Identification of QTLs and Putative Candidate Gene Involved in Rhizome Enlargement of Asian lotus (Nelumbo Nucifera)

Lotus (Nelumbo) is perennial aquatic plant with nutritional, pharmacological, and ornamental significance. Rhizome is an underground lotus stem that act as a storage organ and as a reproductive tissue for asexual production. The enlargement of lotus rhizome is an important adaptive strategy for surviving the cold winter. The aims of this study were to identify quantitative trait loci (QTLs) for rhizome enlargement traits including rhizome enlargement index (REI) and number of enlarged rhizome (NER), and to uncover candidate genes associated with these phenotypic traits. A high-density genetic linkage map was constructed, consisting of 2,935 markers binned from 236,840 SNPs. A total of 14 significant QTLs were detected for REI and NER, which explained 6.67–22.28% of trait variance. Three QTL regions were repeatedly identified in at least two years, and a major QTL, designated cqREI-LG2, with a rhizome-enlargement effect and about 20% of the phenotypic contribution was identified across the three climatic years. A candidate NnBEL6 gene located within the confidence interval of cqREI-LG2 was considered to be putatively involved in lotus rhizome enlargement. The expression of NnBEL6 was exclusively induced by rhizome swelling. Sequence comparison of NnBEL6 among lotus varieties revealed a functional Indel site in its promoter that likely initiates the rhizome enlargement process. Transgenic potato assay was used to confirm the role of NnBEL6 in inducing tuberization. The successful identification QTLs and functional validation of NnBEL6 gene reported in this study will enrich our knowledge on the genetic basis of rhizome enlargement in lotus.

Hypothesis-free detection of gene-interaction effects on biomarker concentration in UK Biobank using variance prioritisation

Blood biomarkers include disease intervention targets that may interact with genetic and environmental factors resulting in subgroups of individuals who respond differently to treatment. Such interactions may be observed in genetic effects on trait variance. Variance prioritisation is an approach to identify genetic loci with interaction effects by estimating their association with trait variance, even where the modifier is unknown or unmeasured. Here, we develop and evaluate a regression-based Brown-Forsythe test and variance effect estimate to detect such interactions. We provide scalable open-source software (varGWAS) for genome-wide association analysis of SNP-variance effects (https://github.com/MRCIEU/varGWAS) and apply our software to 30 blood biomarkers in UK Biobank. We find 468 variance quantitative trait loci across 24 biomarkers and follow up findings to detect 82 gene-environment and six gene-gene interactions independent of strong scale or phantom effects. Our results replicate existing findings and identify novel epistatic effects of TREH rs12225548 x FUT2 rs281379 and TREH rs12225548 x ABO rs635634 on alkaline phosphatase and ZNF827 rs4835265 x NEDD4L rs4503880 on gamma glutamyltransferase. These data could be used to discover possible subgroup effects for a given biomarker during preclinical drug development.

Palm functional trait responses to local environmental factors in the Colombian Amazon

Functional traits play a key role in driving plant community effects on ecosystem function. We examined nine functional traits in various palm (Arecaceae) species and their relationships with moisture, tree-fall gaps, slope, and forest type at 29 transects (500×5 m) in the northeastern region of the Colombian Amazon. Redundancy analysis of mean trait values of species within a plot weighted by their abundance and Pearson correlations were used to evaluate the relationships between traits and environmental factors. The community trait composition was correlated with local environmental factors, which explained 23% of the trait variance. We detected functional dominance of the tallest palms in soils with high moisture and in floodplain forests (p ≤0.05). Palms with relatively long leaves were dominant in the flooded forests. Acaulescent and small palms were dominant on high slopes, and in terra firme forests, long-petioled palms were dominant in forest gaps. The number of seeds per fruit was not correlated with any environmental variable. Thus, hydrology is one of the main drivers of the functional composition of neotropical palm communities at the local scale, segregating tall palms with competitive and evasive strategies from small understory palms, which are mainly stress tolerant.

The Genetic Architecture of Milling Quality in Spring Oat Lines of the Collaborative Oat Research Enterprise

Most oat grains destined for human consumption must possess the ability to pass through an industrial de-hulling process with minimal breakage and waste. Uniform grain size and a high groat to hull ratio are desirable traits related to milling performance. The purpose of this study was to characterize the genetic architecture of traits related to milling quality by identifying quantitative trait loci (QTL) contributing to variation among a diverse collection of elite and foundational spring oat lines important to North American oat breeding programs. A total of 501 lines from the Collaborative Oat Research Enterprise (CORE) panel were evaluated for genome-wide association with 6 key milling traits. Traits were evaluated in 13 location years. Associations for 36,315 markers were evaluated for trait means across and within location years, as well as trait variance across location years, which was used to assess trait stability. Fifty-seven QTL influencing one or more of the milling quality related traits were identified, with fourteen QTL mapped influencing mean and variance across location years. The most prominent QTL was Qkernel.CORE.4D on chromosome 4D at approximately 212 cM, which influenced the mean levels of all traits. QTL were identified that influenced trait variance but not mean, trait mean only and both.

The Development of Vocational Interests in Early Adolescence: Stability, Change, and State-Trait Components

Vocational interests predict major life outcomes such as job performance, college major choice, and life goals. It is therefore important to gain a better understanding of their development during the crucial years of late childhood and early adolescence, when trait-like interests are starting to develop. The present study investigated the development of vocational interests in a longitudinal sample, comprising N = 3,876 participants—assessed at four time points from ages 11 to 14. Stability, state-trait variance components, mean-level development, and gender differences in mean-levels of Realistic, Investigative, Artistic, Social, Enterprising, and Conventional (RIASEC) dimensions were examined. Stabilities were moderate for all dimensions, but Realistic, Investigative, Social, and Conventional interests became more stable over time. For Realistic, Artistic, Social, and Conventional interests, the trait variance increased over time. At age 14, all dimensions had substantial trait variance components. The mean-levels of Realistic, Investigative, Artistic, and Conventional interests decreased over the 3 years (–0.44 < d < –0.24). Initial gender differences—with girls having higher Artistic and Social interests and boys having higher Realistic and Investigative interests—increased over time. By investigating the development of vocational interests in late childhood and early adolescence, we complement previous findings and provide first insights about state-trait proportions in early adolescence.

PRICKLE1 × FOCAD Interaction Revealed by Genome-Wide vQTL Analysis of Human Facial Traits

The human face is a highly complex and variable structure resulting from the intricate coordination of numerous genetic and non-genetic factors. Hundreds of genomic loci impacting quantitative facial features have been identified. While these associations have been shown to influence morphology by altering the mean size and shape of facial measures, their effect on trait variance remains unclear. We conducted a genome-wide association analysis for the variance of 20 quantitative facial measurements in 2,447 European individuals and identified several suggestive variance quantitative trait loci (vQTLs). These vQTLs guided us to conduct an efficient search for gene-by-gene (G × G) interactions, which uncovered an interaction between PRICKLE1 and FOCAD affecting cranial base width. We replicated this G × G interaction signal at the locus level in an additional 5,128 Korean individuals. We used the hypomorphic Prickle1Beetlejuice (Prickle1Bj) mouse line to directly test the function of Prickle1 on the cranial base and observed wider cranial bases in Prickle1Bj/Bj. Importantly, we observed that the Prickle1 and Focadhesin proteins co-localize in murine cranial base chondrocytes, and this co-localization is abnormal in the Prickle1Bj/Bj mutants. Taken together, our findings uncovered a novel G × G interaction effect in humans with strong support from both epidemiological and molecular studies. These results highlight the potential of studying measures of phenotypic variability in gene mapping studies of facial morphology.

The Development of Vocational Interests in Early Adolescence: Stability, Change, and State-Trait Components

Vocational interests predict major life outcomes such as job performance, college major choice, and life goals. It is therefore important to gain a better understanding of their development during the crucial years of late childhood and early adolescence, when trait-like interests are starting to develop. The present study investigated the development of vocational interests in a longitudinal sample, comprising N = 3,876 participants—assessed at four time points from ages 11 to 14. Stability, state-trait variance components, mean-level development, and gender differences in mean-levels of Holland’s (1997) RIASEC dimensions were examined. Stabilities were moderate for all dimensions, but Realistic, Investigative, Social, and Conventional interests became more stable over time. For Realistic, Artistic, Social, and Conventional interests, the trait variance increased over time. At age 14, all dimensions had substantial trait variance components. The mean-levels of Realistic, Investigative, Artistic, and Conventional interests decreased over the 3 years (-0.44 &lt; d &lt; -0.24). Initial gender differences—with girls having higher Artistic and Social interests and boys having higher Realistic and Investigative interests—increased over time. By investigating the development of vocational interests in late childhood and early adolescence, we complement previous findings and provide first insights about state-trait proportions in early adolescence.

Within-species trait diversity reorganizes consumer competitive hierarchy and prey community structure in an experimental microbial ecosystem

Phenotypic trait differences between species are expected to play an essential role in community assembly. However, the magnitude of trait variability between individuals of the same species is increasingly recognized to have significant ecological effects, including maintaining species diversity. Here we ask how within-species trait diversity at the consumer trophic level affects consumer competition and prey community dynamics at lower trophic levels in an experimental microbial ecosystem consisting of ciliated protozoa, nematode worms, and bacterial prey. Although the nematode had an inherent competitive advantage and rapidly excluded ciliates with low trait variance, we found that high trait variance in the ciliate inverted the consumer hierarchy, ultimately excluding the nematode. Competition between the high trait variance ciliate and the nematode altered the temporal trajectories of individual prey species in non-additive ways, mediated by prey traits related to growth rate and defense. We performed pairwise co-cultures with each consumer and prey species and found that high trait variance in the ciliate increased the mean prey consumption rate over the low trait variance ciliate, which led to an increase in selective feeding in the presence of all prey species. Overall, our results are consistent with predictions from the coexistence theory framework and are compelling evidence that intraspecific trait diversity in consumer species 1) modulates competitive differences between species at higher trophic levels and 2) generates cascading effects on the community composition at lower trophic levels.

Proprioceptive Genes as a Source of Genetic Variation Underlying Robustness for Flight Performance in Drosophila

A central challenge of quantitative genetics is partitioning phenotypic variation into genetic and non-genetic components. These non-genetic components are usually interpreted as environmental effects; however, variation between genetically identical individuals in a common environment can still exhibit phenotypic variation. A trait's resistance to variation is called robustness, though the genetics underlying it are poorly understood. Accordingly, we performed an association study on a previously studied, whole organism trait: robustness for flight performance. Using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, we surveyed variation across single nucleotide polymorphisms, whole genes, and epistatic interactions to find genetic modifiers robustness for flight performance. There was an abundance of genes involved in the development of sensory organs and processing of external stimuli, supporting previous work that processing proprioceptive cues is important for affecting variation in flight performance. Additionally, we tested insertional mutants for their effect on robustness using candidate genes found to modify flight performance. These results suggest several genes involved in modulating a trait mean are also important for affecting trait variance, or robustness, as well.

More Error than Attitude in Implicit Association Tests (IATs), a CFA-MTMM analysis of measurement error.

Many design characteristics of the popular Implicit Association Test (IAT) appear to make the task highly susceptible to measurement error. This study examined potential sources of measurement error for two types of IAT, the classic verbal IAT (VIAT) and a fully pictorial IAT (PIAT). A CFA-MTMM analytical approach was used to estimate the influence of both random error and method variance on the IAT scores. Four empirical IATs were employed to assess implicit bias towards Middle Eastern and European people (‘Racial’ VIAT and PIAT) and countries (‘Country’ VIAT and PIAT). They were completed by 198 student participants from an Australian University. The CFA-MTMM analysis provided clear evidence of measurement error confounding IAT scores. Specifically, IAT data was shown to be, on average, comprised of just over 50% random error variance, nearly 30% method variance and under 20% trait variance. These results demonstrate unequivocally that IAT scores are predominantly composed of measurement error not implicit attitudes. These findings have significant implications for the use of IATs in applied research. Options for minimising the impact of high error variance in future implicit attitudinal research are considered.