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We the scientists : how a daring team of parents and doctors forged a new path for medicine
\"Pulitzer Prize-winning reporter Amy Dockser Marcus shows what happened when a group of parents joined forces with doctors and researchers to try to save children's lives. Parents whose children had been diagnosed with the rare and fatal genetic condition Niemann-Pick Type C disease recognized there would never be a treatment in time to save their children if things stayed the same, so the parents set up a collaboration with researchers and doctors in search of a cure. Their social experiment reveals new pathways for treating disease and conducting research\"-- Provided by publisher.
Book
Strong photoperiod sensitivity is controlled by cooperation and competition among Hd1, Ghd7 and DTH8 in rice heading
• Rice (Oryza sativa) is a short-day (SD) plant originally having strong photoperiod sensitivity (PS), with SDs promoting and long days (LDs) suppressing flowering. Although the evolution of PS in rice has been extensively studied, there are few studies that combine the genetic effects and underlying mechanism of different PS gene combinations with variations in PS.
• We created a set of isogenic lines among the core PS-flowering genes Hd1, Ghd7 and DTH8 using CRISPR mutagenesis, to systematically dissect their genetic relationships under different day-lengths. We investigated their monogenic, digenic, and trigenic effects on target gene regulation and PS variation.
• We found that Hd1 and Ghd7 have the primary functions for promoting and repressing flowering, respectively, regardless of day-length. However, under LD conditions, Hd1 promotes Ghd7 expression and is recruited by Ghd7 and/or DTH8 to form repressive complexes that collaboratively suppress the Ehd1-Hd3a/RFT1 pathway to block heading, but under SD conditions Hd1 competes with the complexes to promote Hd3a/RFT1 expression, playing a tradeoff relationship with PS flowering. Natural allelic variations of Hd1, Ghd7 and DTH8 in rice populations have resulted in various PS performances.
• Our findings reveal that rice PS flowering is controlled by crosstalk of two modules – Hd1–Hd3a/RFT1 in SD conditions and (Hd1/Ghd7/DTH8)–Ehd1–Hd3a/RFT1 in LD conditions – and the divergences of these genes provide the basis for rice adaptation to broad regions.
Journal Article
Salt in my soul : an unfinished life
\"Diagnosed with cystic fibrosis at the age of three, Mallory Smith grew into a determined, talented young woman who inspired others even as she raged against her illness. Despite the daily challenges of endless medical treatments and a deep understanding that she'd never lead a normal life, Mallory was determined to 'live happy,' a mantra she followed until her death\"-- Provided by publisher.
Book
Chromosome-specific painting in Thinopyrum species using bulked oligonucleotides
Key messageChromosome-specific painting probes were developed to identify the individual chromosomes from 1 to 7E in Thinopyrum species and detect alien genetic material of the E genome in a wheat background.The E genome of Thinopyrum is closely related to the ABD genome of wheat (Triticum aestivum L.) and harbors genes conferring beneficial traits to wheat, including high yield, disease resistance, and unique end-use quality. Species of Thinopyrum vary from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70), and chromosome structural variation and differentiation have arisen during polyploidization. To investigate the variation and evolution of the E genome, we developed a complete set of E genome-specific painting probes for identification of the individual chromosomes 1E to 7E based on the genome sequences of Th. elongatum (Host) D. R. Dewey and wheat. By using these new probes in oligonucleotide-based chromosome painting, we showed that Th. bessarabicum (PI 531711, EbEb) has a close genetic relationship with diploid Th. elongatum (EeEe), with five chromosomes (1E, 2E, 3E, 6E, and 7E) maintaining complete synteny in the two species except for a reciprocal translocation between 4 and 5Eb. All 14 pairs of chromosomes of tetraploid Th. elongatum have maintained complete synteny with those of diploid Th. elongatum (Thy14), but the two sets of E genomes have diverged. This study also demonstrated that the E genome-specific painting probes are useful for rapid and effective detection of the alien genetic material of E genome in wheat–Thinopyrum derived lines.
Journal Article
The ethics of species : an introduction
\"We are causing species to go extinct at extraordinary rates, altering existing species in unprecedented ways and creating entirely new species. More than ever before, we require an ethic of species to guide our interactions with them. In this book, Ronald L. Sandler examines the value of species and the ethical significance of species boundaries and discusses what these mean for species preservation in the light of global climate change, species engineering and human enhancement. He argues that species possess several varieties of value, but they are not sacred. It is sometimes permissible to alter species, let them go extinct (even when we are a cause of the extinction) and invent new ones. Philosophically rigorous, accessible and illustrated with examples drawn from contemporary science, this book will be of interest to students of philosophy, bioethics, environmental ethics and conservation biology\"-- Provided by publisher.
Book
A draft genome assembly and resequencing analysis of Chinese cherry (Cerasus pseudocerasus) reveal structural variants associated with fruit traits
Chinese cherry (Cerasus pseudocerasus) is a significant fruit crop that enjoys widespread cultivation in China. Here, we report a draft autotetraploid genome assembly of the Chinese cherry cultivar ‘Huangguo’, characterized by a size of 340.99 Mb and comprised of 261,760 contig sequences. We further obtained resequencing data of eight Chinese cherry varieties, with an average sequencing depth of approximately 57 × per individual. Population structure analysis revealed that the eight varieties were partitioned into two distinct groups. Additionally, the genetic relationship matrix analysis indicated that ‘Changbing’ and ‘Duanbing’ shared the closest genetic background. Moreover, we have creatively established a workflow for transforming heterozygous genotypes from diploid format to tetraploid format by conducting secondary genotyping in deletion structural variations. Through this process, we initially screened out structural variants associated with the fruit peel color and size of Chinese cherry. In summary, this study provides valuable resources for population genetic relationships and will advance functional genomics studies in Chinese cherry and other crops.
Journal Article
Genomic prediction of agronomic traits in wheat using different models and cross-validation designs
Key messageGenomic predictions across environments and within populations resulted in moderate to high accuracies but across-population genomic prediction should not be considered in wheat for small population size.Genomic selection (GS) is a marker-based selection suggested to improve the genetic gain of quantitative traits in plant breeding programs. We evaluated the effects of training population (TP) composition, cross-validation design, and genetic relationship between the training and breeding populations on the accuracy of GS in spring wheat (Triticum aestivum L.). Two populations of 231 and 304 spring hexaploid wheat lines that were phenotyped for six agronomic traits and genotyped with the wheat 90 K array were used to assess the accuracy of seven GS models (RR-BLUP, G-BLUP, BayesB, BL, RKHS, GS + de novo GWAS, and reaction norm) using different cross-validation designs. BayesB outperformed the other models for within-population genomic predictions in the presence of few quantitative trait loci (QTL) with large effects. However, including fixed-effect marker covariates gave better performance for an across-population prediction when the same QTL underlie traits in both populations. The accuracy of prediction was highly variable based on the cross-validation design, which suggests the importance to use a design that resembles the variation within a breeding program. Moderate to high accuracies were obtained when predictions were made within populations. In contrast, across-population genomic prediction accuracies were very low, suggesting that the evaluated models are not suitable for prediction across independent populations. On the other hand, across-environment prediction and forward prediction designs using the reaction norm model resulted in moderate to high accuracies, suggesting that GS can be applied in wheat to predict the performance of newly developed lines and lines in incomplete field trials.
Journal Article
Genetic relationship analysis and core collection construction of Eucalyptus grandis from Dongmen improved variety base: the largest eucalypt germplasm resource in China
Background
Eucalyptus grandis
, which was first comprehensively and systematically introduced to China in the 1980s, is one of the most important fast-growing tree species in the forestry industry. However, to date, no core collection has been selected from the germplasm resources of
E. grandis
based on growth and genetic relationship analysis.
Results
In the present study, 545 individuals of
E. grandis
collected from 28 populations across 5 countries were selected for genetic diversity analysis using 16 selected SSR markers. The polymorphism information content (
PIC
) was employed to assess genetic diversity, yielding a mean value of 0.707. Genetic structure analysis was conducted on 492 individuals from 13 combined populations, revealing three clusters as the most suitable number. Principal coordinate analysis (PCoA) demonstrated that the populations were divided into three major clusters. Additionally, the analysis of molecular variance (AMOVA) indicated that the majority of variation occurred within populations.
Conclusions
Based on the criteria for screening the core collection, we constructed a population consisting of 158 individuals and created unique fingerprinting codes. These results provide a crucial theoretical foundation for the protection and utilization of germplasm resources of
E. grandis
in China, which will be helpful in the selection of genetically distant parents for future multigenerational hybridization programs.
Journal Article
Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis Benth
Mesona chinensis Benth (MCB) is one of the main economic crops in tropical and subtropical areas. To understand the codon usage bias (CUB) in M. chinensis Benth, chloroplast genome is essential to study its genetic law, molecular phylogenetic relationships, and exogenous gene expression. Results showed that the GC content of 53 CDS sequences was 37.95%, and GC1, GC2, and GC3 content were 46.02%, 38.26%, and 29.85%, respectively. The general GC content order was GC1>GC2>GC3. Moreover, the majority of genes had an effective number of codon (ENC) value greater than 40, except ndhE, rps8, and rps18. Correlation analysis results revealed that the GC content was significantly correlated with GC1, GC2, GC3, and ENC. Neutrality plot analysis, ENC-plot analysis, and PR2-plot analysis presented that the CUB of M. chinensis Benth chloroplast genome was mainly affected by mutation and selection. In addition, GGG, GCA, and TCC were found to be the optimal codons. Furthermore, results of cluster analysis and evolutionary tree showed that M. chinensis Benth was closely related to Ocimum basilicum, indicating that there was a certain correlation between the CUB of the chloroplast gene and the genetic relationship of plant species. Overall, the study on the CUB of chloroplast genome laid a basis for genetic modification and phylogenetic research of M. chinensis Benth chloroplast genome.
Journal Article
Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus
Key messageA single recessive gene for complete resistance to powdery mildew and a major-effect QTL for partial resistance to downy mildew were co-localized in aCucumis hystrixintrogression line of cucumber.Downy mildew (DM) and powdery mildew (PM) are two major foliar diseases in cucumber. DM resistance (DMR) and PM resistance (PMR) may share common components; however, the genetic relationship between them remains unclear. IL52, a Cucumis hystrix introgression line of cucumber which has been reported to possess DMR, was recently identified to exhibit PMR as well. In this study, a single recessive gene pm for PMR was mapped to an approximately 468-kb region on chromosome 5 with 155 recombinant inbred lines (RILs) and 193 F2 plants derived from the cross between a susceptible line ‘changchunmici’ and IL52. Interestingly, pm was co-localized with the major-effect DMR QTL dm5.2 confirmed by combining linkage analysis and BSA-seq, which was consistent with the observed linkage of DMR and PMR in IL52. Further, phenotype–genotype correlation analysis of DMR and PMR in the RILs indicated that the co-localized locus pm/dm5.2 confers complete resistance to PM and partial resistance to DM. Seven candidate genes for DMR were identified within dm5.2 by BSA-seq analysis, of which Csa5M622800.1, Csa5M622830.1 and Csa5M623490.1 were also the same candidate genes for PMR. A single nucleotide polymorphism that is present in the 3ˊ untranslated region (3′UTR) of Csa5M622830.1 co-segregated perfectly with PMR. The GATA transcriptional factor gene Csa5M622830.1 may be a likely candidate gene for DMR and PMR. This study has provided a clear evidence for the relationship between DMR and PMR in IL52 and sheds new light on the potential value of IL52 for cucumber DMR and PMR breeding program.
Journal Article