Low Levels Of Linkage Disequilibrium Research Articles

The narrow footprint of ancient balancing selection revealed by heterokaryon incompatibility genes in Aspergillus fumigatus.

In fungi, fusion between individuals leads to localized cell death, a phenomenon termed heterokaryon incompatibility. Generally, the genes responsible for this incompatibility are observed to be under balancing selection resulting from negative frequency-dependent selection. Here, we assess this phenomenon in Aspergillus fumigatus, a human pathogenic fungus with a very low level of linkage disequilibrium as well as an extremely high crossover rate. Using complementation of auxotrophic mutations as an assay for hyphal compatibility, we screened sexual progeny for compatibility to identify genes involved in this process, called het genes. In total, 5/148 (3.4%) offspring were compatible with a parent and 166/2142 (7.7%) sibling pairs were compatible, consistent with several segregating incompatibility loci. Genetic mapping identified five loci, four of which could be fine mapped to individual genes, of which we tested three through heterologous expression, confirming their causal relationship. Consistent with long-term balancing selection, trans-species polymorphisms were apparent across several sister species, as well as equal allele frequencies within A. fumigatus. Surprisingly, a sliding window genome-wide population-level analysis of an independent dataset did not show increased Tajima's D near these loci, in contrast to what is often found surrounding loci under balancing selection. Using available de novo assemblies, we show that these balanced polymorphisms are restricted to several hundred base pairs flanking the coding sequence. In addition to identifying the first het genes in an Aspergillus species, this work highlights the interaction of long-term balancing selection with rapid linkage disequilibrium decay.

Identification of genomic characteristics and selective signals in Guizhou black goat

BackgroundGuizhou black goat is one of the indigenous black goat breeds in the southwest region of Guizhou, China, which is an ordinary goat for mutton production. They are characterized by moderate body size, black coat, favorite meat quality with tender meat and lower odor, and tolerance for cold and crude feed. However, little is known about the genetic characteristics or variations underlying their important economic traits.ResultsHere, we resequenced the whole genome of Guizhou black goat from 30 unrelated individuals breeding in the five core farms. A total of 9,835,610 SNPs were detected, and 2,178,818 SNPs were identified specifically in this breed. The population structure analysis revealed that Guizhou black goat shared a common ancestry with Shaanbei white cashmere goat (0.146), Yunshang black goat (0.103), Iran indigenous goat (0.054), and Moroccan goat (0.002). However, Guizhou black goat showed relatively higher genetic diversity and a lower level of linkage disequilibrium than the other seven goat breeds by the analysis of the nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity. Based on FST and θπ values, we identified 645, 813, and 804 selected regions between Guizhou black goat and Yunshang black goat, Iran indigenous goat, and cashmere goats. Combined with the results of XP-EHH, there were 286, 322, and 359 candidate genes, respectively. Functional annotation analysis revealed that these genes are potentially responsible for the immune response (e.g., CD28, CD274, IL1A, TLR2, and SLC25A31), humility-cold resistance (e.g., HBEGF, SOSTDC1, ARNT, COL4A1/2, and EP300), meat quality traits (e.g., CHUK, GAB2, PLAAT3, and EP300), growth (e.g., GAB2, DPYD, and CSF1), fertility (e.g., METTL15 and MEI1), and visual function (e.g., PANK2 and NMNAT2) in Guizhou black goat.ConclusionOur results indicated that Guizhou black goat had a high level of genomic diversity and a low level of linkage disequilibrium in the whole genome. Selection signatures were detected in the genomic regions that were mainly related to growth and development, meat quality, reproduction, disease resistance, and humidity-cold resistance in Guizhou black goat. These results would provide a basis for further resource protection and breeding improvement of this very local breed.

Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea.

Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon's information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker-trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm.

Population structure and genomic analyses of carcass back Length, shoulder width and leg width in purebred and crossbred German Merino sheep

In order to derive suitable breeding strategies for complex traits, it is indispensable that their genetic architecture as well as population specific parameters are thoroughly investigated. Large samples of genotyped individuals are required in order to produce reliable results and to draw adequate inferences. Whereas in cattle, pig and chicken such data are available for many populations, such datasets are rare for sheep. Except for some sheep breeding nations where genomic selection is applied to sheep, the majority of datasets of genotyped sheep come from experiments with often small sample sizes. Pooling data from different breeds and crosses is one way to increase the sample size for genomic analyses but is somehow challenging due to the multi-breed composition of the datasets. Population structure and genetic diversity has an impact on the results of genomic analyses but is often not studied in the populations in which genomic analyses are conducted. Genetically diverse populations as found in sheep often compromise the analyses and the interpretation of results. Here, we investigated the genetic diversity and population structure of purebred Merino and several Merino crossbred lambs as well as in their pooled data and conducted separate and joint genetic analyses. Linkage disequilibrium was studied in the pooled data as well as in the single datasets. Consistency of phase was calculated among crosses. Population structure assessed by principal component analysis. Variance components were estimated and genome-wide association studies were performed for three carcass traits. All investigations based on 50k genotype data. Large genetic diversity was found between and also within crosses. The populations showed low levels of linkage disequilibrium (average r² between 0.155 and 0.171 within crosses and 0.138 in the pooled dataset for inter-marker distances up to 0.059 Mbp) which decayed fast with increasing inter-marker distance which was particularly pronounced when the data were pooled. The population genetic structure of the purebred Merino sample was similar as in Merino crosses and the genetic differentiation between the different populations were small. Variance components could solely be estimated at acceptable standard errors for some of the single crosses and hence genome-wide association studies could not be performed for all crosses. Pooling data drastically reduced standard errors in variance component estimation but did only marginally improve gene mapping results in terms of power but not precision. The heritabilities estimated in the pooled dataset were 0.30, 0.18 and 0.18 for back length, shoulder width and leg width. Only one genome-wide significant SNP for shoulder width was detected. Further, across all traits and datasets, 25 SNPs were found to be putatively trait associated. Larger datasets and denser marker panels are required to utilize such datasets for gene mapping analyses at high power and precision and would improve population genetic investigations. If possible, and to avoid the application of too complex models, data pooling should rather be done by combining several populations of the same breed instead of multiple crosses.

Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto)

As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the micro-evolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.

A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3).

The dopamine transporter gene, SLC6A3, has received substantial attention in genetic association studies of various phenotypes. Although some variable number tandem repeats (VNTRs) present in SLC6A3 have been tested in genetic association studies, results have not been consistent. VNTRs in SLC6A3 that have not been examined genetically were characterized. The Tandem Repeat Annotation Library was used to characterize the VNTRs of 64 unrelated long-read haplotype-phased SLC6A3 sequences. Sequence similarity of each repeat unit of the five VNTRs is reported, along with the correlations of SNP-SNP, SNP-VNTR, and VNTR-VNTR alleles across the gene. One of these VNTRs is a novel hyper-VNTR (hyVNTR) in intron 8 of SLC6A3, which contains a range of 3.4-133.4 repeat copies and has a consensus sequence length of 38 bp, with 82% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. In addition, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it might be a recombination hotspot.

The Association Between Vitamin C and Cancer: A Two-Sample Mendelian Randomization Study.

In recent years, many studies have indicated that vitamin C might be negatively associated with the risk of cancer, but the actual relationship between vitamin C and cancer remains ambivalent. Therefore, we utilized a two-sample Mendelian randomization (MR) study to explore the causal associations of genetically predicted vitamin C with the risk of a variety of cancers. Single-nucleotide polymorphisms (SNPs) associated with vitamin C at a significance level of p < 5 × 10–8 and with a low level of linkage disequilibrium (LD) (r2 < 0.01) were selected from a genome-wide association study (GWAS) meta-analysis of plasmid concentration of vitamin C consisting of 52,018 individuals. The data of the GWAS outcomes were obtained from United Kingdom Biobank, FinnGen Biobank and the datasets of corresponding consortia. In the inverse-variance weight (IVW) method, our results did not support the causal association of genetically predicted vitamin C with the risk of overall cancer and 14 specific types of cancer. Similar results were observed in sensitivity analyses where the weighted median and MR-Egger methods were adopted, and heterogeneity and pleiotropy were not observed in statistical models. Therefore, our study suggested that vitamin C was not causally associated with the risk of cancer. Further studies are warranted to discover the potential protective and therapeutic effects of vitamin C on cancer, and its underlying mechanisms.

Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping.

Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87–110.64%) and a high level of genetic diversity (mean number of alleles, NA = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.

Rapid Adaptation to Temperature via a Potential Genomic Island of Divergence in the Invasive Green Crab, Carcinus maenas

Widespread species often adapt easily to novel conditions – both those found in new habitats and those generated by climate change. However, rapid adaptation may be hindered in the marine realm, where long-distance dispersal and consequently high gene flow are predicted to limit potential for local adaptation. Here, we use a highly dispersive invasive marine crab to test the nature and speed of adaptation to temperature in the sea. Using single nucleotide polymorphisms (SNPs) generated from cardiac transcriptome sequencing, we characterized six populations of the European green crab (Carcinus maenas) located across parallel thermal gradients in their native and invasive ranges. We compared SNP frequencies with local temperatures and previously generated data on cardiac heat and cold tolerance to identify candidate markers associated with population-level differences in thermal physiology. Of 10,790 SNPs, 104 were identified as frequency outliers, a signal that was strongly driven by association with temperature and/or cold tolerance. Seventy-two of these outlier markers, representing 28 different genes, were in a cluster of SNPs identified as a potential inversion polymorphism using linkage disequilibrium network analysis. This SNP cluster was unique in the data set, which was otherwise characterized by low levels of linkage disequilibrium, and markers in this cluster showed a significant enrichment of coding substitutions relative to the full SNP set. These 72 outlier SNPs appear to be transmitted as a unit, and represent a putative genomic island of divergence which varied in frequency with organismal cold tolerance. This relationship was strikingly similar across both native and invasive populations, all of which showed a very strong correlation with cold tolerance (R2 = 0.96 over all six populations). Notably, three of these populations have diverged recently (&amp;lt;100 years) and show little to no neutral divergence, suggesting that this genomic region may be responding to temperature on a relatively short time scale. This relationship indicates adaptation to temperature based on the action of a putative genomic island of divergence, perhaps partially explaining the extraordinary invasive ability of this species.

In the presence of population structure: From genomics to candidate genes underlying local adaptation.

Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis‐regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low‐frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis‐regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic‐acid pathway to local adaptation.

Genotyping more cows increases genetic gain and reduces rate of true inbreeding in a dairy cattle breeding scheme using female reproductive technologies

Both small dairy cattle populations and dairy cattle populations with a low level of linkage disequilibrium (LD) suffer from low reliability of genomic prediction. In this study, we investigated whether adding more genotyped cows to the reference population influences the rate of genetic gain and rate of inbreeding by affecting the reliability. A standard breeding program with a large reference population and high LD, which mimicked a breeding program for Danish Holstein population, was simulated as a reference. A Danish Jersey population with a small reference population and high LD and a Red Dairy Cattle population with a large reference population and low LD were also simulated. Two additional breeding programs were simulated for Danish Jersey and Red Dairy Cattle populations, where 2,000 additional genotyped cows were included in the population for genomic selection. All 5 simulated breeding programs were initiated by a founder population to generate LD resembling the real LD pattern, followed by a 20-yr conventional progeny-testing scheme with 1,000 or 10,000 genotyped progeny-tested bulls and a 10-yr genomic selection scheme with or without 2,000 additional genotyped cows. Evaluation criteria were annual monetary genetic gain and rate of true inbreeding. Our results showed that adding more genotyped cows to the reference in dairy cattle populations has the potential to increase genetic gain and reduce the rate of inbreeding, regardless of reference population size and level of LD. However, it is still not possible to reach the same genetic gain as in the simulated Danish Holstein population with either a small reference population or low LD. Our results also showed that in a small reference population with high LD, it is difficult to manage inbreeding because of lower accuracy compared with the simulated Danish Holstein population and a smaller number of relevant families to select from. Therefore, breeding strategies need to be chosen to match population size and structure. The rate of true inbreeding is always underestimated by pedigree inbreeding and even more in genomic breeding programs, indicating that some forms of genome-wide inbreeding, instead of pedigree-based inbreeding, should be used to monitor inbreeding when genomic selection is implemented.

A test of genomic modularity among life-history adaptations promoting speciation with gene flow.

Speciation with gene flow may require adaptive divergence of multiple traits to generate strong ecologically based reproductive isolation. Extensive negative pleiotropy or physical linkage of genes in the wrong phase affecting these diverging traits may therefore hinder speciation, while genetic independence or "modularity" among phenotypic traits may reduce constraints and facilitate divergence. Here, we test whether the genetics underlying two components of diapause life history, initial diapause intensity and diapause termination timing, constrain differentiation between sympatric hawthorn and apple-infesting host races of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured via genotyping-by-sequencing (GBS). Loci genetically associated with diapause termination timing were mainly observed for SNPs mapping to chromosomes 1-3 in the genome, most notably for SNPs displaying higher levels of linkage disequilibrium (LD), likely due to inversions. In contrast, selection on initial diapause intensity affected loci on all five major chromosomes of the genome, specifically those showing low levels of LD. This lack of overlap in genetically associated loci suggests that the two diapause phenotypes are largely modular. On chromosome 2, however, intermediate level LD loci and a subgroup of high LD loci displayed significant negative relationships between initial diapause intensity and diapause termination time. These gene regions on chromosome 2 therefore affected both traits, while most regions were largely independent. Moreover, loci associated with both measured traits also tended to exhibit highly divergent allele frequencies between the host races. Thus, the presence of nonoverlapping genetic modules likely facilitates simultaneous, adaptive divergence for the measured life-history components.

Gene-gene interaction of single nucleotide polymorphisms in 16p13.3 may contribute to the risk of non-syndromic cleft lip with or without cleft palate in Chinese case-parent trios.

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G × G) and gene-environment (G × E) interactions. We conducted transmission disequilibrium tests on 69 single nucleotide polymorphisms (SNPs) mapping to 16p13.3 among 806 Chinese case-parent trios ascertained through an international consortium where a GWAS of oral clefts was conducted. G × G, as well as G × E interactions involving maternal environmental tobacco smoke (ETS) and multivitamin supplementation, were explored using conditional logistic regression model. We applied Cordell's method as implemented in the R package TRIO to test for possible interactions. While no SNPs showed evidence of linkage and association with NSCL/P after Bonferroni correction, we found signals of G × G interactions between SNPs in 16p13.3. Nine pairs of SNP-SNP interactions attained significance after Bonferroni correction, among which the most significant interaction was found between rs2072346 (ADCY9) and rs11646137 (intergenic region, P = 7.2 × 10-5 ). Linkage disequilibrium (LD) analysis revealed only low level of LD between these SNPs. This study failed to confirm the significant association between SNPs within 16p13.3 and the risk of NSCL/P, but underlined the importance of taking into account potential G × G interactions for the genetic association analysis of NSCL/P.

Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species

The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.

Random forest estimation of genomic breeding values for disease susceptibility over different disease incidences and genomic architectures in simulated cow calibration groups

A simulation study was conducted to investigate the performance of random forest (RF) and genomic BLUP (GBLUP) for genomic predictions of binary disease traits based on cow calibration groups. Training and testing sets were modified in different scenarios according to disease incidence, the quantitative-genetic background of the trait (h2=0.30 and h2=0.10), and the genomic architecture [725 quantitative trait loci (QTL) and 290 QTL, populations with high and low levels of linkage disequilibrium (LD)]. For all scenarios, 10,005 SNP (depicting a low-density 10K SNP chip) and 50,025 SNP (depicting a 50K SNP chip) were evenly spaced along 29 chromosomes. Training and testing sets included 20,000 cows (4,000 sick, 16,000 healthy, disease incidence 20%) from the last 2 generations. Initially, 4,000 sick cows were assigned to the testing set, and the remaining 16,000 healthy cows represented the training set. In the ongoing allocation schemes, the number of sick cows in the training set increased stepwise by moving 10% of the sick animals from the testing set to the training set, and vice versa. The size of the training and testing sets was kept constant. Evaluation criteria for both GBLUP and RF were the correlations between genomic breeding values and true breeding values (prediction accuracy), and the area under the receiving operating characteristic curve (AUROC). Prediction accuracy and AUROC increased for both methods and all scenarios as increasing percentages of sick cows were allocated to the training set. Highest prediction accuracies were observed for disease incidences in training sets that reflected the population disease incidence of 0.20. For this allocation scheme, the largest prediction accuracies of 0.53 for RF and of 0.51 for GBLUP, and the largest AUROC of 0.66 for RF and of 0.64 for GBLUP, were achieved using 50,025 SNP, a heritability of 0.30, and 725 QTL. Heritability decreases from 0.30 to 0.10 and QTL reduction from 725 to 290 were associated with decreasing prediction accuracy and decreasing AUROC for all scenarios. This decrease was more pronounced for RF. Also, the increase of LD had stronger effect on RF results than on GBLUP results. The highest prediction accuracy from the low LD scenario was 0.30 from RF and 0.36 from GBLUP, and increased to 0.39 for both methods in the high LD population. Random forest successfully identified important SNP in close map distance to QTL explaining a high proportion of the phenotypic trait variations.

Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations.

BackgroundQTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data.ResultsAnalysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping.ConclusionsThe use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high.

High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium.

Short read sequencing of diploid individuals does not permit the direct inference of the sequence on each of the two homologous chromosomes. Although various phasing software packages exist, they were primarily tailored for and tested on human data, which differ from other species in factors that influence phasing, such as SNP density, amounts of linkage disequilibrium (LD) and sample sizes. Despite becoming increasingly popular for other species, the reliability of phasing in non-human data has not been evaluated to a sufficient extent. We scrutinized the phasing accuracy for Drosophila melanogaster, a species with high polymorphism levels and reduced LD relative to humans. We phased two D.melanogaster populations and compared the results to the known haplotypes. The performance increased with size of the reference panel and was highest when the reference panel and phased individuals were from the same population. Full genomic SNP data and inclusion of sequence read information also improved phasing. Despite humans and Drosophila having similar switch error rates between polymorphic sites, the distances between switch errors were much shorter in Drosophila with only fragments <300-1500bp being correctly phased with ≥95% confidence. This suggests that the higher SNP density cannot compensate for the higher recombination rate in D.melanogaster. Furthermore, we show that populations that have gone through demographic events such as bottlenecks can be phased with higher accuracy. Our results highlight that statistically phased data are particularly error prone in species with large population sizes or populations lacking suitable reference panels.

Gene by Environment Interaction Linking the Chromosome 15q25 Locus with Cigarette Consumption and Lung Cancer Susceptibility - Are African American Affected Differently? — Authors' Reply

We appreciate Drs. Hopkins' and Young's commentary (Hopkins and Young, 2016) on some of the conclusions and limitations to our investigation (David et al., 2016) of gene by environment interactions for lung cancer in African–Americans. The investigation was not designed to examine underlying biological mechanisms of gene by environment interactions for lung cancer risk, but was instead intended to characterize the nature and directionality of such interactions in a sufficiently powered case–control study of African–Americans. Potential mediating processes, such as can be captured by measurements of airflow limitation resulting from chronic obstructive pulmonary disease and the inflammatory and oxidative stress processes – resulting from altered levels of inhaled, combusted tobacco smoke – are examples of precursor phenotypes, which could shed additional light on genetically-moderated mediation of lung cancer. The present study did not compare genetic interaction effects between different ethnic groups. Therefore, we cannot directly contrast our results with those of Asian-, American–Indian- or European-ancestry studies. Although it may appear that the dose–response of cigarettes smoked per day is lost in smokers with 2 risk alleles, this may not necessarily be the case. It may be more accurate to conclude that the genetic association with lung cancer is most prominent in light smokers. Nonetheless, our results, including the predeceasing genome-wide association studies of smoking quantity and fine mapping studies of lung cancer confirm the importance of the chromosome 15q25.1 region (CHRNA3, CHRNA5, IREB2 and PSMA4) in lung cancer risk in African–Americans. Differences in genetic architecture of this region between African-ancestry and those of non-African ancestry, such as varying prevalence of polymorphisms linked to smoking exposure and lung cancer and lower levels of linkage disequilibrium, necessitate careful evaluation within African-ancestry study populations in order to demonstrate the clinical validity of lung cancer susceptibility variants that have been more widely studied in European-ancestry populations. Overall, these results point to a complex web of causation whereby the chromosome 15q25.1 region represents a lung cancer susceptibility locus in African–Americans vis-a-vis increased smoking exposure and intrinsic lung cancer risk.

Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep

BackgroundKnowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (Ne), heterozygosity, fixation index (FST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates.MethodsIn this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r2 and D′), Ne, heterozygosity, FST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP).ResultsCompared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller Ne than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest FST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection.ConclusionsThis study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0169-6) contains supplementary material, which is available to authorized users.

Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status of Glycine gracilis.

The level of linkage disequilibrium (LD) is a major factor to determine DNA polymorphism pattern of a population and to construct high-resolution maps useful in localizing and gene cloning of complicated traits. Here, we investigated LD level of three soybean populations with different genetic backgrounds and taxonomic status of G.gracilis by comparing the DNA polymorphism patterns of four high-diversity single-copy nuclear genes. A total of 152, 22, and 77 accessions of G.soja, G.gracilis, and G.max were observed. The results indicated that G.max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G.soja. Four gene loci evolved according to neutrality in both G.max and G.gracilis populations, and three gene loci evolved according to neutrality in G.soja population by Tajima's and Fu and Li's test. However, one gene locus deviated from neutrality by Fu and Li's test in the G.soja population. Further, medial level of LD (average r (2)=0.2426) was found in intragene in G.max and G.gracilis populations, but unexpected low level of LD (r (2)≤0.0539) was found in G.soja population. Significant genetic differentiation was detected between G.max and G.soja populations and also between G.max and G.gracilis populations; however, nonsignificant genetic differentiation was found between G.gracilis and G.soja populations. The results suggest that LD level depends on genetic background of soybean population, and implicit that G.gracilis should be regarded as the variant of G.soja, not as an independent species.