Patterns of genomic and phenomic diversity in wine and table grapes.

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes

Navigating Accent Variation: A Developmental Perspective

Adult processing of other-accented speech is fast, dependent on lexical access, and readily generalizable to new words. But what does children's processing of other-accented speech look like? Although many acquisition researchers have emphasized how other-accented speech presents a formidable challenge to young children, we argue that the field has perhaps underestimated children's early accent processing abilities. In support of this view, we present evidence that 2-year-olds’ accent processing abilities appear to be in many respects adult-like, and discuss the growing literature on children's ability to cope with multi-accent input in the natural world. We outline different theoretical outlooks on the transition children make from infancy to later childhood, and discuss how the growing sophistication of infants’ accent processing abilities feeds into their social perception of the world (and perhaps vice versa). We also argue that efficient processing and meaningful interpretation of accent variation are fundamental to human cognition, and that early proficiency with accent variation (along with all of the implied representational and learning capacities) is difficult to explain without assuming the early emergence of abstract speech representations

The effect of accent exposure on children’s sociolinguistic evaluation of peers

Language and accent strongly influence the formation of social groups. By five years of age, children already show strong social preferences for peers who speak their native language with a familiar accent (Kinzler, Shutts, DeJesus, & Spelke, 2009). However, little is known about the factors that modulate the strength and direction of children’s accent-based group preferences. In three experiments, we examine the development of accent-based friendship preferences in children growing up in Toronto, one of the world’s most linguistically and culturally diverse cities. We hypothesized that the speaker’s type of accent and the amount of accent exposure children experienced in their everyday lives would modulate their preferences in a friend selection task. Despite literature suggesting that exposure leads to greater acceptance (Allport, 1954), we find no evidence that routine exposure to different accents leads to greater acceptance of unfamiliarly accented speakers. Children still showed strong preferences for peers who spoke with the locally dominant accent, despite growing up in a linguistically diverse community. However, children’s preference for Canadian-accented in-group members was stronger when they were paired with non native (Korean-accented) speakers compared to when they were paired with regional (British-accented) speakers. We propose that children’s ability to perceptually distinguish between accents may have contributed to this difference. Children showed stronger preferences for in-group members when the difference between accents was easier to perceive. Overall, our findings suggest that although the strength of accent-based social preferences can be modulated by the type of accent, these preferences still persist in the face of significant diversity in children’s accent exposure

Genetic structure and domestication history of the grape

The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germ-plasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity

Phosphoinositide-dependent kinase 1 controls migration and malignant transformation but not cell growth and proliferation in PTEN-null lymphocytes

In normal T cell progenitors, phosphoinositide-dependent kinase l (PDK1)–mediated phosphorylation and activation of protein kinase B (PKB) is essential for the phosphorylation and inactivation of Foxo family transcription factors, and also controls T cell growth and proliferation. The current study has characterized the role of PDK1 in the pathology caused by deletion of the tumor suppressor phosphatase and tensin homologue deleted on chromosome 10 (PTEN). PDK1 is shown to be essential for lymphomagenesis caused by deletion of PTEN in T cell progenitors. However, PTEN deletion bypasses the normal PDK1-controlled signaling pathways that determine thymocyte growth and proliferation. PDK1 does have important functions in PTEN-null thymocytes, notably to control the PKB–Foxo signaling axis and to direct the repertoire of adhesion and chemokine receptors expressed by PTEN-null T cells. The results thus provide two novel insights concerning pathological signaling caused by PTEN loss in lymphocytes. First, PTEN deletion bypasses the normal PDK1-controlled metabolic checkpoints that determine cell growth and proliferation. Second, PDK1 determines the cohort of chemokine and adhesion receptors expressed by PTEN-null cells, thereby controlling their migratory capacity

Input matters: speed of word recognition in 2-year-olds exposed to multiple accents

Although studies investigating language abilities in young children exposed to more than one language have become common, there is still surprisingly little research examining language development in children exposed to more than one accent. Here, we report two looking-while-listening experiments examining the impact of routine home exposure to multiple accents on 2-year-olds’ word recognition abilities. In Experiment 1, we found that monolingual English-learning 24-month-olds who routinely receive exposure to both Canadian English and a non-native variant of English are less efficient in their recognition of familiar words spoken in Canadian English than monolingual English-learning 24-month-olds who hear only Canadian English at home. In Experiment 2, we found that by 34 months of age all children recognize words equally quickly regardless of their accent exposure at home. We conclude that monolingual toddlers in some locations may form a less homogeneous population than past work has assumed, a factor that should be considered when drawing generalizations about language development across different populations

Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation

Genic and nongenic contributions to natural variation of quantitative traits in maize

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene-targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%-59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions