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Forensic Colonialism
Forensic genetic technologies are popularly conceptualized and
revered as important tools of justice. The research and development
of these technologies, however, has been accomplished through the
capture of various Indigenous Peoples' genetic material and a
subsequent ongoing genetic servitude. In Forensic
Colonialism Mark Munsterhjelm explores how controversial
studies of Indigenous Peoples have been used to develop racializing
forensic technologies. Making moral and political claims about
defending the public from criminals and terrorists, international
networks of scientists, police, and security agencies have
developed forensic genetic technologies firmly embedded in
hierarchies that target and exploit many Indigenous Peoples without
their consent. Collections began under the guise of the highly
controversial Human Genome Diversity Project and related efforts,
including the 1987 sampling of Brazilian Indigenous Peoples as they
recovered from near genocide. After 9/11, War on Terror rhetoric
began to be used to justify research on ancestry estimation and
physical appearance (phenotyping) markers, and since 2019,
international research cooperation networks' use of genetic data
from thousands of Uyghurs and other Indigenous Peoples from
Xinjiang and Tibet has contributed to a series of controversies.
Munsterhjelm concludes that technologies produced by forensic
genetics advance the biopolitical security only of privileged
populations, and that this depends on imposing race-based divisions
between who lives and who dies. Meticulously researched,
Forensic Colonialism adds to growing debates over racial
categories, their roots in colonialism, and the political
hierarchies inherent to forensic genetics.
eBook
Fine mapping of the BnaC04.BIL1 gene controlling plant height in Brassica napus L
Background
Plant height is an important architecture trait which is a fundamental yield-determining trait in crops. Variety with dwarf or semi-dwarf phenotype is a major objective in the breeding because dwarfing architecture can help to increase harvest index, increase planting density, enhance lodging resistance, and thus be suitable for mechanization harvest. Although some germplasm or genes associated with dwarfing plant type have been carried out. The molecular mechanisms underlying dwarfism in oilseed rape (
Brassica napus
L.) are poorly understood, restricting the progress of breeding dwarf varieties in this species. Here, we report a new dwarf mutant
Bndwarf2
from our
B. napus
germplasm. We studied its inheritance and mapped the dwarf locus
BnDWARF2
.
Results
The inheritance analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped in an interval of 787.88 kb on the C04 chromosome of
B. napus
by Illumina Brassica 60 K Bead Chip Array. To fine-map
BnDWARF2
, 318 simple sequence repeat (SSR) primers were designed to uniformly cover the mapping interval. Among them, 15 polymorphic primers that narrowed down the
BnDWARF2
locus to 34.62 kb were detected using a F
2:3
family population with 889 individuals. Protein sequence analysis showed that only BnaC04.BIL1 (BnaC04g41660D) had two amino acid residues substitutions (Thr187Ser and Gln399His) between ZS11 and
Bndwarf2
, which encoding a GLYCOGEN SYNTHASE KINASE 3 (GSK3-like). The quantitative real-time PCR (qRT-PCR) analysis showed that the
BnaC04.BIL1
gene expressed in all tissues of oilseed rape. Subcellular localization experiment showed that BnaC04.BIL1 was localized in the nucleus in tobacco leaf cells. Genetic transformation experiments confirmed that the
BnaC04.BIL1
is responsible for the plant dwarf phenotype in the
Bndwarf2
mutants. Overexpression of
BnaC04.BIL1
reduced plant height, but also resulted in compact plant architecture.
Conclusions
A dominant dwarfing gene,
BnaC04.BIL1
, encodes an GSK3-like that negatively regulates plant height, was mapped and isolated. Our identification of a distinct gene locus may help to improve lodging resistance in oilseed rape.
Journal Article
Detection of Expressed Otx mRNA Isoforms in Sea Urchins by Mapping NGS Reads to Single-Gene/Transcript Sequences
The identification of mRNA isoforms in biological samples is crucial for studying tissue- and cell-specific isoform expression, activity of tissue-specific promoters, alternative splicing events, and alternative polyadenylation signals in genes. For single or several genes, expressed mRNA isoforms can be found using RT-PCR and RT-qPCR. Available transcriptome short-read archives deposited in GenBank or as laboratory data can be used to identify mRNA isoforms instead of or prior to wet analysis by other methods in eukaryotic organisms with annotated genomes. However, isoform expression analysis requires advanced bioinformatics skills and may be time-consuming. In addition, this analysis generates a large amount of unnecessary data. To detect mRNA isoforms encoded by one gene of interest, screening of expressed mRNAs in NGS data can be simplified by mapping NGS short reads to a single-gene or transcript sequence. Using single-gene/transcript mapping, we analyzed the expression of the Otx gene at the mRNA isoform level in some embryonic and adult tissue mRNA libraries of the sea urchin Strongylocentrotus purpuratus available in GenBank. The presence of expressed Otx mRNA isoforms was confirmed by RT-qPCR in the same tissues and at the same developmental stages of the closely related species Strongylocentrotus intermedius. We showed that single-gene/transcript mapping is a suitable approach for qualitative evaluation of the expression of mRNA isoforms and recognition of at least two expressed isoforms in the same biological sample.
Journal Article
Novel early‐onset Alzheimer‐associated genes influence risk through dysregulation of glutamate, immune activation, and intracellular signaling pathways
INTRODUCTION Most genetic studies for Alzheimer's disease (AD) have been focused on late‐onset AD (LOAD). There are no large genetic studies on early‐onset AD (EOAD). METHODS We performed a multi‐ancestry (non‐Hispanic European, African, and East Asian) genome‐wide association study (GWAS) including a total of 7,349 cases and 17,887 control. Cases with age at onset younger than 70 years were included. Sensitivity analysis including cases with onset <65 was performed. Only controls older than 70 were included to decrease the risk of developing LOAD. RESULTS We identified eight novel significant loci: six in the ancestry‐specific analyses and two in the trans‐ancestry analysis. By integrating gene‐based analysis, expression quantitative trait loci (eQTL), protein quantitative trait loci (pQTL), and functional annotations, we nominate eight novel genes that are involved in microglia activation, glutamate production, and signaling pathways. DISCUSSION EOAD, although sharing genes with LOAD, harbors unique genes and pathways that could be used to create better prediction models or target identification. Highlights We performed the largest and first multi‐ethnic genetic screening for early‐onset Alzheimer's disease (AD). We identified eight novel significant loci: six in the ancestry‐specific analyses and two in the trans‐ancestry analysis. The novel genes are implicated microglia activation, glutamate production, and signaling pathways. EOAD, although sharing many genes with LOAD, harbors unique genes and pathways that could be used to create better prediction models or target identification for this type of AD.
Journal Article
Combinations of Independent Dominant Loci Conferring Clubroot Resistance in All Four Turnip Accessions (Brassica rapa) From the European Clubroot Differential Set
Clubroot disease is devastating to
crop production when susceptible cultivars are planted in infected fields. European turnips are the most resistant sources and their resistance genes have been introduced into other crops such oilseed rape (
L.), Chinese cabbage and other
vegetables. The European clubroot differential (ECD) set contains four turnip accessions (ECD1-4). These ECD turnips exhibited high levels of resistance to clubroot when they were tested under controlled environmental conditions with Canadian field isolates. Gene mapping of the clubroot resistance genes in ECD1-4 were performed and three independent dominant resistance loci were identified. Two resistance loci were mapped on chromosome A03 and the third on chromosome A08. Each ECD turnip accession contained two of these three resistance loci. Some resistance loci were homozygous in ECD accessions while others showed heterozygosity based on the segregation of clubroot resistance in 20 BC
families derived from ECD1 to 4. Molecular markers were developed linked to each clubroot resistance loci for the resistance gene introgression in different germplasm.
Journal Article
A Robust and Rapid Candidate Gene Mapping Pipeline Based on M2 Populations
The whole-genome sequencing-based bulked segregant analysis (WGS-BSA) has facilitated the mapping candidate causal variations for cloning target plant genes. Here, we report an improved WGS-BSA method termed as M2-seq to expedite the mapping candidate mutant loci by studying just M 2 generation. It is an efficient mutant gene mapping tool, rapid, and comparable to the previously reported approaches, such as Mutmap and Mutmap+ that require studying M 3 or advanced selfed generations. In M2-seq, background variations among the M 2 populations can be removed efficiently without knowledge of the variations of the wild-type progenitor plant. Furthermore, the use of absolute delta single-nucleotide polymorphism (SNP) index values can effectively remove the background variation caused by repulsion phase linkages of adjacent mutant alleles; and thereby facilitating the identification of the causal mutation in target genes. Here, we demonstrated the application of M2-seq in successfully mapping the genomic regions harboring causal mutations for mutant phenotypes among 10 independent M 2 populations of soybean. The mapping candidate mutant genes just in M 2 generation with the aid of the M2-seq method should be particularly useful in expediting gene cloning especially among the plant species with long generation time.
Journal Article
Mapping and validation of all-stage resistance to stem rust in four South African winter wheat cultivars
Several South African winter wheat cultivars express all-stage resistance to local races of Puccinia graminis f. sp. tritici (Pgt). To study the inheritance of resistance, cultivars Komati, Koonap, Limpopo and SST 387 were crossed with the stem rust susceptible Line 37-07. Segregation of reaction to Pgt race PTKST in each of the four F2 populations indicated the presence of a single dominant resistance gene. Allelism tests among the resistant parents indicated that the same gene, alleles of the same gene, or closely linked genes were involved. The resistance gene(s) mapped to the short arm of chromosome 6D and was flanked by SSR markers barc183 and wms4862. The four cultivars tested negative using single nucleotide polymorphism (SNP) markers linked to Sr42, SrTmp and SrCad also located on chromosome arm 6DS. Allelism tests between the resistant cultivars and Norin 40 (Sr42) and CnsSrTmp (SrTmp) also suggested common genes for resistance. Multi-race phenotyping ruled out involvement of Sr42 and SrCad in all tested cultivars. The available evidence suggested the presence of previously uncharacterised gene(s) or alleles of Sr42, SrTmp or SrCad in all four cultivars. SNP marker BS00085937 and SSR markers psp3200 and wms4862 were 90.9–92.7% effective in predicting stem rust resistance among 55 South African genotypes and could be useful for marker-assisted selection.
Journal Article
Mapping genomic loci implicates genes and synaptic biology in schizophrenia
Schizophrenia has a heritability of 60-80%1, much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies.
Journal Article