Tianhua He

Improved yield potential is the goal of barley domestication and cultivation. During this process, two- and six-rowed barley types emerged and have been utilised in breeding and production. The six-rowed type could produce three times as many grains as its ancestral two-rowed forms, thus dominating barley cultivation for thousands of years. The deficiens form of the two-rowed type, characterised by extremely suppressed lateral spikelets, has gained dominance over the past few decades in barley-growing regions worldwide. We hypothesised that the absence of lateral spikelets in deficiens barley affects spike architecture and spike-related traits, contributing to its superior yield potential of deficiens barley cultivation. Currently, a deficiens barley variety, RGT Planet, is the most popular barley variety in the world. In this study, we used two F2 populations derived from crossing RGT Planet with two canonical two-rowed barley and identified the functional allele Vrs1.t1 associated with deficiens morphology. We observed that the Vrs1.t1 allele may contribute to high yield potential by optimising spike architecture through increased spikelet length, grain number, and grain size. Phylogenetic analysis suggests that the deficiens mutation was likely present from the early stages of barley cultivation in the Fertile Crescent and spread to Ethiopia and beyond with agricultural expansion. We conclude that the ancient deficiens allele Vrs1.t1 has been a critical driver for the recent success of modern barley improvement by optimising spike architecture.

Aim
It is usually assumed that low biodiversity of arid regions is due to the inability of most lineages to adapt to their low/unreliable rainfall. However, species requiring fire-stimulated seed-dormancy release are also at a fitness disadvantage in deserts that rarely burn. We hypothesized that a hard-seeded, temperate-climate genus is not absent from Australia's deserts because it is insufficiently adapted to aridity but that the dearth of fire means its germination requirements cannot be met.

Location
Earth, mainly Australia.

Taxa
Many fire-prone and fire-free clades, with Cryptandra (Rhamnaceae) as a case study.

Methods
We document clades with/lacking fire-stimulated-seed-dormancy release and compare their occurrences under different climates and degrees of fire exposure. We compare drought-related traits of Cryptandra species in southwestern Australia with matched species in Central Australia. Grid cells were overlain onto maps to document co-occurrences of Cryptandras and climate type/vegetation cover/rainfall reliability and fire activity, and a distribution model was created. The phylogenetic signal was quantified, and ancestral trait reconstruction was undertaken for that part of the Rhamnaceae bearing Cryptandras.

Results
Species fire-proneness peaks at intermediate levels of aridity. A sample of eight worldwide lineages is drought-adapted but not fire-dependent and thus colonises arid regions; 23 clades with fire-stimulated-seed-dormancy release possess species that no longer require fire and have migrated into arid regions; and eight clades, where non-fire-stimulated-seed-dormancy release has not evolved, remain in fire-prone regions, despite apparent arid-tolerant traits. Leaf/stem/habitat traits of selected Cryptandras appear as drought-tolerant as matched species in arid Australia. Abundance of fire-dependent Cryptandras in Western Australia is greatest in the well-vegetated zones with a mediterranean climate and rare/absent in the fire-free deserts.

Conclusions
Many xeromorphic clades with fire-stimulated-seed-dormancy release in temperate/(sub)tropical regions possess recent sister lineages with non-fire-stimulated-seed-dormancy release in arid regions, whereas others appear incapable of evolving lineages that no longer benefit from fire. As drought-adapted, hard-seeded Cryptandras and other Rhamnaceae universally require occasional fires to break seed dormancy, this may explain their absence in rarely burnt deserts that cannot satisfy this requirement.

Secondary metabolites (SMs) are crucial for plant survival and adaptation and play multiple roles in mediating ecological interactions, such as defense and stress tolerance. Specialized transporters relocate SMs from synthesis sites to defense tissues or storage organs. The spatiotemporal distribution of defense-related SMs is a key determinant of plant fitness. However, the accumulation of anti-nutritional SMs in crop seeds or fruits may pose health risks to humans and livestock. Recent advances have highlighted the significant role of SM transporters in optimizing the allocation of metabolites. This review explores the transport mechanisms for both defense and anti-nutritional SMs, focusing on long-distance transporters that regulate source-sink dynamics and their potential implications in agricultural biotechnology. We highlight innovative approaches to manipulating transporter activities, ranging from multi-omics integration to precision engineering, and discuss how these tools can be used to design crops with enhanced defense capacity, increased levels of beneficial compounds, and more palatable seeds and fruits. We explore the technologies and frameworks for the discovery and characterization of long-distance transporters of SMs for crop improvement. Transporter-focused frameworks offer a promising solution to global agricultural challenges and present exciting opportunities for advancing crop improvement in the context of global food supply.

Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

Ribulose bisphosphate carboxylase (RuBisCO) is the primary regulator of carbon fixation in the plant kingdom. Although the large subunit (RBCL) is the site of catalysis, RuBisCO efficiency is also influenced by the sequence divergence of the small subunit (RBCS). This project compared the RBCS gene family in C3 and C4 grasses to identify genetic targets for improved crop photosynthesis. Triticeae/Aveneae phylogeny groups exhibited a syntenic tandem duplication array averaging 326.1 Kbp on ancestral chromosomes 2 and 3, with additional copies on other chromosomes. Promoter analysis revealed a paired I-box element promoter arrangement in chromosome 5 RBCS of H. vulgare, S. cereale, and A. tauschii. The I-box pair was associated with significantly enhanced expression, suggesting functional adaptation of specific RBCS gene copies in Triticaeae. H. vulgare-derived pan-transcriptome data showed that RBCS expression was 50.32% and 28.44% higher in winter-type accessions compared to spring types for coleoptile (p < 0.05) and shoot, respectively (p < 0.01). Molecular dynamics simulations of a mutant H. vulgare Rubisco carrying a C4-like amino acid substitution (G59C) in RBCS significantly enhanced the stability of the Rubisco complex. Given the known structural efficiency of C4 Rubisco complexes, G59C could serve as an engineering target for enhanced RBCS in economically crucial crop species which, in comparison, possess less efficient Rubisco complexes.

Crop wild relatives (CWRs) are invaluable for crop improvement. Among these, Hordeum I-genome species exhibit exceptional tolerance to alkali and salt stresses. Here we present a chromosome-scale genome assembly of Hordeum brevisubulatum (II, 2n = 2x =14) and genome resequencing of 38 diploid germplasms spanning 7 I-genome species. We reveal that the adaptive evolution of the H. brevisubulatum genome is shaped by structural variations, some of which may contribute to its adaptation to high alkali and salt environments. Evolutionary duplication of the stress sensor-responder module CaBP-NRT2 and the horizontally transferred fungal gene Fhb7 were identified as novel alkaline-saline tolerance mechanisms. We also demonstrate the potential of the Hordeum I genome in crop breeding through the newly synthesized hexaploid Tritordeum (AABBII) with enhanced alkaline-saline tolerance. Our study fills critical gaps in Hordeum genomics and CWR research, advancing introgression of CWR resources into current crops for sustainable agriculture.Crop wild relatives (CWRs) are invaluable for crop improvement. Among these, Hordeum I-genome species exhibit exceptional tolerance to alkali and salt stresses. Here we present a chromosome-scale genome assembly of Hordeum brevisubulatum (II, 2n = 2x =14) and genome resequencing of 38 diploid germplasms spanning 7 I-genome species. We reveal that the adaptive evolution of the H. brevisubulatum genome is shaped by structural variations, some of which may contribute to its adaptation to high alkali and salt environments. Evolutionary duplication of the stress sensor-responder module CaBP-NRT2 and the horizontally transferred fungal gene Fhb7 were identified as novel alkaline-saline tolerance mechanisms. We also demonstrate the potential of the Hordeum I genome in crop breeding through the newly synthesized hexaploid Tritordeum (AABBII) with enhanced alkaline-saline tolerance. Our study fills critical gaps in Hordeum genomics and CWR research, advancing introgression of CWR resources into current crops for sustainable agriculture.

Agriculture is a major contributor to global environmental challenges and is highly vulnerable to climate change. High-technology greenhouse farming provides efficient, secure and climate-resilient food production but costs significant energy to operate. We designed and constructed a greenhouse with high-transparency photovoltaic windows used as roof- and wall-mounted components of building envelope and demonstrated its significant potential to improve the sustainability of greenhouse farming. This innovative structure reduced energy consumption by 57% and water usage by 29% in research-scale greenhouse production. We showed that several crops commonly produced in greenhouses exhibited no yield loss when grown in solar greenhouses, including tomato, snow pea, spinach mustard, dwarf bean, bell pepper and lettuce. Due to a limitation in the experimental design, solar windows were not fully installed on the greenhouse, which led to an underestimation of the potential energy savings. A computing model showed that a fully glazed solar greenhouse has the potential to offset up to 100% of the energy consumption in worldwide locations by using adaptable and efficient temperature control techniques, thereby potentially enabling completely self-sustainable greenhouse farming on a global scale. The potential of self-sustainable greenhouse farming could be further enhanced by refining its wavelength-selective transmittance and using genetic manipulation to engineer crops that thrive in the solar greenhouse environment. The solar greenhouse technology represents significant opportunities to make substantial progress towards achieving net-zero emissions in global food systems by 2050.

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.
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.
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.
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 GA
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.
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.

The centres of diversification of the iconic family Proteaceae are in South Africa and southern Australia. Since the ancestors of the family can be traced to NW Africa our task was to explain how all subfamilies (Proteoideae, Grevilleoideae, Persoonioideae) managed to reach Australia and we propose the pathway: (Africa (N South America (S South America (Antarctica (Australia))))). Our dated molecular phylogeny shows that the family arose 132 million years ago (Ma), and by 125 Ma had separated into the three subfamilies that remain dominant today. The age and location of records for 420 fossil pollen with Proteaceae affinities were collated per continent and submitted to curve-fitting analysis. This showed spread of early Proteaceae into N South America from ∼121 Ma that was able to continue for another 20–25 My. These three subfamilies (plus Carnarvonia) travelled south through South America and Antarctica, crossing the Weddellian Isthmus from ∼110 Ma, to reach southern Australia by ∼104 Ma. The history of Proteaceae in South America mimics that of Africa, where Grevilleoideae diversified instead of Proteoideae that died out. Entry to Australia via Antarctica was possible until ∼70 Ma at its SW corner and 45 Ma at its SE (Tasmanian) corner enabling the three subfamilies (and Carnarvonia) restricted entry into Australia over 35–60 million years. The SW Australian sclerophyll flora became the centre of diversification and emigration at the species level of all but the rainforest (mesophyll) Grevilleoid/Proteoid clades within Australia. Close genetic links between clades in South Africa (the centre of diversification of the sclerophyll flora in Africa) and SW Australia are the product of disparate migratory histories from their common ancestor in NW Africa, differential survival among subfamilies and parallel evolution in matched environments. SE Australia became the centre of diversification at the subtribe level. Close genetic links between clades in South America and SE Australia are the product of long-distance dispersal from their common ancestor in N South America, genetic stability in matched environments and eventual vicariance.