A Three-Stage Genome-Wide Association Study of General Cognitive Ability: Hunting the Small Effects

Childhood general cognitive ability (g) is important for a wide range of outcomes in later life, from school achievement to occupational success and life expectancy. Large-scale association studies will be essential in the quest to identify variants that make up the substantial genetic component implicated by quantitative genetic studies. We conducted a three-stage genome-wide association study for general cognitive ability using over 350,000 single nucleotide polymorphisms (SNPs) in the quantitative extremes of a population sample of 7,900 7-year-old children from the UK Twins Early Development Study. Using two DNA pooling stages to enrich true positives, each of around 1,000 children selected from the extremes of the distribution, and a third individual genotyping stage of over 3,000 children to test for quantitative associations across the normal range, we aimed to home in on genes of small effect. Genome-wide results suggested that our approach was successful in enriching true associations and 28 SNPs were taken forward to individual genotyping in an unselected population sample. However, although we found an enrichment of low P values and identified nine SNPs nominally associated with g (P < 0.05) that show interesting characteristics for follow-up, further replication will be necessary to meet rigorous standards of association. These replications may take advantage of SNP sets to overcome limitations of statistical power. Despite our large sample size and three-stage design, the genes associated with childhood g remain tantalizingly beyond our current reach, providing further evidence for the small effect sizes of individual loci. Larger samples, denser arrays and multiple replications will be necessary in the hunt for the genetic variants that influence human cognitive ability

Genomic Analysis of Individual Differences in Ethanol Drinking: Evidence for Non-Genetic Factors in C57BL/6 Mice

Genetic analysis of factors affecting risk to develop excessive ethanol drinking has been extensively studied in humans and animal models for over 20 years. However, little progress has been made in determining molecular mechanisms underlying environmental or non-genetic events contributing to variation in ethanol drinking. Here, we identify persistent and substantial variation in ethanol drinking behavior within an inbred mouse strain and utilize this model to identify gene networks influencing such “non-genetic” variation in ethanol intake. C57BL/6NCrl mice showed persistent inter-individual variation of ethanol intake in a two-bottle choice paradigm over a three-week period, ranging from less than 1 g/kg to over 14 g/kg ethanol in an 18 h interval. Differences in sweet or bitter taste susceptibility or litter effects did not appreciably correlate with ethanol intake variation. Whole genome microarray expression analysis in nucleus accumbens, prefrontal cortex and ventral midbrain region of individual animals identified gene expression patterns correlated with ethanol intake. Results included several gene networks previously implicated in ethanol behaviors, such as glutamate signaling, BDNF and genes involved in synaptic vesicle function. Additionally, genes functioning in epigenetic chromatin or DNA modifications such as acetylation and/or methylation also had expression patterns correlated with ethanol intake. In verification for the significance of the expression findings, we found that a histone deacetylase inhibitor, trichostatin A, caused an increase in 2-bottle ethanol intake. Our results thus implicate specific brain regional gene networks, including chromatin modification factors, as potentially important mechanisms underlying individual variation in ethanol intake

A Retrospective Analysis of White Clover ( Trifolium repens L.) Content Fluctuation in Perennial Ryegrass ( Lolium perenne L.) Swards under 4 Years of Intensive Rotational Dairy Grazing

International audienceThe objective of this study was to examine fluctuations in white clover (Trifolium repens L.) content in perennial ryegrass (Lolium perenne L.) swards within a high nitrogen (250 kg N/ha) input grazing dairy system. The data came from a larger, overall system experiment within which all management and growing condition variables were categorised each year for the 40 paddocks that contained perennial ryegrass-white clover swards, over four growing years. Within that study, eight perennial ryegrass cultivars were examined, each sown individually with two white clover cultivars in a 50:50 mix of ‘Chieftain’ and ‘Crusader’. To determine management associations and meteorological patterns with white clover content and rate/direction of change, separate generalised linear models were used to analyse each individual management or meteorological variable. Paddocks with high white clover contents were associated with lower pre- and post-grazing sward heights, lower pasture cover over the winter period and shorter over-winter period. Perennial ryegrass cultivars with lower pre- and post-grazing height, lower pre-grazing pasture mass and pasture yield removed, all retained more white clover in their swards. Soil fertility remained a key factor that affected white clover persistence influencing the degree of responses in all treatments, particularly soil phosphorus (P) levels. Beyond this, higher white clover contents and lower rates of white clover decline were associated with paddocks that received lower rainfall, had higher soil moisture deficits and received more radiation into the base of the sward, particularly around the time of grazing

DNA markers associated with general and specific cognitive abilities

Multivariate quantitative genetic research suggests a hierarchical model of cognitive abilities where genetic effects are largely general, cutting across most cognitive abilities. Some genetic effects, however, are specific to certain cognitive abilities. These results lead to a hypothesis for molecular genetic research: Although most genes associated with one cognitive ability will be related to other cognitive abilities, some genes will be specific to a particular cognitive ability. The current research explored this hypothesis in an analysis of data on specific cognitive abilities from 86 children from 6 to 12 years of age from a larger allelic association study of general cognitive ability. Eight DNA markers were entered simultaneously in separate multiple regression analyses predicting each of four specific cognitive ability factors (Verbal, Spatial, Perceptual Speed, Memory), as well as WISC-R subtest scores. Four markers (CTGB33, EST00083, HLA, and SOD2) showed similar effects across the cognitive ability scales. suggesting that they are related to general cognitive ability (g). These associations became negligible when the effects of 'g' (WISC-R IQ) were removed. Three markers (ADH5, DM, and NGFB) continued to be significantly associated with specific cognitive ability scales after the effects of 'g' were removed. Although preliminary, these molecular genetic results support the hierarchical model predicted by quantitative genetic research

A polymorphism in mitochondrial DNA associated with IQ?

In an allelic association study of 100 DNA markers in or near genes of neurological relevance, one restriction fragment length polymorphism (RFLP) yielded significant differences between high- and low-IQ groups in two independent samples. The goal of this article is to describe how we tracked down the specific gene marked by the RFLP and to introduce some current techniques used to apply molecular genetics to complex traits like IQ. The RFLP, EST00083, is a brain-expressed sequence tag site (BESTS) derived from a cDNA hippocampal library. The cDNA clone was shown to involve a chimera between genomic DNA on Chromosome 6 and mitochondrial DNA (mtDNA). The RFLP was localized in the mtDNA rather than the genomic DNA. The RFLP is an MspI restriction site (CCGG) at 15,925 base pairs of the complete mitochondrial genome in a gene that codes for the transfer RNA for threonine. The mitochondrial origin of the EST00083 RFLP explains why the RFLP is maternally transmitted and never yields heterozygotes. Although mtDNA could be associated with IQ, such an unusual result requires further replication

Failure to replicate a QTL association between a DNA marker identified by EST00083 and IQ

In a paper published in this journal, a possible QTL association was reported between general cognitive ability and a marker, identified by an expressed sequence tag, EST00083 (Skuder et al., 1995). In two small samples, the frequency of the common allele of this DNA marker, which was shown to be in the threonine transfer RNA gene in mitochondrial DNA, was significantly greater in a high-Iq group than in a low-IQ group. As part of the ongoing IQ QTL Project (Plomin et al., 1995), we have attempted to replicate this QTL association. First, we found that the QTL association remained significant when we compared 51 high- and 51-average IQ subjects, drawn in part from the samples used in the previous report. However, when we examined the association in new samples of 40 extremely high-IQ subjects and 50 average-IQ subjects, the association did not replicate. This underlies the need for replication in case-control studies of allelic association

Allelic associations between 100 DNA markers and high versus low IQ

For DNA markers in or near genes of neurological relevance, allelic frequencies were compared for groups of White children high and low in IQ in an attempt to identify specific genes responsible for the substantial heritability of IQ scores. We previously reported results for 60 DNA markers and we now describe results for 40 additional markers. One sample consisted of high- and low-IQ groups with average IQs of 130 (N = 24) and 82 (N = 18), respectively. A replication sample was more extreme, including groups with average IQs of 142 (N = 27) and 59 (N = 17). Three of the 40 markers yielded significant allelic frequency differences between the high- and low-IQ groups in the original sample. In the replication sample, two of these markers (alcohol dehydrogenase 5 and the beta polypeptide of nerve growth factor) yielded results in the same direction but were not significant. The third marker (EST00083), derived from a cDNA hippocampal library, was also significant in the replication sample. As described in another article (Skuder et al., 1995) in this issue, this marker was found to involve mitochondrial DNA (mtDNA) rather than nuclear DNA. The unexpected nature of this marker suggests caution in claiming that the replicated association for EST00083 is indeed a quantitative trait loci (QTL) for IQ until the association receives additional support. This study provides statistical power to detect associations that account for about 2% of the IQ variance in the population. We are currently obtaining samples four times larger that will provide statistical power to detect allelic associations that account for considerably less than 1% of the variance