Prospects for rice in 2050

A key to achieve the goals put forward in the UN's 2030 Agenda for Sustainable Development, it will need transformative change to our agrifood systems. We must mount to the global challenge to achieve food security in a sustainable manner in the context of climate change, population growth, urbanization, and depletion of natural resources. Rice is one of the major staple cereal crops that has contributed, is contributing, and will still contribute to the global food security. To date, rice yield has held pace with increasing demands, due to advances in both fundamental and biological studies, as well as genomic and molecular breeding practices. However, future rice production depends largely on the planting of resilient cultivars that can acclimate and adapt to changing environmental conditions. This Special Issue highlight with reviews and original research articles the exciting and growing field of rice-environment interactions that could benefit future rice breeding. We also outline open questions and propose future directions of 2050 rice research, calling for more attentions to develop environment-resilient rice especially hybrid rice, upland rice and perennial rice.Jianxin Shi, Gynheung An, Andreas P. M. Weber, Dabing Zhan

Arabidopsis A BOUT DE SOUFFLE is a putative mitochondrial transporter involved in photorespiratory metabolism and is required for meristem growth at ambient CO2 levels

Photorespiratory metabolism is essential in all oxygenic photosynthetic organisms. In plants, it is a highly compartmentalized pathway that involves chloroplasts, peroxisomes, mitochondria and the cytoplasm. The metabolic pathway itself is well characterized, and the enzymes required for its function have been identified. However, very little information is available on the transport proteins that catalyze the high metabolic flux between the involved compartments. Here we show that the A BOUT DE SOUFFLE (BOU) gene, which encodes a mitochondrial carrier, is involved in photorespiration in Arabidopsis. BOU was found to be co-expressed with photorespiratory genes in leaf tissues. The knockout mutant bou-2 showed the hallmarks of a photorespiratory growth phenotype, an elevated CO2 compensation point, and excessive accumulation of glycine. Furthermore, degradation of the P-protein, a subunit of glycine decarboxylase, was demonstrated for bou-2, and is reflected in strongly reduced glycine decarboxylase activity. The photorespiration defect in bou-2 has dramatic consequences early in the seedling stage, which are highlighted by transcriptome studies. In bou-2 seedlings, as in shm1, another photorespiratory mutant, the shoot apical meristem organization is severely compromised. Cell divisions are arrested, leading to growth arrest at ambient CO2. Although the specific substrate for the BOU transporter protein remains elusive, we show that it is essential for the function of the photorespiratory metabolism. We hypothesize that BOU function is linked with glycine decarboxylase activity, and is required for normal apical meristems functioning in seedlings

D-2-hydroxyglutarate metabolism is linked to photorespiration in the shm1-1 mutant

The Arabidopsis mutant shm1-1 is defective in mitochondrial serine hydroxymethyltransferase 1 activity and displays a lethal photorespiratory phenotype at ambient CO2 concentration but grows normally at high CO2. After transferring high CO2-grown shm1-1 plants to ambient CO2, the younger leaves remain photosynthetically active while developed leaves display increased yellowing and decreased FV/FM values. Metabolite analysis of plants transferred from high CO2 to ambient air indicates a massive light-dependent (photorespiratory) accumulation of glycine, 2-oxoglutarate (2OG) and D-2-hydroxyglutarate (D-2HG). Amino acid markers of senescence accumulated in ambient air in wild-type and shm1-1 plants maintained in darkness and also build up in shm1-1 in the light. This, together with an enhanced transcription of the senescence marker SAG12 in shm1-1, suggests the initiation of senescence in shm1-1 under photorespiratory conditions. Mitochondrial D-2HG dehydrogenase (D-2HGDH) converts D-2HG into 2OG. In vitro studies indicate that 2OG exerts competitive inhibition on D-2HGDH with a Ki of 1.96 mm. 2OG is therefore a suitable candidate as inhibitor of the in vivo D-2HGDH activity, as 2OG is produced and accumulates in mitochondria. Inhibition of the D-2HGDH by 2OG is likely a mechanism by which D-2HG accumulates in shm1-1, however it cannot be ruled out that D-2HG may also accumulate due to an active senescence programme that is initiated in these plants after transfer to photorespiratory conditions. Thus, a novel interaction of the photorespiratory pathway with cellular processes involving D-2HG has been identified

Gene and genome duplications and the origin fo C4 photosysnthesis: Birth of a trait in the Cleomaceae

C4 photosynthesis is a trait that has evolved in 66 independent plant lineages and increases the efficiency of carbon fixation. The shift from C3 to C4 photosynthesis requires substantial changes to genes and gene functions effecting phenotypic, physiological and enzymatic changes. We investigate the role of ancient whole genome duplications (WGD) as a source of new genes in the development of this trait and compare expression between paralog copies. We compare Gynandropsis gynandra, the closest relative of Arabidopsis that uses C4 photosynthesis, with its C3 relative Tarenaya hassleriana that underwent a WGD named Th-a. We establish through comparison of paralog synonymous substitution rate that both species share this paleohexaploidy. Homologous clusters of photosynthetic gene families show that gene copy numbers are similar to what would be expected given their duplication history and that no significant difference between the C3 and C4 species exists in terms of gene copy number. This is further confirmed by syntenic analysis of T. hassleriana, Arabidopsis thaliana and Aethionema arabicum, where syntenic region copy number ratios lie close to what could be theoretically expected. Expression levels of C4 photosynthesis orthologs show that regulation of transcript abundance in T. hassleriana is much less strictly controlled than in G. gynandra, where orthologs have extremely similar expression patterns in different organs, seedlings and seeds. We conclude that the Th-a and older paleopolyploidy events have had a significant influence on the specific genetic makeup of Cleomaceae versus Brassicaceae. Because the copy number of various essential genes involved in C4 photosynthesis is not significantly influenced by polyploidy combined with the fact that transcript abundance in G. gynandra is more strictly controlled, we also conclude that recruitment of existing genes through regulatory changes is more likely to have played a role in the shift to C4 than the neofunctionalization of duplicated genes

Gene and genome duplications and the origin fo C4 photosysnthesis: Birth of a trait in the Cleomaceae

C4 photosynthesis is a trait that has evolved in 66 independent plant lineages and increases the efficiency of carbon fixation. The shift from C3 to C4 photosynthesis requires substantial changes to genes and gene functions effecting phenotypic, physiological and enzymatic changes. We investigate the role of ancient whole genome duplications (WGD) as a source of new genes in the development of this trait and compare expression between paralog copies. We compare Gynandropsis gynandra, the closest relative of Arabidopsis that uses C4 photosynthesis, with its C3 relative Tarenaya hassleriana that underwent a WGD named Th-a. We establish through comparison of paralog synonymous substitution rate that both species share this paleohexaploidy. Homologous clusters of photosynthetic gene families show that gene copy numbers are similar to what would be expected given their duplication history and that no significant difference between the C3 and C4 species exists in terms of gene copy number. This is further confirmed by syntenic analysis of T. hassleriana, Arabidopsis thaliana and Aethionema arabicum, where syntenic region copy number ratios lie close to what could be theoretically expected. Expression levels of C4 photosynthesis orthologs show that regulation of transcript abundance in T. hassleriana is much less strictly controlled than in G. gynandra, where orthologs have extremely similar expression patterns in different organs, seedlings and seeds. We conclude that the Th-a and older paleopolyploidy events have had a significant influence on the specific genetic makeup of Cleomaceae versus Brassicaceae. Because the copy number of various essential genes involved in C4 photosynthesis is not significantly influenced by polyploidy combined with the fact that transcript abundance in G. gynandra is more strictly controlled, we also conclude that recruitment of existing genes through regulatory changes is more likely to have played a role in the shift to C4 than the neofunctionalization of duplicated genes

Azolla domestication towards a biobased economy?

Due to its phenomenal growth requiring neither nitrogen fertilizer nor arable land and its biomass composition, the mosquito fern Azolla is a candidate crop to yield food, fuels and chemicals sustainably. To advance Azolla domestication, we research its dissemination, storage and transcriptome. Methods for dissemination, cross-fertilization and cryopreservation of the symbiosis Azolla filiculoides–Nostoc azollae are tested based on the fern spores. To study molecular processes in Azolla including spore induction, a database of 37 649 unigenes from RNAseq of microsporocarps, megasporocarps and sporophytes was assembled, then validated. Spores obtained year-round germinated in vitro within 26 d. In vitro fertilization rates reached 25%. Cryopreservation permitted storage for at least 7 months. The unigene database entirely covered central metabolism and to a large degree covered cellular processes and regulatory networks. Analysis of genes engaged in transition to sexual reproduction revealed a FLOWERING LOCUS T-like protein in ferns with special features induced in sporulating Azolla fronds. Although domestication of a fern–cyanobacteria symbiosis may seem a daunting task, we conclude that the time is ripe and that results generated will serve to more widely access biochemicals in fern biomass for a biobased economy

Past and future milestones of plant breeding

In honour of the 25th anniversary of Trends in Plant Science, we wanted to take a look back over some of the milestones from recent decades. Here, we asked authors of the June 2021 special issue to reflect on the changes that have occurred within the field of plant breeding during the past 25 years, as well as to contemplate what the future might hold

The genome of Gynandropsis gynandra provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to Arabidopsis. Here, we present a high-quality genome sequence of G. gynandra, anchored onto 17 main super- scaffolds with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. We revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1x) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3 T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the impact of gene duplication and gene retention on the evolution of C4 photosynthesis in Cleomaceae