Edward S. Buckler | bioRxiv Science

bioRxiv2016

Non-Mendelian inheritance of SNP markers reveals extensive chromosomal translocations in dioecious hops (Humulus lupulus L.)

Genome-wide meiotic recombination structures, sex chromosomes, and candidate genes for sex determination were discovered among Humulus spp. by application of a novel, high-density molecular marker system: ~1.2M single nucleotide polymorphisms (SNPs) were profiled with genotyping-by-sequencing (GBS) among 4512 worldwide accessions, including 4396 cultivars and landraces and 116 wild accessions of hops. Pre-qualified GBS markers were validated by inferences on families, population structures and phylogeny. Candidate genes discovered for several traits, including sex and drought stress-resistance, demonstrate the quality and utility of GBS SNPs for genome-wide association studies (GWAS) and Fst analysis in hops. Most importantly, pseudo-testcross mappings in F1 families delineated non-random linkage of Mendelian and non-Mendelian markers: structures that are indicative of unusual meiotic events which may have driven the evolution and cultivation of hops.

Genomics↗

bioRxiv2015

Independent molecular basis of convergent highland adaptation in maize

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection, and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation, and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

Evolutionary Biology↗