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Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)

Many apple cultivars are subject to biennial fluctuations in flowering and fruiting. It is believed that this phenomenon is caused by a repressive effect of developing fruit on the initiation of flowers in the apex of proximal bourse shoots. However, the genetic pathways of floral initiation are incompletely described in apple, and the biological nature of floral repession by fruit is currently unknown. In this study, we characterize the transcriptional landscape of bourse shoot apices in the biennial cultivar, 'Honeycrisp', during the period of floral initiation, in trees bearing a high fruit load and in trees without fruit. Trees with high fruit load produced almost exclusively vegetative growth in the subsequent year, whereas the trees without fruit produced flowers on the majority of the potential flowering nodes. Using RNA-based sequence data, we documented gene expression at high resolution, identifying >11,000 transcripts that had not been previously annotated, and characterized expression profiles associated with vegetative growth and flowering. We also conducted a census of genes related to known flowering genes, organized the phylogenetic and syntenic relationships of these genes, and compared expression among homologs. Several genes closely related to AP1, FT, FUL, LFY, and SPLS were more strongly expressed in apices from non-bearing, floral-determined trees, consistent with their presumed floral-promotive roles. In contast, a homolog of TFL1 exhibited strong and persistent up-regulation only in apices from bearing, vegetative-determined trees, suggesting a roles in floral repression. Additionally, we identified four GIBBERELLIC ACID (GA) 2 OXIDASE genes that were expressed to relatively high levels in apices from bearing trees. These results define the flowering-related transcriptional landscape in apple, and strongly support previous studies implicating both gibberellins and TFL1 as key components in repression of flowering by fruit.

Genetic structure in populations of Euterpe precatoria Mart. in the Brazilian Amazon

Euterpe precatoria is a palm tree belonging to the Arecaceae family, occurring in Western and Central Brazilian Amazonia Its fruit, which is very appreciated in the Amazon region, produces pulp that is consumed in fresh form. Its production is carried out almost exclusively by extractive farmers. In order to establish adequate strategies to sustain this genetic resource. We need knowledge about its diversity and genetic structure in natural populations. This study aimed to evaluate the influence of geographic distance on genetic structure in the main extractive populations of E. precatoria in the Brazilian Amazon. Leaves from 377 plants were collected in 19 populations located in 16 municipalities in the State of Amazonas and three in the State of Rondônia. Twelve microsatellite loci were used to genotype the plants. The diversity and genetic structure among populations were estimated. The average number of alleles per locus was 5.97. The observed heterozygosity means (HO) were higher than expected (HE) at the population level (HO = 0.72, HE = 0.66) and fixation index (f = -0.100) was negative. The FST value (0.1820) and the AMOVA results (17.961) showed population structure. The populations were clustered into three groups (K = 3) in Bayesian analysis. The Discriminant Analysis of Principal Components (DAPC) confirmed eight clusters, with the populations close to those identified by the Bayesian analysis. The geographic differentiation was confirmed by the groupings obtained in the analyses by the Structure program and the DACP function. Information related to phenotypic, genetic and environmental characterization of populations is important to guide conservation and management strategies and the formulation of public species management policies in Amazonian.

Genetic insights into the globally invasive and taxonomically problematic tree genus Prosopis

Accurate taxonomic identification of alien species is crucial to detect new incursions, prevent or reduce the arrival of new invaders and implement management options such as biological control. Globally, the taxonomy of non-native Prosopis species is problematic due to misidentification and extensive hybridization. We performed a genetic analysis on several Prosopis species, and their putative hybrids, including both native and non-native populations, with a special focus on Prosopis invasions in Eastern Africa (Ethiopia, Kenya and Tanzania). We aimed to clarify the taxonomic placement of non-native populations and to infer the introduction histories of Prosopis in Eastern Africa. DNA sequencing data from nuclear and chloroplast markers showed high homology (almost 100%) between most species analysed. Analyses based on seven nuclear microsatellites confirmed weak population genetic structure among Prosopis species. Hybrids and polyploid individuals were recorded in both native and non-native populations. Invasive genotypes of P. juliflora in Kenya and Ethiopia could have a similar native Mexican origin, while Tanzanian genotypes likely are from a different source. Native Peruvian Prosopis pallida genotypes showed high similarity with non-invasive genotypes from Kenya. Levels of introduced genetic diversity, relative to native populations, suggest that multiple introductions of P. juliflora and P. pallida occurred to Eastern Africa. Polyploidy may explain the successful invasion of P. juliflora in Eastern Africa. The polyploid Prosopis juliflora was highly differentiated from the rest of the (diploid) species within the genus. The lack of genetic differentiation between most diploid species in their native ranges supports the notion that hybridization between allopatric species may occur frequently when they are co-introduced into non-native areas. For regulatory purposes, we propose to treat diploid Prosopis taxa from the Americas as a single taxonomic unit in non-native ranges.

FIGURE S1. Automatic Barcode Gap Discovery genetic distances calculated for 18 Asteronotus Ehrenberg, 1831 in A tale of two genera: the revival of Hoplodoris (Nudibranchia: Discodorididae) with the description of new species of Hoplodoris and Asteronotus

FIGURE S1. Automatic Barcode Gap Discovery genetic distances calculated for 18 Asteronotus Ehrenberg, 1831 and Hoplodoris Bergh, 1880 COI sequences using three genetic distance calculations: (A) Jukes-Cantor (JC69); (B) Kimura (K80); (C) Simple Distance. Presumed intraspecific variation is shown in white, interspecific variation in grey.

Data from: Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney

The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterise the effects of BP index variants from genome-wide association studies (GWAS) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired 49 BP-GWAS kidney genes with 210 licensed drugs. Our colocalisation and Mendelian randomisation analyses identified 179 unique kidney genes with evidence of putatively causal effects on BP. Through Mendelian randomisation we uncovered effects of BP on renal outcomes commonly affecting hypertensive patients. Collectively, our studies identified genetic variants, kidney genes, molecular mechanisms and biological pathways of key relevance to the genetic regulation of BP and inherited susceptibility to hypertension.

Rapid reversal of a potentially constraining genetic covariance between leaf and flower traits in Silene latifolia

Genetic covariance between two traits generates correlated responses to selection, and may either enhance or constrain adaptation. Silene latifolia exhibits potentially constraining genetic covariance between specific leaf area and flower number in males. Flower number is likely to increase via fecundity selection but the correlated increase in specific leaf area increases mortality, and specific leaf area is under selection to decrease in dry habitats. We selected on trait combinations in two selection lines for four generations to test whether genetic covariance could be reduced without significantly altering trait means. In one selection line, the genetic covariance changed sign and eigenstructure changed significantly, while in the other selection line eigenstructure remained similar to the control line. Changes in genetic variance-covariance structure are therefore possible without the introduction of new alleles, and the responses we observed suggest that founder effects and changes in frequency of alleles of major effect may be acting to produce the changes.

opencc-zeroOct 2021View details →

Asymmetric acoustic signal recognition led to asymmetric genetic introgression between two parapatric rhacophorid treefrogs

Correct discrimination between courtship signals could help maintain genetic integrity between closely related species. However, asymmetric usage of signals might cause asymmetric magnitude of gene flow across the contact zone. Buergeria japonica and B. otai are sibling species with parapatric distribution pattern in Taiwan, forming two narrow contact zones in eastern and western sides of the island. Both species use a shared acoustic signal of calls (Type 1a/1b), whereas B. otai presents another unique call type (Type 2) which never appears in B. japonica. Combining behavioral experiments with genome-wide RAD-seq analyses, we aim to test whether the ability of signal recognition influences genetic introgression across their species boundary. The playback experiments showed that the western population of B. otai has evolved a stronger level of reproductive character displacement by showing the inclusive usage of their unique Type 2 signal. In contrast, the eastern population used both unique and shared signals and has a stronger preference for the latter. Consistent with behavioral difference, genetic introgression across the contact zone was detected only in the eastern boundary but not in the western one. Furthermore, the gene flow in this contact zone tends to be unidirectional from B. japonica toward B. otai. Our results support the prediction that a more specialized signal user might have a higher probability to maintain their genetic integrity compared to a generalized signal user.

Genetic barcoding of museum eggshell improves data integrity of avian biological collections

Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three sampling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird's egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen's appearance or integrity. This method proved superior to swabbing the external surface or sampling the interior; however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species' accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.

Data from: Genetic diversity of the rain tree (Albizia saman) in Colombian seasonally dry tropical forest for informing conservation and restoration interventions

Albizia saman is a multipurpose tree species of seasonally dry tropical forests (SDTFs) of Mesoamerica and northern South America typically cultivated in silvopastoral and other agroforestry systems around the world, a trend that is bound to increase in light of multimillion hectare commitments for forest and landscape restoration. The effective conservation and sustainable use of A. saman requires detailed knowledge of its genetic diversity across its native distribution range of which surprisingly little is known to date. We assessed the genetic diversity and structure of A.saman across twelve representative locations of SDTF in Colombia, and how they may have been shaped by past climatic changes and human influence. We found four different genetic groups which may be the result of differentiation due to isolation of populations in pre-glacial times. The current distribution and mixture of genetic groups across STDF fragments we observed might be the result of range expansion of SDTFs during the last glacial period followed by range contraction during the Holocene and human-influenced movement of germplasm associated with cattle ranching. Despite the fragmented state of the presumed natural A. saman stands we sampled we did not find any signs of inbreeding, suggesting that gene flow is not jeopardized in humanized landscapes. However, further research is needed to assess potential deleterious effects of fragmentation on progeny. Climate change is not expected to seriously threaten the in situ persistence of A. saman populations and might present opportunities for future range expansion. However, the sourcing of germplasm for tree planting activities needs to be aligned with the genetic affinity of reference populations across the distribution of Colombian SDTFs. We identify priority source populations for in situ conservation based on their high genetic diversity, lack or limited signs of admixture and/or genetic uniqueness.

Quantitative genetics of phosphorus content in the freshwater herbivore, Daphnia pulicaria

1. Phosphorus (P) is essential for growth of all organisms, and P content is correlated with growth in most taxa. Although P content was initially considered to be a trait fixed at the species level, there is growing evidence for considerable intraspecific variation. Selection on such variation can thus alter the rates at which P fluxes through food webs. 2. Nevertheless, prior work describing the sources and extent of intraspecific variation in P content were not genetically explicit, confounded by unknown genetic background and evolutionary history. We constructed an F2 recombinant population of the dominant freshwater grazer, Daphnia pulicaria to mitigate such issues. 3. F2 recombinants exhibited considerable variation in growth rate, P content (0.49% to 1.97%), P use efficiency (PUE; 51 to 208 mg biomass/mg P), and correlated traits such as hatching time of resting eggs, in common garden conditions. 4. These results clearly demonstrate the scope of genetic recombination in generating variation in ecologically-relevant traits. The absence of environmental selection is a likely component driving such variation not observed in natural settings. 5. Although phosphoglucose isomerase (PGI) genotype was significantly associated with variation in hatching time of resting eggs, contrary to prior work with less rigorous designs, allelic variation at the PGI locus did not explain variation in P content and PUE of Daphnia, indicating that such quantitative traits are under polygenic control. 6. Together, these results suggest that although there is considerable genetic scope for variation in key ecologically-relevant traits, such as P content and efficiency of P use, these traits are likely under strong stabilizing selection, most likely due to selection on growth rate and size. Importantly, our observations suggest that anthropogenic alterations to P supply due to eutrophication could alter selection on these traits, thereby rapidly altering the role Daphnia plays in the P cycle of lakes.

Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering

Molecular epidemiology using genomic data can help identify relationships between malaria parasite population structure, malaria transmission intensity, and ultimately help generate actionable data to assess the effectiveness of malaria control strategies. Genomic data, coupled with geographic information systems data, can further identify clusters or hotspots of malaria transmission, parasite genetic and spatial connectivity, and parasite movement by human or mosquito mobility over time and space. In this study, we performed longitudinal genomic surveillance in a cohort of 70 participants over four years from different neighborhoods and households in Thiès, Senegal—a region of exceptionally low malaria transmission (entomological inoculation rate (EIR) less than 1). Genetic identity (identity by state) was established using a 24 single nucleotide polymorphism molecular barcode and a multivariable linear regression model was used to establish genetic and spatial relationships. Our results show clustering of genetically similar parasites within households and a decline in genetic similarity of parasites with increasing distance. One household showed extremely high diversity and warrants further investigation as to the source of these diverse genetic types. This study illustrates the utility of genomic data with traditional epidemiological approaches for surveillance and detection of trends and patterns in malaria transmission not only by neighborhood but also by household. This approach can be implemented regionally and countrywide to strengthen and support malaria control and elimination efforts.

opencc-zeroDec 2021View details →

Comparative analysis of genetic and morphological variation within the Platanthera hyperborea complex (Orchidaceae)

Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America.

The distribution and spread of naturally occurring Medea selfish genetic elements in the United States

Selfish genetic elements (SGEs) are DNA sequences that are transmitted to viable offspring in greater than Mendelian frequencies. Medea SGEs occur naturally in some populations of red flour beetle (Tribolium castaneum) and are expected to increase in frequency within populations and spread among populations. The large-scale USA distributions of Medea-4 (M4) had been mapped based on samples from 1993-1995. We sampled beetles in 2011-2014 and show that the distribution of M4 in the United States is dynamic and has shifted southward. By using a genetic marker of Medea-1 (M1), we found five unique geographic clusters with high- and low M1 frequencies in a pattern not predicted by microsatellite-based analysis of population structure. Our results indicate absence of rigid barriers to Medea spread in the USA, so assessment of what factors have limited its current distribution require further investigation. There is great interest in using synthetic SGEs, including synthetic Medea, to alter or suppress pest populations, but there is concern about unpredicted spread of these SGE's and potential for populations to become resistant to them. The finding of patchy distributions of Medea elements suggests that released synthetic SGEs cannot always be expected to spread uniformly, especially in target species with limited dispersal.

opencc-zeroNov 2019View details →

Eco-genetic additivity of diploids in allopolyploid wild wheats

Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modeling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonized wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.

FIGURE 7 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

FIGURE 7. Scatter plot of Multivariate Principal Component Analysis (PCA) for male individuals using 13 morphometric characters marked as * Supplementary file Table 1 transformed to their ratio to SVL for Minervarya species A (M. species A) and Minervarya species B (M. species B)

FIGURE 3 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

FIGURE 3. Morphological characters of Minervarya species A and Minervarya species B. Minervarya species A (A) and Minervarya species B (B) in life. Note the longitudinal skin folds on dorsal side of Minervarya species A and granular blotches on Minervarya species B. Difference in the webbing pattern on the foot of Minervarya species A (C) and Minervarya species B (D).

FIGURE 10 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

FIGURE 10. Morphological variation in Minervarya syhadrensis frogs from different localities in the Western Ghats. (A and B) Coorg, (C) Goa, (D) Koyna, (E) Silvasa and (F) Calicut.

FIGURE 9 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

FIGURE 9. Dorsal view of M. syhadrensis (Minervarya species A collected for the present study, ZSI/WRC/A/2255) and M. caperata (type specimen BNHS4657). Note the presence of longitudinal skin folds on dorsal side. Scale bar = 1cm.

FIGURE 5 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

FIGURE 5. Advertisement call of Minervarya species B. Microtemporal structure (A) and spectrogram (B) of a call group. (C) Microtemporal structure of a call depicting its pulsatile nature.

FIGURE 2 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

FIGURE 2. Type specimen of Minervarya syhadrensis (ZSI 19764). Note the presence of longitudinal skin folds on dorsal side. Scale bar = 1cm.