FORTRAN 90 source code to perform the PCIT algorithm is available as Supplementary File 1.

Genome-wide association mapping is highly sensitive to environmental changes, but network analysis allows rapid causal gene identification.

With the improvement and decline in cost of high-throughput genotyping and phenotyping technologies, genome-wide association (GWA) studies are fast becoming a preferred approach for dissecting complex quantitative traits. Glucosinolate (GSL) secondary metabolites within Arabidopsis spp. can serve as a model system to understand the genomic architecture of quantitative traits. GSLs are key defenses against insects in the wild and the relatively large number of cloned quantitative trait locus (QTL) controlling GSL traits allows comparison of GWA to previous QTL analyses. To better understand the specieswide genomic architecture controlling plant-insect interactions and the relative strengths of GWA and QTL studies, we conducted a GWA mapping study using 96 A. thaliana accessions, 43 GSL phenotypes, and $230,000 SNPs. Our GWA analysis identified the two major polymorphic loci controlling GSL variation (AOP and MAM) in natural populations within large blocks of positive associations encompassing dozens of genes. These blocks of positive associations showed extended linkage disequilibrium (LD) that we hypothesize to have arisen from balancing or fluctuating selective sweeps at both the AOP and MAM loci. These potential sweep blocks are likely linked with the formation of new defensive chemistries that alter plant fitness in natural environments. Interestingly, this GWA analysis did not identify the majority of previously identified QTL even though these polymorphisms were present in the GWA population. This may be partly explained by a nonrandom distribution of phenotypic variation across population subgroups that links population structure and GSL variation, suggesting that natural selection can hinder the detection of phenotype-genotype associations in natural populations. N ATURAL phenotypic variation within a species or population is largely quantitative, polygenic, and controlled by the interaction of environmental and genetic factors (Fisher 1930;Falconer and Mackay 1996;Lynch and Walsh 1998). Advances in both highthroughput genotyping and phenotyping has enabled the use of intraspecific natural variation to identify the molecular and genetic bases of complex traits such as disease resistance, growth and development and correspondingly provide a preliminary view of the ecological and evolutionary consequences of this variation. While quantitative trait locus (QTL) mapping has been the standard approach to studying complex traits in the past, its application to self-incompatible and longgeneration species has been limited by the labor and time required to generate and genotype mapping populations (Liu 1998;Lynch and Walsh 1998;Mauricio 2001). As such, the molecular basis of most quantitative traits remains unknown.Genome-wide association (GWA) mapping has become a popular alternative to QTL mapping in recent years for studying natural genetic variation. GWA identifies association between phenotypes and genotypes, at a genome-wide level, using ''unrelated'' individuals that have been simultaneously genoty...

Discovering links between the genotype of an organism and its metabolite levels can increase our understanding of metabolism, its controls, and the indirect effects of metabolism on other quantitative traits. Recent technological advances in both DNA sequencing and metabolite profiling allow the use of broad-spectrum, untargeted metabolite profiling to generate phenotypic data for genome-wide association studies that investigate quantitative genetic control of metabolism within species. We conducted a genome-wide association study of natural variation in plant metabolism using the results of untargeted metabolite analyses performed on a collection of wild Arabidopsis thaliana accessions. Testing 327 metabolites against >200,000 single nucleotide polymorphisms identified numerous genotype–metabolite associations distributed non-randomly within the genome. These clusters of genotype–metabolite associations (hotspots) included regions of the A. thaliana genome previously identified as subject to recent strong positive selection (selective sweeps) and regions showing trans-linkage to these putative sweeps, suggesting that these selective forces have impacted genome-wide control of A. thaliana metabolism. Comparing the metabolic variation detected within this collection of wild accessions to a laboratory-derived population of recombinant inbred lines (derived from two of the accessions used in this study) showed that the higher level of genetic variation present within the wild accessions did not correspond to higher variance in metabolic phenotypes, suggesting that evolutionary constraints limit metabolic variation. While a major goal of genome-wide association studies is to develop catalogues of intraspecific variation, the results of multiple independent experiments performed for this study showed that the genotype–metabolite associations identified are sensitive to environmental fluctuations. Thus, studies of intraspecific variation conducted via genome-wide association will require analyses of genotype by environment interaction. Interestingly, the network structure of metabolite linkages was also sensitive to environmental differences, suggesting that key aspects of network architecture are malleable.

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.

Background The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. Findings Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. Conclusions GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.

No abstract

The view that changes to the control of gene expression rather than alterations to protein sequence are central to the evolution of organisms has become something of a truism in molecular biology. In reality, the direct evidence for this is limited, and only recently have we had the ability to look more globally at how genetic variation influences gene expression, focusing upon inter-individual variation in gene expression and using microarrays to test for differences in mRNA levels. Here, we review the scope of these experimental analyses, what they are designed to tell us about genetic variation, and what are their limitations from both a technical and a conceptual viewpoint. We conclude that while we are starting to understand the impact of this class of genetic variation upon steady-state mRNA levels, we are still far from identifying the potential phenotypic and evolutionary outcomes.