Biology subjects

Schmid, K. J.

Publications and source records attributed to Schmid, K. J..

3 recordsLinked to original sources

bioRxiv2018

Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley

Temperature compensation, expressed as the ability to maintain clock characteristics (mainly period) in face of temperature changes, is considered a key feature of circadian clock systems. In this study, we explore the genetic basis for circadian clock plasticity under high temperatures by utilizing a new doubled haploid (DH) population derived from two reciprocal Hordeum vulgare sps. spontaneum hybrids genotypes (crosses between B1K-50-04 and B1K-09-07). Genotyping by sequencing of DH lines indicated a rich recombination landscape, with minor fixation (less than 8%), for one of the parental alleles, yet with prevalent and varied segregation distortion across seven barley chromosomes. Phenotyping was conducted with a high-throughput platform under optimal and high temperature environments. Genetic analysis, which included QxE and binary-threshold models, identified a significant influence of the maternal organelle genome (the plasmotype), as well as several nuclear quantitative trait loci (QTL), on clock phenotypes (free-running period and amplitude). Moreover, it showed the differential contribution of cytoplasmic genome clock rhythm buffering against high temperature. Resequencing of the parental chloroplast indicated the presence of several candidate genes underlying these significant effects. This first reported plasmotype-driven clock plasticity paves the way for identifying an hitherto unknown impact of nuclear and plasmotype variations on clock robustness and on plant adaptation to changing environments.\n\nHighlightCircadian clock robustness to high temperature is controlled by nuclear and plasmotype quantitative trait loci in a wild barley (Hordeum vulgare ssp. spontaneum) reciprocal doubled haploid population.

genetics↗

bioRxiv2017

Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

Cauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material and our results suggest that it may be useful to incorporate routine genotyping into accession management and seed regeneration to monitor the diversity present in ex situ collections and to reduce the loss of genetic diversity during seed regeneration.

plant biology↗

bioRxiv2016

Phylogenetic relationships and genome size evolution within the genus Amaranthus indicate the ancestors of an ancient crop

The genus Amaranthus consists of 50 to 70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joing tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.

evolutionary biology↗