The combined effect of SNP-marker and phenotype attributes in genome-wide association studies

The last decade has seen rapid improvements in high-throughput single nucleotide polymorphism (SNP) genotyping technologies that have consequently made genome-wide association studies (GWAS) possible. With tens to hundreds of thousands of SNP markers being tested simultaneously in GWAS, it is imperative to appropriately pre-process, or filter out, those SNPs that may lead to false associations. This paper explores the relationships between various SNP genotype and phenotype attributes and their effects on false associations. We show that (i) uniformly distributed ordinal data as well as binary data are more easily influenced, though not necessarily negatively, by differences in various SNP attributes compared with normally distributed data; (ii) filtering SNPs on minor allele frequency (MAF) and extent of Hardy–Weinberg equilibrium (HWE) deviation has little effect on the overall false positive rate; (iii) in some cases, filtering on MAF only serves to exclude SNPs from the analysis without reduction of the overall proportion of false associations; and (iv) HWE, MAF and heterozygosity are all dependent on minor genotype frequency, a newly proposed measure for genotype integrity.     

Testing for local adaptation in Avena barbata: a classic example of ecotypic divergence

Forty years ago, Robert Allard and colleagues documented that the slender wild oat, Avena barbata , occurred in California as two multi-locus allozyme genotypes, associated with mesic and xeric habitats. This is arguably the first example of ecotypes identified by molecular techniques. Despite widespread citation, however, the inference of local adaptation of these ecotypes rested primarily on the allozyme pattern. This study tests for local adaptation of these ecotypes using reciprocal transplant and quantitative trait locus (QTL) mapping techniques. Both ecotypes and 188 recombinant inbred lines (RILs) derived from a cross between them were grown in common garden plots established at two sites representative of the environments in which the ecotypes were first described. Across four growing seasons at each site, three observations consistently emerged. First, despite significant genotype by environment interaction, the mesic ecotype consistently showed higher lifetime reproductive success across all years and sites. Second, the RILs showed no evidence of a trade-off in performance across sites or years, and fitness was positively correlated across environments. Third, at QTL affecting lifetime reproductive success, selection favoured the same allele in all environments. None of these observations are consistent with local adaptation but suggest that a single genotype is selectively favoured at both moist and dry sites. I propose an alternative hypothesis that A. barbata may be an example of contemporary evolution – whereby the favoured genotype is spreading and increasing in frequency – rather than local adaptation.     

Diversity and compatibility of peanut (Arachis hypogaea L.) bradyrhizobia and their host plants

A high degree of genetic diversity among 125 peanut bradyrhizobial strains and among 32 peanut cultivars collected from different regions of China was revealed by using the amplified fragment length polymorphism (AFLP) technique. Eighteen different peanut bradyrhizobial genotypes and six peanut cultivars were selected for symbiotic cross-inoculation experiments. The genomic diversity was reflected in the symbiotic diversity. The peanut cultivars varied in their ability to nodulate with the strains used. Some cultivars had a more restricted host range than the others. Also the strains displayed a range of nodulation patterns. In yield formation there were clear differences between the plant cultivar/bradyrhizobium combinations. There was good compatibility between some peanut bradyrhizobial strains and selected cultivars, with inoculation resulting in well-nodulated, high-yielding symbiotic combinations, but no plant cultivar was compatible with all strains used. The strains displayed a varying degree of effectiveness, with some strains being fairly effective with all cultivars and others with selected ones. The AFLP genotypes of the strains did not explain the symbiotic behavior, whereas the yield formation of the plant cultivars was more related to the genotype. It is concluded that to obtain optimal nitrogen fixation efficiency of peanut in the field, compatible plant cultivar-bradyrhizobium combinations should be selected either by finding inoculant strains compatible with the plant cultivars used, or plant cultivars compatible with the indigenous bradyrhizobia.     

A comparison of alternative methods to compute conditional genotype probabilities for genetic evaluation with finite locus models

An increased availability of genotypes at marker loci has prompted the development of models that include the effect of individual genes. Selection based on these models is known as marker-assisted selection (MAS). MAS is known to be efficient especially for traits that have low heritability and non-additive gene action. BLUP methodology under non-additive gene action is not feasible for large inbred or crossbred pedigrees. It is easy to incorporate non-additive gene action in a finite locus model. Under such a model, the unobservable genotypic values can be predicted using the conditional mean of the genotypic values given the data. To compute this conditional mean, conditional genotype probabilities must be computed. In this study these probabilities were computed using iterative peeling, and three Markov chain Monte Carlo (MCMC) methods – scalar Gibbs, blocking Gibbs, and a sampler that combines the Elston Stewart algorithm with iterative peeling (ESIP). The performance of these four methods was assessed using simulated data. For pedigrees with loops, iterative peeling fails to provide accurate genotype probability estimates for some pedigree members. Also, computing time is exponentially related to the number of loci in the model. For MCMC methods, a linear relationship can be maintained by sampling genotypes one locus at a time. Out of the three MCMC methods considered, ESIP, performed the best while scalar Gibbs performed the worst.     

Direct shoot regeneration from mature embryo as a rapid and genotype-independent pathway in tissue culture of heterogeneous diverse sets of cumin (Cuminum cyminum L.) genotypes

Summary A rapid and one-step protocol for direct regeneration of shoots from cumin embryo explants has been developed. Embryo explants with shoot meristems were cultured on shoot regeneration medium for 15–22 d. After embryo culture, shoots were regenerated from the area adjacent to the region between the cotyledons and embryo axis within 2 wk, without any intermediate callus phase. Shoot proliferation and elongation were achieved on shoot regeneration medium without subculture. Among the different combinations of 6-benzylaminopurine, α-naphthaleneacetic acid (NAA), and indole-3-acetic acid (IAA) tested, 0.8 mgl^−1 (4.3 μM) NAA in combination with 0.3 mgl^−1 (1.71 μM) IAA in the B5 medium resulted in the most efficient direct shoot regeneration. No significant difference was detected for the number of regenerated explants when different heterogeneous endemic varieties were compared. This plant regeneration procedure was applicable to different cumin genotypes and regenerated plants were phenotypically normal.     

Genetic Identity of Populus tremuloides Litter Influences Decomposition and Nutrient Release in a Mixed Forest Stand

Recent research has shown that genetic variation can directly impact community and ecosystem level processes. Populus tremuloides (trembling aspen) is an extremely widespread and genetically diverse tree species important to many North American forest ecosystems. Using leaf litter from five genotypes grown in a common garden under two nutrient treatments, we tracked litter decomposition in a natural aspen stand for 1 year. Here we show that aspen leaf litter decomposes and releases carbon, nitrogen, and sulfur in relation to its genetic identity. In a secondary experiment, we show that the genetic diversity of aspen litter mixtures can influence decomposition, however weakly so. Overall, nutrient treatments influenced leaf litter decomposition the most, followed by genetic identity, and then by genetic diversity (if at all in some cases). In this widespread, genetically diverse, and dominant species, genetic variation within a single species is important to ecosystem functioning. The relatively weak effect of genetic diversity on the processes measured here does not preclude its importance to ecosystem functioning, but does suggest that genetic identity and composition are more important than genetic diversity per se.     

Efficient and repetitive production of leaf-derived somatic embryos of Oncidium

Oncidium cultivars gave different embryogenic responses of leaf explants when affected by auxins (2,4-D, IAA, IBA and NAA), cytokinins (2iP, BA, kinetin, TDZ and zeatin), sucrose, NaH₂PO₄, casein hydrolysate, peptone, and glutamine. The best embryogenic responses of cv. Sweet Sugar were at 20 g dm⁻³ sucrose, 85 mg dm⁻³ NaH₂PO₄ and 3 mg dm⁻³ kinetin, respectively. The development of somatic embryos on leaf explants of cv. Sweet Sugar was delayed for about 10 – 20 d in comparison with cv. Gower Ramsey. On growth regulator-free medium, about 40 % of leaf derived embryos of cv. Gower Ramsey were fused together in their basal parts and so called multiple-state embryos. However, under the same condition, the embryos of cv. Sweet Sugar were all in multiple-state form.     

Does COMT genotype influence the effects of d‐amphetamine on executive functioning?

In a widely cited study, Mattay et al. reported that amphetamine (0.25 mg/kg oral, or 17 mg for a 68 kg individual) impaired behavioral and brain indices of executive functioning, measured using the Wisconsin Card Sorting Task (WCST) and N‐Back working memory task, in 6 individuals homozygous for the met allele of the val158met polymorphism in the catechol‐O‐methyltransferase (COMT) gene, whereas it improved executive functioning in 10 individuals homozygous for the more active val allele. We attempted to replicate their behavioral findings in a larger sample, using similar executive functioning tasks and a broader range of amphetamine doses. Over four sessions, n = 200 healthy normal adults received oral placebo, d‐amphetamine 5, 10, and 20 mg (average of 0.07, 0.15 and 0.29 mg/kg), under counterbalanced double‐blind conditions and completed WCST and N‐back tests of executive functioning. Amphetamine had typical effects on blood pressure and processing speed but did not affect executive functioning. COMT genotype (val158met) was not related to executive functioning under placebo or amphetamine conditions, even when we compared only the homozygous val/val and met/met genotypes at the highest dose of amphetamine (20 mg). Thus, we were not able to replicate the behavioral interaction between COMT and amphetamine seen in Mattay et al. We discuss possible differences between the studies and the implications of our findings for the use of COMT genotyping to predict clinical responses to dopaminergic drugs, and the use of intermediate phenotypes in genetic research.     

Apolipoprotein E,brain injury and neurodevelopmental outcome of children

Apolipoprotein E plays an important role in neurodegenerative processes in adulthood, whereas its neurodevelopmental role is uncertain. We aimed to study the effect of apolipoprotein E on neurodevelopment in a cohort liable to neurodevelopmental changes. The cohort consisted of very preterm (<32 gestational weeks) and/or very low birth weight (<1500 g) children, and the longitudinal follow‐up protocol included sequential cranial ultrasounds during infancy, brain magnetic resonance imaging at term‐equivalent age, neurological and cognitive assessment (Mental Developmental Index) at the corrected age of 2 years and cognitive and neuropsychological assessments (Wechsler Preschool and Primary Scale of Intelligence and Developmental NEuroPSYchological Assessment) at the chronological age of 5 years. Apolipoprotein E genotypes were determined from 322 children. Ultrasound and magnetic resonance imaging data were available for 321 (99.7%) and 151 (46.9%) children, respectively. Neurodevelopmental assessment data were available for 138 (42.9%) to 171 (53.1%) children. Abnormal findings in ultrasounds and magnetic resonance imaging were found in 163 (50.8%) and 64 (42.4%) children, respectively. Mild cognitive delay at the corrected age of 2 years and the chronological age of 5 years was suspected in 21 (12.3%) of 171 and 19 (13.8%) of 138 children, respectively. In the Developmental NEuroPSYchological Assessment, 47 (32.6%) of 144 children had significantly impaired performances in more than one study subtest. No associations between the apolipoprotein E genotypes and imaging findings or measured neurodevelopmental variables were found. Apolipoprotein E genotypes do not appear to have major impact on brain vulnerability or neurodevelopment in children .     

Association between a rare novel TP53 variant (rs78378222) and melanoma,squamous cell carcinoma of head and neck and lung cancer susceptibility in non‐Hispanic Whites

Recently, several studies have investigated the association between a newly reported rare functional single nucleotide polymorphism (SNP) in TP53 (rs78378222) and cancer risk, but generated inconsistent findings. The present study further investigated this association with risk of melanoma, squamous cell carcinoma of head and neck (SCCHN) and lung cancer. Using volunteers of non‐Hispanic Whites recruited for three large case–control studies, we genotyped the TP53 rs78378222 SNP in 1329 patients with melanoma, 1096 with SCCHN, 1013 with lung cancer and 3000 cancer‐free controls. Overall, we did not observe any variant homozygotes in this study population, nor significant associations between the TP53 rs78378222AC genotype or C allele and risk for melanoma (P = 0.680 and 0.682 respectively) and lung cancer (P = 0.379 and 0.382 respectively), but a protection against SCCHN (P = 0.008 and 0.008 respectively), compared with the AA genotype or A allele. An additional meta‐analysis including 19,423 cancer patients and 54,050 controls did not support such a risk association either. Our studies did not provide statistical evidence of an association between this rare TP53 variant and increased risk of melanoma, nor of lung cancer, but a possible protection against SCCHN.