The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley.
Understanding the genetic architecture of complex traits is a major objective in biology. The standard approach for doing so is genome-wide association studies (GWAS), which aim to identify genetic polymorphisms responsible for variation in traits of interest. In human genetics, consistency across studies is commonly used as an indicator of reliability. However, if traits are involved in adaptation to the local environment, we do not necessarily expect reproducibility. On the contrary, results may depend on where you sample, and sampling across a wide range of environments may decrease the power of GWAS because of increased genetic heterogeneity. In this study, we examine how sampling affects GWAS in the model plant species Arabidopsis thaliana. We show that traits like flowering time are indeed influenced by distinct genetic effects in local populations. Furthermore, using gene expression as a molecular phenotype, we show that some genes are globally affected by shared variants, while others are affected by variants specific to subpopulations. Remarkably, the former are essentially all cis-regulated, whereas the latter are predominately affected by trans-acting variants. Our result illustrate that conclusions about genetic architecture can be extremely sensitive to sampling and population structure.
Silphium spp. have garnered interest in Europe as a bioenergy crop and in North America as a perennial oilseed crop. However, very little has been done at this early stage of domestication to characterize wild collections for many key characteristics, including important oilseed traits. The objective of this work was to develop a basic understanding of how biogeography and associated population genetic forces have shaped seed phenotypes in plant collections across the native range of Silphium integrifolium Michx. (Asteraceae: Heliantheae), the primary domestication candidate for oilseed use. A collection of 53 accessions was grown in a common environment in Salina, KS, which is a location well within the native range of the species in central North America. Plants from each collection site were randomly mated by hand to produce seed representative of each accession, and the seeds subjected to seed dimensional trait, oil content and oil composition analyses. Kernel width varied along a latitudinal cline of collection site, while kernel length varied across a longitudinal cline. Palmitic and linoleic acids were inversely correlated with each other and varied along a longitudinal cline of the collection site. The results indicate that accessions collected from more southwesterly sites tended to have larger seed and those from more westerly sites had higher linoleic acid content and lower palmitic and myristic acids, which are all desirable phenotypes for an oilseed Silphium.
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