Biology subjects

Henry, R. J.

Publications and source records attributed to Henry, R. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Poly Pipeline: A Polyvalent Spatial Transcriptomics Workflow Validated Across Polyploid and Diploid Organisms

Spatial transcriptomics (ST) has emerged as a transformative approach for visualizing tissue landscapes, yet it faces significant challenges regarding data standardization, sparsity, and the analysis of complex genomes, particularly polyploid plants. To address these limitations, we introduce Poly Pipeline, a robust and universal bioinformatic workflow designed to streamline analysis across diverse plant and animal genomes. The pipeline integrates a comprehensive converter for proprietary formats, clustering algorithms, and hdWGCNA co-expression networks, which indirectly preserves the expression signatures of low-expressed duplicated genes. Benchmarking across datasets from wheat, rice, Arabidopsis, and mouse demonstrated the broad applicability of the pipeline in identifying relevant clusters, showing effectiveness across diverse organisms and data types. By providing a unified and reproducible framework, Poly Pipeline addresses a critical gap in analyzing genomic redundancy, especially that related to polyploidy, and promotes FAIR data principles for the broader scientific community.

bioinformatics↗

bioRxiv2026

Genomic and pedigree-based approaches to predict parental breeding values for nut and kernel traits in almond (Prunus dulcis Mill. D. A. Webb)

The self-incompatibility, perennial growth habit, large tree size, and long juvenility present challenges in applying traditional breeding approaches in almond (Prunus dulcis Mill. D. A. Webb). Moreover, nut and kernel traits in almond are mainly controlled by a large number of small-effect quantitative trait loci (QTLs) and improving complex traits through conventional breeding approaches is slow and often inefficient. Genome-wide selection represents a promising strategy to enhance the efficiency of cultivar identification and selection of superior parents in almond breeding programs by estimating the breeding values (BVs) at early maturity. The main aim of this study was to implement genomic (GBLUP) and pedigree-based (ABLUP) prediction approaches to estimate BVs to identify the superior parental candidates for improving nut and kernel traits in almond. Here, we estimated BVs for nine traits that are commonly used in the primary evaluation stage of the almond breeding using genomic data from 61 parents and phenotypic data of 15,281 progeny derived from 205 unique families. Breeding values obtained from both approaches showed a strong correlation (r [≥] 0.94) for all traits except shell seal (r = 0.87). The population structure analysis conducted using high-quality 90K single nucleotide polymorphisms (SNPs) indicated clear separation of the Californian, European and some old Australian almond cultivars, with considerable admixture across some cultivars. Following further validation, both prediction approaches could be useful in early identification of superior candidates. The slightly higher breeding values obtained using the GBLUP compared to the ABLUP approach suggest that accounting for within-family variations and realised genomic relationships can enhance prediction accuracy, reliability, and overall genomic prediction performance in almond.

genetics↗

bioRxiv2025

Going Against the Grain: Investigating the C4 Wheat Hypothesis with Spatial Transcriptomics

The possibility of a C4 photosynthetic pathway present in the developing grain of wheat, a C3 plant, has been the source of scientific debate. Wheat is critical to food security and may benefit greatly from the biological advantages conferred by C4 photosynthesis under heat and drought stress. Therefore, significant research has gone towards engineering wheat to use C4 biochemistry, resulting in the discovery of a unique photosynthetic pathway in the grain that has been suggested to be C4 specific. Here, we employed a spatial transcriptomics analysis of the developing wheat grain to further investigate the spatial expression patterns of C4 specific genes. Our results showed that most of the genes related to C4 photosynthesis were expressed in the grain in the theorised tissue locations, including phosphoenolpyruvate carboxylase (ppc) and pyruvate orthophosphate dikinase (ppdk). The photosynthetic pericarp cells were the site of ppc synthesis while the endosperm was the site of ppc carboxylation activity. Notably, isoforms of aspartate aminotransferase, alanine aminotransferase and malate dehydrogenase exhibited spatially distinct expression patterns, with tissue specificity, possibly linked to the unique functions of individual isoforms. As wheat performance under stress has been associated with the levels of expression of these C4 genes, confirmation of an active C4 pathway in the grain would have significant agronomic implications. Our results provide novel gene expression data for key genes related to photosynthesis, which could contribute to future development of highly productive, climate change resilient wheat varieties.

genetics↗

bioRxiv2025

Chromosome-scale haplotype genome assemblies for the Australian mango 'Kensington Pride' 1 and a wild relative, Mangifera laurina, provide insights into anthracnose-resistance and volatile 2 compound biosynthesis genes

Mango (Mangifera indica) is one of the most popular fruits cultivated in tropical and subtropical regions of the world. The availability of reference genomes helps to identify the genetic basis of important traits. Here we report assembled high-quality chromosome-level genomes for the Australian mango cultivar Kensington Pride, and M. laurina; a wild relative, which shows resistance to anthracnose disease. PacBio HiFi sequencing with higher genome coverage enabled the assembly of both genomes with 100% completeness. Genome sizes of Kensington Pride and M. laurina were 367 Mb and 379 Mb, respectively, with all 20 chromosomes in both genomes having telomeres at both ends. K-mer analysis revealed that these genomes are highly heterozygous and significant structural variations were identified between Kensington Pride, M. laurina, and the recently published genome of the cultivar Irwin. Functional annotation identified key genes involved in carotenoid, anthocyanin, and terpenoid biosynthesis, responsible for fruit color and flavour in mango. Furthermore, the presence of a SNP in {beta}-1,3-glucanase 2 gene associated with anthracnose resistance was analyzed. Whole genome duplication analysis confirmed that mangoes have undergone two polyploidization events during their evolution. Analysis revealed a conserved pattern of colinear genes, although many colinear blocks were also identified on non-homologous chromosomes. Practitioner PointsO_LIPacBio HiFi sequencing and high coverage produced genomes for Kensington Pride mango and M. laurina with 100% completeness, identifying all the telomeres in the assembled chromosomes. C_LIO_LISignificant structural variations were identified between Kensington Pride, M. laurina, and the published Irwin genome. C_LIO_LIGenes linked in the biosynthesis of unique terpenoids were identified, and the structural differences in the annotated {beta}-1,3-glucanase 2 genes associated with anthracnose resistance provide a resource for gene expression analysis in susceptible and resistant cultivars. C_LI

plant biology↗

bioRxiv2025

Genetic diversity and variation in heterozygosity in Macadamia

BackgroundMacadamia is a diploid (2n =28) rainforest tree of the Proteaceae family, native to Australia. Single-nucleotide polymorphisms (SNPs) have proven to be effective tools for evaluating genetic diversity and heterozygosity. SNPs from the whole genome were used to determine allelic diversity within different species and breeding populations, and to investigate the heterozygosity of genotypes ResultsA total of 349 samples, including wild and domesticated genotypes, were whole genome sequenced, generating 4,180,786 - 7,661,269, 2,446,762 - 7,356,187, 2,829,944 - 4,391,600, 1601519 - 3,182,089 and 3,123,715 to 9,620,640 single nucleotide polymorphism (SNP) positions at the whole genome level for M. integrifolia, M. tetraphylla, M. ternifolia, M. jansenii and the domesticated cultivars and breeding selections respectively. The overall SNP diversity for wild M. integrifolia, M. tetraphylla, M. ternifolia and M. jansenii was 4.43%, 4.33%, 1.80% and 1.1%, respectively. Domesticated M. integrifolia showed an overall SNP diversity of 3.4%, 1.03% lower than wild M. integrifolia, providing evidence of a genetic bottleneck during domestication. Genetic diversity at the individual level for the domesticated gene pool varied from 0.4% to 1.24%, with an overall diversity of 6.10%. Results across different breeding groups revealed that the Australian breeding selections (NMBPA) had the highest diversity, and HAES cultivars had the lowest diversity. Wild M. integrifolia and M. tetraphylla exhibited heterozygosity ranging from 0.36% to 0.71% and 0.30% to 0.71% respectively. The two non-edible species, M. ternifolia and M. jansenii, displayed relatively low heterozygosity (From 0.29% to 0.42% and 0.19% to 0.34% respectively). Domesticated macadamia exhibited a wide range of heterozygosity (0.33% to 1.15%). Additionally, heterozygosity correlated with yield efficiency (kernel yield/tree volume), cumulative kernel yield at age 8 and cumulative nut in shell (NIS) yield at age 8 and showed that performance increased with heterozygosity to an optimal level and declined thereafter. ConclusionThese findings confirmed that there is substantial genetic variation among the different macadamia genotypes. The results also revealed that the greatest diversity is present in wild germplasm. The data will greatly support future genome-wide studies and breeding programs.

plant biology↗

bioRxiv2025

Spatial transcriptomics of developing wheat seed reveals radial expression patterns in endosperm and subgenome biased expression of key genes

Gene expression of developing seeds drives essential processes such as nutrient storage, stress tolerance and germination. However, the spatial organisation of gene expression within the complex structure of the seed remains largely unexplored. Here we report the use of the STOmics spatial transcriptomics platform to visualise spatial expression patterns in the wheat (Triticum aestivum) seed at the critical period of grain filling in mid seed development. We analysed >4,000,000 spatially resolved transcripts, achieving subcellular resolution of transcript localization across multiple tissue domains, and identified gene expression clusters linked to eight functional cellular groups. Notably, our analysis characterised four distinct clusters within the endosperm, which exhibited radial expression patterns from the inner to outer regions of the grain, and identified novel marker gene candidates for the clusters found. We further investigated known tissue-specific genes and identified subgenome biased expression between paralogs of puroindoline-B, metallothionein protein, and -amylase/subtilisin inhibitor. These findings provide new detail about gene expression across and within different functional cellular groups of the developing seed and demonstrate that spatial transcriptomics could further our understanding of subgenome differences in polyploid plants.

plant biology↗

bioRxiv2024

Re-calibration of flow cytometry standards for plant genome size estimation

The evolution of long-read sequencing technologies has advanced the development of genome assemblies that are now frequently presented as gap-free or nearly gapless, reflecting substantial improvements in sequencing accuracy and completeness. However, discrepancies between the genome size estimates derived from genome assemblies and flow cytometry create ambiguity regarding the accuracy of these complementary approaches. Accurate genome size estimation via flow cytometry relies on use of an internal standard with a genome of known size. Historically, the genome size of these standards was often calibrated against incomplete genome assemblies or non-plant genomes, such as the human male genome, which was previously considered to be 7 pg but is now known to be around 6.15 pg after 20 years of advancements. Calibrating plant references against non-plant standards is not recommended due to differential staining properties. Therefore, we recalibrated the size of five plant genomes commonly used as reference standards in flow cytometry, by utilizing a recent gapless, telomere-to-telomere (T2T) genome assembly of Nipponbare rice. Our results indicate a significant overestimation of around 20% in previous flow cytometry-based estimates for Pisum sativum and Nicotiana benthamiana, around 10% for Arabidopsis thaliana, and less than 5% for Sorghum bicolor, and Gossypium hirsutum. The close alignment of the recalibrated GS estimates to the reference genome assemblies and recalculated estimates from different studies confirms their suitability as reference standards for more accurate measurement of plant genome size.

molecular biology↗

bioRxiv2024

Centromeres are Hotspots for Chromosomal Inversions and Breeding Traits in Mango

Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits, indicating that chromosomal inversions have likely facilitated their selection. The results from this study have important implications for selective breeding of favorable combinations of alleles in regions of low recombination. Significance StatementChromosomal inversions and other low recombination regions of the genome can drive trait evolution. Fewer recombination events can assist in maintaining favorable combinations of alleles, but it can also make disentangling favorable and deleterious alleles difficult. Understanding whether these low recombination regions contain favorable or deleterious loci could drive our decision to increase or decrease the frequency of these regions in target breeding populations. Breeding for large segments of the genome based on presence or absence of an inversion can rapidly drive large trait differences within few generations. Harnessing the impact of large low recombination regions of the genome could have major implications for future genetic improvement in breeding.

genomics↗

bioRxiv2023

An improved haplotype resolved genome reveals more rice genes

The rice reference genome (Oryza sativa ssp. japonica cv. Nipponbare) has been an important resource in plant science. We now report an improved and haplotype resolved genome sequence based upon more accurate sequencing technology. This improved assembly includes regions missing in earlier genomes sequences and the annotation of more than 3,000 new genes due to greater sequence accuracy.

genomics↗

bioRxiv2023

The genomes of the Macadamia genus

Macadamia, a genus native to Eastern Australia, comprises four species, Macadamia integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii. Macadamia was recently domesticated largely from a limited gene pool of Hawaiian germplasm and has become a commercially significant nut crop. Disease susceptibility and climate adaptability challenges, highlight the need for use of a wider range of genetic resources for macadamia production. High quality haploid resolved genome assemblies were generated using HiFiasm to allow comparison of the genomes of the four species. Assembly sizes ranged from 735 Mb to 795 Mb and N50 from 53.7 Mb to 56 Mb, indicating high assembly continuity with most of the chromosomes covered telomere to telomere. Repeat analysis revealed that approximately 61% of the genomes were repetitive sequence. The BUSCO completeness scores ranged from 95.0% to 98.9%, confirming good coverage of the genomes. Gene prediction identified 37198 to 40534 genes. The ks distribution plot of Macadamia and Telopea suggests Macadamia has undergone a whole genome duplication event prior to divergence of the four species and that Telopea genome was duplicated more recently. Synteny analysis revealed a high conservation and similarity of the genome structure in all four species. Differences in the content of genes of fatty acid and cyanogenic glycoside biosynthesis were found between the species. An antimicrobial gene with a conserved cysteine motif was found in all four species. The four genomes provide reference genomes for exploring genetic variation across the genus in wild and domesticated germplasm to support plant breeding.

genomics↗

bioRxiv2023

Determination of phylogenetic relationships in the genus Mangifera based on whole chloroplast genome and nuclear genome sequences

The genus Mangifera (Anacardiaceae) includes 69 species of which Mangifera indica L. is the most important and primarily cultivated species for commercial mango production. Although the species are classified based on morphological descriptors, molecular evidence has proposed the hybrid origin of two species suggesting the possibility that more of the species may be of hybrid origin. To analyze evolutionary relationships within the genus, 13 samples representing 11 Mangifera species were sequenced and whole chloroplast (Cp) genomes and 47 common single-copy nuclear gene sequences were assembled and used for phylogenetic analysis using concatenation and coalescence-based methods. The Cp genome size varied from 151,752 to 158,965 bp with M. caesia and M. laurina having the smallest and largest genomes, respectively. Genome annotation revealed 80 protein-coding genes, 31 tRNA and four rRNA genes across all the species. Comparative analysis of whole Cp genome sequence and nuclear gene-based phylogenies revealed topological conflicts suggesting chloroplast capture or cross hybridization. The Cp genomes of M. altissima, M. applanata, M. caloneura and M. lalijiwa were similar to those of M. indica (99.9% sequence similarity). Their close sequence relationship suggests a common ancestry and likely cross-hybridization between wild relatives and M. indica. This study provides improved knowledge of phylogenetic relationships in Mangifera, indicating extensive gene flow among the different species, suggesting that hybrids may be common within the genus.

plant biology↗

bioRxiv2023

Interaction of high-fat diet and brain trauma alters adipose tissue macrophages and brain microglia associated with exacerbated cognitive dysfunction.

Obesity increases the morbidity and mortality of traumatic brain injury (TBI). We performed a detailed analysis of transcriptomic changes in the brain and adipose tissue to examine the interactive effects between high-fat diet-induced obesity (DIO) and TBI in relation to central and peripheral inflammatory pathways, as well as neurological function. Adult male mice were fed a high-fat diet (HFD) for 12 weeks prior to experimental TBI and continuing after injury. Combined TBI and HFD resulted in additive dysfunction in the Y-Maze, novel object recognition (NOR), and Morris water maze (MWM) cognitive function tests. We also performed high-throughput transcriptomic analysis using Nanostring panels of cellular compartments in the brain and total visceral adipose tissue (VAT), followed by unsupervised clustering, principal component analysis, and IPA pathway analysis to determine shifts in gene expression programs and molecular pathway activity. Analysis of cellular populations in the cortex and hippocampus as well as in visceral adipose tissue during the chronic phase after combined TBI-HFD showed amplification of central and peripheral microglia/macrophage responses, including superadditive changes in select gene expression signatures and pathways. These data suggest that HFD-induced obesity and TBI can independently prime and support the development of altered states in brain microglia and visceral adipose tissue macrophages, including the disease-associated microglia/macrophage (DAM) phenotype observed in neurodegenerative disorders. The interaction between HFD and TBI promotes a shift toward chronic reactive microglia/macrophage transcriptomic signatures and associated pro-inflammatory disease-altered states that may, in part, underlie the exacerbation of cognitive deficits. Targeting of HFD-induced reactive cellular phenotypes, including in peripheral adipose tissue macrophages, may serve to reduce microglial maladaptive states after TBI, attenuating post-traumatic neurodegeneration and neurological dysfunction.

neuroscience↗

bioRxiv2023

Genetic basis of expression and splicing underlying spike architecture in wheat (Triticum aestivum L.)

IntroductionWheat is one of the most important staple crops worldwide, and an important source of human protein and mineral element intake. Continuously increasing stable production of wheat is critical for global food security under the challenge of population growth and limited resource input. ObjectiveSpike architecture determines the potential grain yield of wheat. However, the mechanisms of transcriptional regulation of spike architecture in wheat remain largely unknown, limiting further genetic improvement of wheat yield. In this study we explored the genetic basis of spike architecture in wheat. MethodsPopulation RNA-seq methods were used to identify the eQTLs and sQTLs associated with spike architecture and applied this to dissection of the genetic basis of gene expression and splicing controlling these complex yield-related traits. ResultsIn total, 4,143 expression quantitative trait loci (eQTLs) and 12,933 splice QTLs (sQTLs) were identified in wheat based on 178 RNA-seq samples, revealing 774 cis-eQTLs and 321 cis-sQTLs for 86 eGenes and 73 sGenes, respectively. Integration of eQTLs and sQTLs with genome-wide association study (GWAS) identified dozens of additional novel candidate genes that may contribute to spike-related traits. Gene network analysis showed that eQTLs and sQTLs were widely involved in the co-expression modules that regulate wheat spike architecture. Notably, the eQTL locus AX-108754757 regulated the expression of 5 eGenes that negatively controled grain number per spike. AX-111592099 regulated both the splicing and expression of TraesCS7B02G442100, encoding an E3 ubiquitin ligase, and playing a central role in regulating spike length. ConclusionThis study provides new insights into the genetic basis of spike architecture. This improved understanding of spike-related traits in wheat will contribute to more rapid genetic improvement.

plant biology↗

bioRxiv2023

Region-specific homeostatic identity of astrocytes is essential for defining their reactive phenotypes following pathological insults

The transformation of astrocytes into reactive states constitutes a biological response of the central nervous system under a variety of pathological insults. Astrocytes display diverse homeostatic identities, which are developmentally predetermined and regionally specified. Upon transformation into reactive states associated with neurodegenerative diseases and other neurological disorders, astrocytes acquire diverse reactive phenotypes. However, it is not clear whether their reactive phenotypes are dictated by regionspecific homeostatic identity or, alternatively, by the nature of an insult. To address this question, regionspecific gene expression profiling was performed for four brain regions (cortex, hippocampus, thalamus and hypothalamus) in mice using a custom Nanostring panel consisting of selected sets of genes that report on astrocyte functions and their reactivity for five conditions: prion disease, traumatic brain injury, brain ischemia, 5XFAD Alzheimers disease model and normal aging. Upon transformation into reactive states, genes that are associated predominantly with astrocytes were found to preserve region-specific signatures suggesting that they respond to insults in a region-specific manner. A common gene set was found to be involved in astrocyte remodeling across insults and normal aging. Regardless of the nature of an insult or insult-specificity of astrocyte response, strong correlations between the degree of astrocyte reactivity and perturbations in their homeostasis-associated genes were observed within each individual brain region. The insult-specific populations did not separate well from each other and instead partially overlapped, forming continuums of phenotypes. The current study demonstrates that astrocytes acquire their reactive phenotypes according to their region-specific homeostatic identities. Within these region-specified identities, reactive phenotypes show continuums of states, partially overlapping between individual insults.

neuroscience↗

bioRxiv2022

Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes

Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus. Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased, with the available genomes of varying accuracy and completeness. We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species; Citrus australis (round lime) using highly accurate PacBio HiFi long reads, complemented with Hi-C scaffolding. Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C. australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness (BUSCO). Repeat analysis showed that more than 50% of the genome contained interspersed repeats. Among them, LTR elements were the predominant type (21.0%), of which LTR Gypsy (9.8 %) and LTR copia (7.7 %) elements were the most abundant repeats. A total of 29,464 genes and 32,009 transcripts were identified in the genome. Of these, 28,222 CDS (25,753 genes) had BLAST hits and 21,401 CDS (75.8%) were annotated with at least one GO term. Citrus specific genes for antimicrobial peptides, defense, volatile compounds and acidity regulation were identified. This chromosome scale, and haplotype resolved C. australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.

plant biology↗

bioRxiv2022

SEQUENCE VARIATIONS ASSOCIATED WITH NOVEL PURPLE-PERICARP SUPER-SWEETCORN COMPARED TO ITS PURPLE-PERICARP MAIZE AND WHITE SUPER-SWEETCORN PARENTS

Recently, a novel purple-pericarp super-sweetcorn line, Tim1 (A1A1.sh2sh2) is derived from the purple-pericarp maize Costa Rica (A1Sh2.A1Sh2) and white shrunken2 (sh2) super-sweetcorn Tims-white (a1sh2.a1sh2), however information regarding purple colour controlling anthocyanin biosynthesis genes and sweetcorn gene is lacking. Specific sequence differences in the CDS (coding DNA sequence) and promoter regions of the anthocyanin biosynthesis structural genes, anthocyanin1 (A1), purple aleurone1 (Pr1) and regulatory genes, purple plant1 (Pl1), plant colour1 (B1), coloured1 (R1), and the sweetcorn structural gene, shrunken2 (sh2) were investigated using the publicly available annotated yellow starchy maize, B73 (NAM5.0) as a reference genome. In the CDS region, the A1, Pl1 and R1 gene sequence differences of Tim1 and Costa Rica were similar, as they control purple-pericarp pigmentation, however the B1 gene showed similarity between the Tim1 and Tims-white lines, which may indicate that it does not have a role in controlling pericarp colour, unlike a previous study. In case of Pr1 gene, unlike Costa Rica, 6- and 8-bp dinucleotide (TA) repeats were observed in the promoter region of the Tims-white and Tim1 lines, respectively, indicating the defective functionality (redder colour in Tim1 than purple in Costa Rica) of the recessive pr1 allele. In the sweetcorn structural gene (sh2), sequence similarity was observed between purple-sweet Tim1 and its white-sweet parent Tims-white, as both display a shrunken phenotype in their mature kernels. These findings revealed that the developed purple-sweet line is different than the reference yellow-nonsweet line regarding both the anthocyanin biosynthesis and sweetcorn genes.

genomics↗

bioRxiv2022

BREAKING THE TIGHT GENETIC LINKAGE BETWEEN THE a1 AND sh2 GENES LED TO THE DEVELOPMENT OF ANTHOCYANIN-RICH PURPLE-PERICARP SUPER-SWEETCORN

The existence of purple-pericarp super-sweetcorn based on the most common supersweet mutation, shrunken2 (sh2), has not been previously reported, partly due to its extremely tight genetic linkage to a non-functional anthocyanin biosynthesis gene, anthocyaninless1 (a1). Generally, both aleurone- and pericarp-pigmented purple corn is starchy, the latter of which contains significantly higher anthocyanin compared to the former. The development of purple-pericarp super-sweetcorn is dependent on breaking the a1-sh2 tight genetic linkage, which occurs at a very low frequency of <1 in 1000 meiotic crossovers. Here, to develop purple-pericarp super-sweetcorn, an initial cross between a male purple-pericarp maize (purple-round seed), Costa Rica (A1Sh2.A1Sh2) and a female white shrunken2 super-sweetcorn (white-shrunken seed), Tims-white (a1sh2.a1sh2), was conducted. Subsequent self-pollination based on purple-pericarp-shrunken kernels identified a small frequency (0.08%) of initial heterozygous F3 segregants (A1a1.sh2sh2) producing a fully sh2 cob with a purple-pericarp phenotype, enabled by breaking the close genetic linkage between the a1 and sh2 genes. Resulting rounds of self-pollination generated a F6 homozygous purple-pericarp super-sweetcorn (A1A1.sh2sh2) line, Tim1. Genome sequencing revealed a recombination break between the a1 and yz1 genes of the a1-yz1-x1-sh2 multigenic interval, with the sequence pattern of Tim1 similar to the Costa Rica parent, and after the linkage break, similar to the Tims-white parent. The novel purple-pericarp super-sweetcorn produced a similar concentration of anthocyanin and sugar as in its purple-pericarp maize and white super-sweetcorn parents, respectively, potentially adding a broader range of health benefits than currently exists with standard yellow/white sweetcorn.

plant biology↗

bioRxiv2022

Brain injury accelerates the onset of a reversible age-related microglial phenotype associated with hyperphagocytosis and inflammatory neurodegeneration

Lipofuscin is an autofluorescent (AF) pigment formed by lipids and misfolded proteins that accumulates in post-mitotic cells with advanced age. Here we immunophenotyped microglia in the brain of old C57BL/6 mice (>18 months-old) and demonstrate that in comparison to young mice, one third of old microglia are AF, characterized by profound changes in lipid and iron content, phagocytic activity, and oxidative stress. Pharmacological depletion of microglia in old mice eliminated the AF microglia following repopulation and reversed microglial dysfunction. Age-related neurological deficits and neurodegeneration after traumatic brain injury (TBI) were attenuated in old mice lacking AF microglia. Furthermore, hyperphagocytic activity and lipid accumulation in microglia persisted for up to one year after TBI, were modified by Apoe4 genotype, and chronically driven by phagocyte-mediated oxidative stress. Thus, AF may reflect a pathological state in aging microglia associated with hyperphagocytosis and inflammatory neurodegeneration that can be further accelerated by TBI. TeaserTraumatic brain injury accelerates age-related pathological phagocytosis and lipofuscin formation in microglia.

neuroscience↗