Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement.

INTRODUCTION: Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known. OBJECTIVES: This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits. METHODS: Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes. RESULTS: There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed. CONCLUSION: Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate.

High-quality wild barley genome assemblies and annotation with Nanopore long reads and Hi-C sequencing data.

Wild barley, from "Evolution Canyon (EC)" in Mount Carmel, Israel, are ideal models for cereal chromosome evolution studies. Here, the wild barley EC_S1 is from the south slope with higher daily temperatures and drought, while EC_N1 is from the north slope with a cooler climate and higher relative humidity, which results in a differentiated selection due to contrasting environments. We assembled a 5.03 Gb genome with contig N50 of 3.53 Mb for wild barley EC_S1 and a 5.05 Gb genome with contig N50 of 3.45 Mb for EC_N1 using 145 Gb and 160.0 Gb Illumina sequencing data, 295.6 Gb and 285.35 Gb Nanopore sequencing data and 555.1 Gb and 514.5 Gb Hi-C sequencing data, respectively. BUSCOs and CEGMA evaluation suggested highly complete assemblies. Using full-length transcriptome data, we predicted 39,179 and 38,373 high-confidence genes in EC_S1 and EC_N1, in which 93.6% and 95.2% were functionally annotated, respectively. We annotated repetitive elements and non-coding RNAs. These two wild barley genome assemblies will provide a rich gene pool for domesticated barley.

Knockdown of Yap attenuates TAA-induced hepatic fibrosis by interaction with hedgehog signals.

Liver fibrosis is an aberrant wound healing response to tissue injury characterized by excessive extracellular matrix deposition and loss of normal liver architecture. Hepatic stellate cells (HSCs) activation is regards to be the major process in liver fibrogenesis which is dynamic and reversible. Both Hippo signaling core factor Yap and Hedgehog (Hh) signaling promote HSCs transdifferentiation thereby regulating the repair process of liver injury. However, the molecular function of YAP and the regulation between Yap and Hh during fibrogenesis remain uncertain. In this study, the essential roles of Yap in liver fibrosis were investigated. Yap was detected to be increased in liver fibrotic tissue by the thioacetamide (TAA)-induced zebrafish embryonic and adult models. Inhibition of Yap by both embryonic morpholino interference and adult's inhibitor treatment was proved to alleviate TAA-induced liver lesions by and histology and gene expression examination. Transcriptomic analysis and gene expression detection showed that Yap and Hh signaling pathway have a cross talking upon TAA-induced liver fibrosis. In addition, TAA induction promoted the nuclear colocalization of YAP and Hh signaling factor GLI2α. This study demonstrates that Yap and Hh play synergistic protective roles in liver fibrotic response and provides new theoretical insight concerning the mechanisms of fibrosis progression.

Fossil pollen resolves origin of the South African Proteaceae as transcontinental not transoceanic.

BACKGROUND AND AIMS: The prevailing view from the areocladogenesis of molecular phylogenies is that the iconic South African Cape Proteaceae (subfamily Proteoideae) arrived from Australia across the Indian Ocean in the Upper Cretaceous (100‒65 million years ago, Ma). Since fossil pollen indicates that the family probably arose in North-West Africa during the early Cretaceous, an alternative view is that it migrated to the Cape from North-Central Africa. The plan therefore was to collate fossil pollen records throughout Africa to determine if they are consistent with an African (para-autochthonous) origin for the Cape Proteaceae, and to seek further support from other paleo-disciplines. METHODS: Palynology (identity, date and location of records), molecular phylogeny and chronogram preparation, biogeography of plate tectonics, and paleo-atmospheric and ocean circulation models. KEY RESULTS: Our collation of the rich assemblage of Proteaceae palynomorphs stretching back to 107 Ma (Triorites africaensis) in North-West Africa showed its progressive overland migration to the Cape by 75‒65 Ma. No key palynomorphs recorded in Australia-Antarctica have morphological affinities with African fossils but specific clade assignment of the preMiocene records is not currently possible. The Cape Proteaceae encompass three molecular-based clades (tribes) whose most-recent apparent ancestors are sisters to those in Australia. However, our chronogram shows that the major Adenanthos/Leucadendron-related clade, originating 54‒34 Ma, would have 'arrived' too late as species with Proteaceae affinities were already present ~20 My earlier. The Franklandia/Protea-related clade arose 118‒81 Ma so its distinctive pollen should have been the foundation for the scores of palynomorphs recorded at 100‒80 Ma but it was not. Also, the prevailing winds and ocean currents trended away from South Africa rather than towards, as the 'out-of-Australia' hypothesis requires. Based on the evidence assembled here, we list three points favouring an Australian origin and nine against; four points favouring an Antarctic origin and seven against; and nine points favouring a North-Central African origin and three against. CONCLUSIONS: We conclude that a gradual migration of the Proteaceae from North-Central Africa southeast→south→southwest to the Cape and surrounds occurred via adaptation and speciation during the period 90‒70 Ma. We caution that incorrect conclusions may be drawn from literal interpretations of molecular phylogenies that neglect the fossil record and do not recognize the possible confounding effects of selection under matched environments leading to parallel evolution and extinction of bona fide sister clades.

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection.

Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a diverse barley (Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in diverse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.

Global beta-diversity of angiosperm trees is shaped by Quaternary climate change.

As Earth's climate has varied strongly through geological time, studying the impacts of past climate change on biodiversity helps to understand the risks from future climate change. However, it remains unclear how paleoclimate shapes spatial variation in biodiversity. Here, we assessed the influence of Quaternary climate change on spatial dissimilarity in taxonomic, phylogenetic, and functional composition among neighboring 200-kilometer cells (beta-diversity) for angiosperm trees worldwide. We found that larger glacial-interglacial temperature change was strongly associated with lower spatial turnover (species replacements) and higher nestedness (richness changes) components of beta-diversity across all three biodiversity facets. Moreover, phylogenetic and functional turnover was lower and nestedness higher than random expectations based on taxonomic beta-diversity in regions that experienced large temperature change, reflecting phylogenetically and functionally selective processes in species replacement, extinction, and colonization during glacial-interglacial oscillations. Our results suggest that future human-driven climate change could cause local homogenization and reduction in taxonomic, phylogenetic, and functional diversity of angiosperm trees worldwide.

Relative growth rate (RGR) and other confounded variables: mathematical problems and biological solutions.

BACKGROUND: Relative growth rate (RGR) has a long history of use in biology. In its logged form, RGR = ln[(M + ΔM)/M], where M is size of the organism at the commencement of the study, and ΔM is new growth over time interval Δt. It illustrates the general problem of comparing non-independent (confounded) variables, e.g. (X + Y) vs. X. Thus, RGR depends on what starting M(X) is used even within the same growth phase. Equally, RGR lacks independence from its derived components, net assimilation rate (NAR) and leaf mass ratio (LMR), as RGR = NAR × LMR, so that they cannot legitimately be compared by standard regression or correlation analysis. FINDINGS: The mathematical properties of RGR exemplify the general problem of 'spurious' correlations that compare expressions derived from various combinations of the same component terms X and Y. This is particularly acute when X >> Y, the variance of X or Y is large, or there is little range overlap of X and Y values among datasets being compared. Relationships (direction, curvilinearity) between such confounded variables are essentially predetermined and so should not be reported as if they are a finding of the study. Standardizing by M rather than time does not solve the problem. We propose the inherent growth rate (IGR), lnΔM/lnM, as a simple, robust alternative to RGR that is independent of M within the same growth phase. CONCLUSIONS: Although the preferred alternative is to avoid the practice altogether, we discuss cases where comparing expressions with components in common may still have utility. These may provide insights if (1) the regression slope between pairs yields a new variable of biological interest, (2) the statistical significance of the relationship remains supported using suitable methods, such as our specially devised randomization test, or (3) multiple datasets are compared and found to be statistically different. Distinguishing true biological relationships from spurious ones, which arise from comparing non-independent expressions, is essential when dealing with derived variables associated with plant growth analyses.

Protective Effects of Lactobacillus gasseri against High-Cholesterol Diet-Induced Fatty Liver and Regulation of Host Gene Expression Profiles.

Fatty liver is one of the most pervasive liver diseases worldwide. Probiotics play an important role in the progression of liver disease, but their effects on host regulation are poorly understood. This study investigated the protective effects of lactobacillus gasseri (L. gasseri) against high-cholesterol diet (HCD)-induced fatty liver injury using a zebrafish larvae model. Liver pathology, lipid accumulation, oxidative stress and hepatic inflammation were evaluated to demonstrate the changes in a spectrum of hepatic injury. Moreover, multiple indexes on host gene expression profiles were comprehensively characterized by RNA screening. The results showed that treatment with L. gasseri ameliorated HCD-induced morphological and histological alterations, lipid regulations, oxidative stress and macrophage aggregation in the liver of zebrafish larvae. Furthermore, the enrichment of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that the core pathways of L. gasseri regulation were interleukin-17 (IL-17) signaling, phosphoinositide 3-kinase (PI3K)-AKT signaling pathway, the regulation of lipolysis and adipocytes and fatty acid elongation and estrogen signaling. The genes at key junction nodes, hsp90aa1.1, kyat3, hsd17b7, irs2a, myl9b, ptgs2b, cdk21 and papss2a were significantly regulated by L. gasseri administration. To conclude, the current research extends our understanding of the protective effects of L. gasseri against fatty liver and provides potential therapeutic options for fatty liver treatment.

New semi-dwarfing alleles with increased coleoptile length by gene editing of gibberellin 3-oxidase 1 using CRISPR-Cas9 in barley (Hordeum vulgare L.).

The green revolution was based on genetic modification of the gibberellin (GA) hormone system with "dwarfing" gene mutations that reduces GA signals, conferring shorter stature, thus enabling plant adaptation to modern farming conditions. Strong GA-related mutants with shorter stature often have reduced coleoptile length, discounting yield gain due to their unsatisfactory seedling emergence under drought conditions. Here we present gibberellin (GA) 3-oxidase1 (GA3ox1) as an alternative semi-dwarfing gene in barley that combines an optimal reduction in plant height without restricting coleoptile and seedling growth. Using large-scale field trials with an extensive collection of barley accessions, we showed that a natural GA3ox1 haplotype moderately reduced plant height by 5-10 cm. We used CRISPR/Cas9 technology, generated several novel GA3ox1 mutants and validated the function of GA3ox1. We showed that altered GA3ox1 activities changed the level of active GA isoforms and consequently increased coleoptile length by an average of 8.2 mm, which could provide essential adaptation to maintain yield under climate change. We revealed that CRISPR/Cas9-induced GA3ox1 mutations increased seed dormancy to an ideal level that could benefit the malting industry. We conclude that selecting HvGA3ox1 alleles offers a new opportunity for developing barley varieties with optimal stature, longer coleoptile and additional agronomic traits.

Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

Fossil flowers of Phylica support a 250 Ma origin for Rhamnaceae.

A new fossil discovery reported by Shi et al. changes our understanding of the biogeographic history of the cosmopolitan family, Rhamnaceae. Flowering shoots of the African genus Phylica (Rhamnaceae) dated at 100 million years ago (Ma) imply a 250 Ma origin of the family in fire-prone Gondwanan vegetation that enabled overland dispersal to all continents where it is currently widespread.

Ancient Rhamnaceae flowers impute an origin for flowering plants exceeding 250-million-years ago.

Setting the molecular clock to newly described 100-million-year-old flowering shoots of Phylica in Burmese amber enabled us to recalibrate the phylogenetic history of Rhamnaceae. We traced its origin to ∼260 million years ago (Ma) that can explain its migration within and beyond Gondwana since that time and implies an origin for flowering plants that stretches well beyond 290 Ma. Ancestral trait assignments also revealed that hard-seededness, fire-proneness, and to a lesser extent, heat-released seed dormancy, have a similarly long history in this clade.

Pancreatic involvement in Erdheim-Chester disease: a case report and review of the literature.

BACKGROUND: Erdheim-Chester disease (ECD) is a rare form of non-Langerhans cell histiocytosis characterized by infiltration of lipid-laden foamy macrophages within different tissues. Clinical manifestations of ECD are highly heterogeneous. Bone lesions are found in 80%-95% of patients, while extraosseous lesions usually involve the cardiovascular system, retroperitoneum, central nervous system (CNS), and skin. Pancreatic involvement in ECD has barely been reported. CASE PRESENTATION: A 29-year-old female initially presented with menoxenia, diabetes insipidus and diabetes mellitus. 18F-fluorodeoxyglucose positron emission tomography-computed tomography (18F-FDG-PET/CT) revealed hypermetabolic foci in the bilateral frontal lobe, saddle area, and pancreas. A 99mTc-MDP bone scrintigraphy scan revealed symmetrical increased uptake in distal femoral and proximal tibial metaphysis, which was confirmed to be osteosclerosis by high-resolution peripheral quantitative computed tomography. The patient underwent incomplete resection of the sellar mass. Histological examination of biopsies showed histiocytic aggregates, which were positive for S100 and negative for CD1a and CD207 on immunohistochemistry. Enhanced abdominal CT scan showed hypointense nodules within the body and tail of the pancreas. Endoscopic ultrasonography guided fine-needle aspiration (EUS-FNA) found no evidence of malignancy. She was diagnosed with ECD and treated with high-dose IFN-α. Repeated examinations at three-and eight-months post treatment revealed markedly reduction of both intracranial and pancreatic lesions. CONCLUSIONS: ECD is a rare histiocytic neoplasm that can involve almost every organ, whereas pancreatic involvement has barely been reported to date. Here, we present the rare case of pancreatic lesions in ECD that responded well to interferon-α. We further reviewed reports of pancreatic involvement in histiocytic disorders and concluded the characteristics of such lesions to help diagnosis and treatment, in which these lesions mimicked pancreatic adenocarcinoma and caused unnecessary invasive surgeries.

Adaptive genetic diversity of dominant species contributes to species co-existence and community assembly.

The synthesis of evolutionary biology and community ecology aims to understand how genetic variation within one species can shape community properties and how the ecological properties of a community can drive the evolution of a species. A rarely explored aspect is whether the interaction of genetic variation and community properties depends on the species' ecological role. Here we investigated the interactions among environmental factors, species diversity, and the within-species genetic diversity of species with different ecological roles. Using high-throughput DNA sequencing, we genotyped a canopy-dominant tree species, Parashorea chinensis, and an understory-abundant species, Pittosporopsis kerrii, from fifteen plots in Xishuangbanna tropical seasonal rainforest and estimated their adaptive, neutral and total genetic diversity; we also surveyed species diversity and assayed key soil nutrients. Structural equation modelling revealed that soil nitrogen availability created an opposing effect in species diversity and adaptive genetic diversity of the canopy-dominant Pa. chinensis. The increased adaptive genetic diversity of Pa. chinensis led to greater species diversity by promoting co-existence. Increased species diversity reduced the adaptive genetic diversity of the dominant understory species, Pi. kerrii, which was promoted by the adaptive genetic diversity of the canopy-dominant Pa. chinensis. However, such relationships were absent when neutral genetic diversity or total genetic diversity were used in the model. Our results demonstrated the important ecological interaction between adaptive genetic diversity and species diversity, but the pattern of the interaction depends on the identity of the species. Our results highlight the significant ecological role of dominant species in competitive interactions and regulation of community structure.

High exposure of global tree diversity to human pressure.

Safeguarding Earth's tree diversity is a conservation priority due to the importance of trees for biodiversity and ecosystem functions and services such as carbon sequestration. Here, we improve the foundation for effective conservation of global tree diversity by analyzing a recently developed database of tree species covering 46,752 species. We quantify range protection and anthropogenic pressures for each species and develop conservation priorities across taxonomic, phylogenetic, and functional diversity dimensions. We also assess the effectiveness of several influential proposed conservation prioritization frameworks to protect the top 17% and top 50% of tree priority areas. We find that an average of 50.2% of a tree species' range occurs in 110-km grid cells without any protected areas (PAs), with 6,377 small-range tree species fully unprotected, and that 83% of tree species experience nonnegligible human pressure across their range on average. Protecting high-priority areas for the top 17% and 50% priority thresholds would increase the average protected proportion of each tree species' range to 65.5% and 82.6%, respectively, leaving many fewer species (2,151 and 2,010) completely unprotected. The priority areas identified for trees match well to the Global 200 Ecoregions framework, revealing that priority areas for trees would in large part also optimize protection for terrestrial biodiversity overall. Based on range estimates for >46,000 tree species, our findings show that a large proportion of tree species receive limited protection by current PAs and are under substantial human pressure. Improved protection of biodiversity overall would also strongly benefit global tree diversity.

Climatic and soil factors explain the two-dimensional spectrum of global plant trait variation.

Plant functional traits can predict community assembly and ecosystem functioning and are thus widely used in global models of vegetation dynamics and land-climate feedbacks. Still, we lack a global understanding of how land and climate affect plant traits. A previous global analysis of six traits observed two main axes of variation: (1) size variation at the organ and plant level and (2) leaf economics balancing leaf persistence against plant growth potential. The orthogonality of these two axes suggests they are differently influenced by environmental drivers. We find that these axes persist in a global dataset of 17 traits across more than 20,000 species. We find a dominant joint effect of climate and soil on trait variation. Additional independent climate effects are also observed across most traits, whereas independent soil effects are almost exclusively observed for economics traits. Variation in size traits correlates well with a latitudinal gradient related to water or energy limitation. In contrast, variation in economics traits is better explained by interactions of climate with soil fertility. These findings have the potential to improve our understanding of biodiversity patterns and our predictions of climate change impacts on biogeochemical cycles.

Fire-mediated germination syndromes in Leucadendron (Proteaceae) and their functional correlates.

A mechanistic understanding of fire-driven seedling recruitment is essential for effective conservation management of fire-prone vegetation, such as South African fynbos, especially with rare and threatened taxa. The genus Leucadendron (Proteaceae) is an ideal candidate for comparative germination studies, comprising 85 species with a mixture of contrasting life-history traits (killed by fire vs able to resprout; serotinous vs geosporous) and seed morphologies (nutlets vs winged achenes). Individual and combined effects of heat and smoke on seed germination of 40 species were quantified in the laboratory, and Bayesian inference applied to distinguish biologically meaningful treatment effects from non-zero, but biologically trivial, effects. Three germination syndromes were identified based on whether germination was dependent on, enhanced by, or independent of direct fire cues (heat and smoke). Seed storage location was the most reliable predictor of germination syndromes, with soil-stored seeds c. 80% more likely to respond to direct fire cues (primarily smoke) than canopy-stored seeds. Notable exceptions were L. linifolium, with an absolute requirement for smoke to germinate (the third serotinous species so reported), and two other serotinous species with smoke-enhanced germination. Nutlet-bearing species, whether serotinous or geosporous, were c. 70% more likely to respond to fire cues than winged seeds, but there was no evidence for an effect of phylogeny or persistence strategy on germination. This comprehensive account of seed germination characteristics and identification of germination syndromes and their predictors, supports propagation, conservation and restoration initiatives in this iconic fynbos genus and other fire-prone shrubs with canopy or soil-stored seeds.

Genomic structural equation modelling provides a whole-system approach for the future crop breeding.

KEY MESSAGE: Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For example, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content; we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding.

Whole-genome assembly and resequencing reveal genomic imprint and key genes of rapid domestication in narrow-leafed lupin.

Shifting from a livestock-based protein diet to a plant-based protein diet has been proposed as an essential requirement to maintain global food sustainability, which requires the increased production of protein-rich crops for direct human consumption. Meanwhile, the lack of sufficient genetic diversity in crop varieties is an increasing concern for sustainable food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics. Narrow-leafed lupin (Lupinus angustifolius L.) has experienced rapid domestication and has become a new legume crop over the past century, with the potential to provide protein-rich seeds. Here, using long-read whole-genome sequencing, we assembled the third-generation reference genome for the narrow-leafed lupin cultivar Tanjil, comprising 20 chromosomes with a total genome size of 615.8 Mb and contig N50 = 5.65 Mb. We characterized the original mutation and putative biological pathway resulting in low seed alkaloid level that initiated the recent domestication of narrow-leafed lupin. We identified a 1133-bp insertion in the cis-regulatory region of a putative gene that may be associated with reduced pod shattering (lentus). A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as precisely predicted by the original model of the bottleneck effect on genetic variability in populations. Our results identify the key domestication genetic loci and provide direct genomic evidence for a domestication bottleneck, and open up the possibility of knowledge-driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low-carbon emission agriculture.