Global diversity in the TAS2R38 bitter taste receptor: Revisiting a classic evolutionary PROPosal

The ability to taste phenylthiocarbamide (PTC) and 6-n-propylthiouracil (PROP) is a polymorphic trait mediated by the TAS2R38 bitter taste receptor gene. It has long been hypothesized that global genetic diversity at this locus evolved under pervasive pressures from balancing natural selection. However, recent high-resolution population genetic studies of TAS2Rs suggest that demographic events have played a critical role in the evolution of these genes. We here utilized the largest TAS2R38 database yet analyzed, consisting of 5,589 individuals from 105 populations, to examine natural selection, haplotype frequencies and linkage disequilibrium to estimate the effects of both selection and demography on contemporary patterns of variation at this locus. We found signs of an ancient balancing selection acting on this gene but no post Out-Of-Africa departures from neutrality, implying that the current observed patterns of variation can be predominantly explained by demographic, rather than selective events. In addition, we found signatures of ancient selective forces acting on different African TAS2R38 haplotypes. Collectively our results provide evidence for a relaxation of recent selective forces acting on this gene and a revised hypothesis for the origins of the present-day worldwide distribution of TAS2R38 haplotypes

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt

Genetic variants of HvCbf14 are statistically associated with frost tolerance in a European germplasm collection of Hordeum vulgare

Two quantitative trait loci (Fr-H1 and Fr-H2) for frost tolerance (FT) have been discovered on the long arm of chromosome 5H in barley. Two tightly linked groups of CBF genes, known to play a key role in the FT regulatory network in A. thaliana, have been found to co-segregate with Fr-H2. Here, we investigate the allelic variations of four barley CBF genes (HvCbf3, HvCbf6, HvCbf9 and HvCbf14) in a panel of European cultivars, landraces and H. spontaneum accessions. In the cultivars a reduction of nucleotide and haplotype diversities in CBFs compared with the landraces and the wild ancestor H. spontaneum, was evident. In particular, in cultivars the loss of HvCbf9 genetic variants was higher compared to other sequences. In order to verify if the pattern of CBF genetic variants correlated with the level of FT, an association procedure was adopted. The pairwise analysis of linkage disequilibrium (LD) among the genetic variants in four CBF genes was computed to evaluate the resolution of the association procedure. The pairwise plotting revealed a low level of LD in cultivated varieties, despite the tight physical linkage of CBF genes analysed. A structured association procedure based on a general liner model was implemented, including the variants in CBFs, of Vrn-H1, and of two reference genes not involved in FT (α-Amy1 and Gapdh) and considering the phenotypic data for FT. Association analysis recovered two nucleotide variants of HvCbf14 and one nucleotide variant of Vrn-H1 as statistically associated to FT

Evaluation of frost resistance in oat

Resistance to biotic and abiotic stress is a crucial aspect for cultivar adaptation to agriculture environments. Among winter cereals, oat is the most frost sensitive and its insufficient level of winterhardiness is the main factor limiting sowing of winter oat in Northern Italy and Central Europe. Frost resistance, the most important component of winterhardiness, is an inducible process promoted by cold exposure and associated with a number of biochemical and molecular changes. We employed field tests and physiological parameters in a set of cultivars released during the last 40 years to explore the genetic variability in frost resistance and identify resistant genotypes. Plants were hardened at +3/+1°C and exposed to freezing temperatures. The efficiency of the excitation capture by open Photosystyem II (PSII) reaction centres was evaluated after freezing, through the chlorophyll fluorescence parameter Fv/Fm, according to Rizza et al. (2001). Different hardening length and pre-hardening temperature (+12/+7°C) were also employed to investigate if a higher level of resistance is associated with the ability to induce early hardening. This capacity is of advantage under field conditions, where temperature falls progressively, because it enables resistant plants to prepare for cold before the susceptible ones. Some significant molecular traits associated to frost resistance such as the accumulation of cor14 (Cattivelli et al., 1995) were also investigated on selected cultivars. Fv/Fm analysis appears as an attractive test being rapid, non invasive and able to monitor a trait related to a crucial mechanism of the resistance acquisition. Significant differences in frost resistance were detected within winter cultivars. The most resistant showed a behaviour similar to that of winter barley, suggesting that it should be possible to improve the resistance of winter oat to a level similar to that of winter barley. Rizza, F. Pagani, D. Cattivelli, C. Stanca, A.M. 2001. Plant Breeding 120: 389-396; Cattivelli, L. Crosatti, C. Rizza, F. 1995 Journal of Genetics & Breeding 49:333-338.vokMyynti MTT tietopalvelu

First Application of a Distance-Based Outlier Approach to Detect Highly Differentiated Genomic Regions Across Human Populations

Genomic scans for positive selection or population differentiation are often used in evolutionary genetics to shortlist genetic loci with potentially adaptive biological functions. However, the vast majority of such tests relies on empirical ranking methods, which suffer from high false positive rates. In this work we computed a modified genetic distance on a 10,000 bp sliding window between sets of three samples each from CHB, CEU and YRI samples from the 1000 Genomes Project. We applied SOLVINGSET, a distance-based outlier detection method capable of mining hundreds of thousands of multivariate entries in a computationally efficient manner, to the average pairwise distances obtained from each window for each CHB-CEU, CHB-YRI and CEU-YRI to compute the top-n genic windows exhibiting the highest scores for the three distances. The outliers detected by this approach were screened for their biological significance, showing good overlap with previously known targets of differentiation and positive selection in human populations

Barley Developmental Mutants: The High Road to Understand the Cereal Spike Morphology

A better understanding of the developmental plan of a cereal spike is of relevance when designing the plant for the future, in which innovative traits can be implemented through pre-breeding strategies. Barley developmental mutants can be a Mendelian solution for identifying genes controlling key steps in the establishment of the spike morphology. Among cereals, barley (Hordeum vulgare L.) is one of the best investigated crop plants and is a model species for the Triticeae tribe, thanks to several characteristics, including, among others, its adaptability to a wide range of environments, its diploid genome, and its self-pollinating mating system, as well as the availability of its genome sequence and a wide array of genomic resources. Among them, large collections of natural and induced mutants have been developed since the 1920s, with the aim of understanding developmental and physiological processes and exploiting mutation breeding in crop improvement. The collections are not only comprehensive in terms of single Mendelian spike mutants, but with regards to double and triple mutants derived from crosses between simple mutants, as well as near isogenic lines (NILs) that are useful for genetic studies. In recent years the integration of the most advanced omic technologies with historical mutation-genetics research has helped in the isolation and validation of some of the genes involved in spike development. New interrogatives have raised the question about how the behavior of a single developmental gene in different genetic backgrounds can help in understanding phenomena like expressivity, penetrance, phenotypic plasticity, and instability. In this paper, some genetic and epigenetic studies on this topic are reviewed

Transcriptome changes associated with cold acclimation in leaves of olive tree (Olea europaea L.)

Olea europaea L. ssp. sativa is an evergreen fruit tree well adapted to the climate conditions of the Mediterranean basin. Its cultivation in northern regions may expose the plants to cold and frost damages during winter, although the maturation of olive fruit in cool environments may provide olive oil with peculiar qualitative characteristics. Thisworkaimsatstudyingshort-andlong-termtranscriptional changes occurring in leaves of olive trees cv. Leccino exposed to a progressive lowering of temperatures, till −4 °C. Followinga RNA-Seqanalysis, a leaf transcriptome comprising 44,332 transcripts has been de novo assembled and 5464 differentially expressed genes (DEGs) identified. Transcriptomic data identified almost all the typical components of the known and conserved molecular repertoire of the plant cold response, including changes in membrane composition-related genes, induction of cold-regulated genes (cor), and transcription factors, and downregulation of photosynthesis-relatedgenes.Besidestheknowncomponents of cold response, we also identified some specific features characterizing the cold response of olive tree. Indeed, during cold acclimation, olive tree leaves induced genes of the glutathione cycle, polyamine and flavonoid pathways, likely to support reactive oxygen species (ROS) scavenging, as well as genes of the raffinose and trehalose biosynthetic pathways to sustain the accumulation of osmolytes. Further, the signaling pathway of abscisic acid (ABA) was strongly implicated, while induction of genes responsible for synthesis of callose and lignins indicated changes in composition of cell wall. In parallel to the transcriptome analysis, a CBF-like transcript has been identified and its expression profile studied in the reference cv. Leccino as well as in seven cvs. differing for cold tolerance

Agrobiodiversity for Adaptive and Yield Traits in Romanian and Italian Barley Cultivars across Four Continental Environments

Within temperate climates the frequency and severity of high and low temperature stresses vary with continentality. The current study reports on the assessment of the performance of 49 barley cultivars across four environments. The cultivars stem from 50 years of breeding activities in Romania and Italy, in two temperate climates that differ in continentality. The plants were phenotyped through stress monitoring, measurements of yield and yield related traits as well as laboratory stress tolerance tests. Genotypes for alleles of vernalisation and photoperiod genes were determined. These genes were significantly associated with frost damage in the field and frost tolerance in laboratory tests. Grain yield (GY) was more closely correlated with the number of grain sinks than with the degree of grain filling indicating major limitations in the vegetative growth phase and during grain initiation. High temperature stress during the grain filling phase significantly reduced GY. Frost damage due to freezing temperatures below −10 °C when plants were not protected by snow cover significantly reduced GY of sensitive cultivars. The characterisation of environmental cues that cause stresses with yield penalties as well as the susceptibility of genetically different cultivars lay the ground for future targeted selection