected 8 479 581 single nucleotide polymorphisms (SNPs) covered with an average sequencing depth per site population ranging 17.0× to 32.2×. Population diversity varied 0.10 0.15, linkage disequilibrium decayed very rapidly. combined differentiation-based methods, correlation allele frequencies environmental variables detect outlier SNPs. Outlier SNPs displayed significant clustering. From clusters, identified 47 candidate regions. further modified a haplotype-based method incorporate genotype uncertainties haplotype calling, applied it retrieved evidence for level 53% our regions, 70% cases same was selected lowland or recovered region located within previously characterized inversion on chromosome 1. found soft sweep locus involved leaf macrohair variation. Finally, results revealed frequent colocalization between regions loci variation traits associated plant-soil interactions such as root morphology, aluminium low phosphorus tolerance. Soil therefore appears be major driver teosintes.