Catálogo de publicaciones - revistas

<jats:title>SUMMARY</jats:title><jats:p>Nitrogen (N) is an essential factor for limiting crop yields, and cultivation of crops with low nitrogen‐use efficiency (NUE) exhibits increasing environmental and ecological risks. Hence, it is crucial to mine valuable NUE improvement genes, which is very important to develop and breed new crop varieties with high NUE in sustainable agriculture system. Quantitative trait locus (QTL) and genome‐wide association study (GWAS) analysis are the most common methods for dissecting genetic variations underlying complex traits. In addition, with the advancement of biotechnology, multi‐omics technologies can be used to accelerate the process of exploring genetic variations. In this study, we integrate the substantial data of QTLs, quantitative trait nucleotides (QTNs) from GWAS, and multi‐omics data including transcriptome, proteome, and metabolome and further analyze their interactions to predict some NUE‐related candidate genes. We also provide the genic resources for NUE improvement among maize, rice, wheat, and sorghum by homologous alignment and collinearity analysis. Furthermore, we propose to utilize the knowledge gained from classical cases to provide the frameworks for improving NUE and breeding N‐efficient varieties through integrated genomics, systems biology, and modern breeding technologies.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Genome‐wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High‐throughput omics technologies, such as genomics, transcriptomics, proteomics and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalise on a diverse canola population with 477 spring‐type lines which was previously analysed by high‐throughput phenotyping of growth‐related traits and by RNA sequencing and metabolite profiling for multi‐omics‐based hybrid performance prediction. We deepened the phenotypic data analysis, now providing 123 time‐resolved image‐based traits, to gain insight into the complex relations during early vegetative growth and reanalysed the transcriptome data based on the latest Darmor‐<jats:italic>bzh</jats:italic> v10 genome assembly. Genome‐wide association testing revealed 61 298 robust quantitative trait loci (QTL) including 187 metabolite QTL, 56814 expression QTL and 4297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritised candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1) and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the <jats:italic>Brassica</jats:italic> A and C subgenomes on early biomass production.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome‐wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA‐seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non‐seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp‐specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene‐related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Heterosis, also known as hybrid vigor, is the phenomenon wherein a progeny exhibits superior traits relative to one or both parents. In terms of crop breeding, this usually refers to the yield advantage of F<jats:sub>1</jats:sub> hybrids over both inbred parents. The development of high‐yielding hybrid cultivars across a wider range of crops is key to meeting future food demands. However, conventional hybrid breeding strategies are proving to be exceptionally challenging to apply commercially in many self‐pollinating crops, particularly wheat and barley. Currently in these crops, the relative performance advantage of hybrids over inbred line cultivars does not outweigh the cost of hybrid seed production. Here, we review the genetic basis of heterosis, discuss the challenges in hybrid breeding, and propose a strategy to recruit multiple heterosis‐associated genes to develop lines with improved agronomic characteristics. This strategy leverages modern genetic engineering tools to synthesize supergenes by fusing multiple heterotic alleles across multiple heterosis‐associated loci. We outline a plan to assess the feasibility of this approach to improve line performance using barley (<jats:italic>Hordeum vulgare</jats:italic>) as the model self‐pollinating crop species, and a few heterosis‐associated genes. The proposed method can be applied to all crops for which heterotic gene combinations can be identified.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Formation of secondary cell wall (SCW) is tightly regulated spatiotemporally by various developmental and environmental signals. Successful fine‐tuning of the trade‐off between SCW biosynthesis and stress responses requires a better understanding of how plant growth is regulated under environmental stress conditions. However, the current understanding of the interplay between environmental signaling and SCW formation is limited. The lipid‐derived plant hormone jasmonate (JA) and its derivatives are important signaling components involved in various physiological processes including plant growth, development, and abiotic/biotic stress responses. Recent studies suggest that JA is involved in SCW formation but the signaling pathway has not been studied for how JA regulates SCW formation. We tested this hypothesis using the transcription factor MYB46, a master switch for SCW biosynthesis, and JA treatments. Both the transcript and protein levels of MYB46, a master switch for SCW formation, were significantly increased by JA treatment, resulting in the upregulation of SCW biosynthesis. We then show that this JA‐induced upregulation of MYB46 is mediated by MYC2, a central regulator of JA signaling, which binds to the promoter of MYB46. We conclude that this MYC2‐MYB46 module is a key component of the plant response to JA in SCW formation.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Sorbitol is a critical photosynthate and storage substance in the Rosaceae family. Sorbitol transporters (SOTs) play a vital role in facilitating sorbitol allocation from source to sink organs and sugar accumulation in sink organs. While prior research has addressed gene duplications within the SOT gene family in Rosaceae, the precise origin and evolutionary dynamics of these duplications remain unclear, largely due to the complicated interplay of whole genome duplications and tandem duplications. Here, we investigated the synteny relationships among all identified Polyol/Monosaccharide Transporter (PLT) genes in 61 angiosperm genomes and SOT genes in representative genomes within the Rosaceae family. By integrating phylogenetic analyses, we elucidated the lineage‐specific expansion and syntenic conservation of PLTs and SOTs across diverse plant lineages. We found that Rosaceae SOTs, as PLT family members, originated from a pair of tandemly duplicated PLT genes within Class III‐A. Furthermore, our investigation highlights the role of lineage‐specific and synergistic duplications in Amygdaloideae in contributing to the expansion of SOTs in Rosaceae plants. Collectively, our findings provide insights into the genomic origins, duplication events, and subsequent divergence of SOT gene family members. Such insights lay a crucial foundation for comprehensive functional characterizations in future studies.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Ascorbate plays an indispensable role in plants, functioning as both an antioxidant and a cellular redox buffer. It is widely acknowledged that the ascorbate biosynthesis in the photosynthetic tissues of land plants is governed by light‐mediated regulation of the D‐mannose/L‐galactose (D‐Man/L‐Gal) pathway. At the core of this light‐dependent regulation lies the <jats:italic>VTC2</jats:italic> gene, encoding the rate‐limiting enzyme GDP‐L‐Gal phosphorylase. The <jats:italic>VTC2</jats:italic> expression is regulated by signals <jats:italic>via</jats:italic> the photosynthetic electron transport system. In this study, we directed our attention to the liverwort <jats:italic>Marchantia polymorpha</jats:italic>, representing one of the basal land plants, enabling us to conduct an in‐depth analysis of its ascorbate biosynthesis. The <jats:italic>M. polymorpha</jats:italic> genome harbors a solitary gene for each enzyme involved in the D‐Man/L‐Gal pathway, including <jats:italic>VTC2</jats:italic>, along with three lactonase orthologs, which may be involved in the alternative ascorbate biosynthesis pathway. Through supplementation experiments with potential precursors, we observed that only L‐Gal exhibited effectiveness in ascorbate biosynthesis. Furthermore, the generation of <jats:italic>VTC2</jats:italic>‐deficient mutants through genome editing unveiled the inability of thallus regeneration in the absence of L‐Gal supplementation, thereby revealing the importance of the D‐Man/L‐Gal pathway in ascorbate biosynthesis within <jats:italic>M.  polymorpha</jats:italic>. Interestingly, gene expression analyses unveiled a distinct characteristic of <jats:italic>M. polymorpha</jats:italic>, where none of the genes associated with the D‐Man/L‐Gal pathway, including <jats:italic>VTC2</jats:italic>, showed upregulation in response to light, unlike other known land plants. This study sheds light on the exceptional nature of <jats:italic>M. polymorpha</jats:italic> as a land plant that has evolved distinctive mechanisms concerning ascorbate biosynthesis and its regulation.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Leaf plastids harbor a plethora of biochemical reactions including photosynthesis, one of the most important metabolic pathways on Earth. Scientists are eager to unveil the physiological processes within the organelle but also their interconnection with the rest of the plant cell. An increasingly important feature of this venture is to use experimental data in the design of metabolic models. A remaining obstacle has been the limited in situ volume information of plastids and other cell organelles. To fill this gap for chloroplasts, we established three microscopy protocols delivering <jats:italic>in situ</jats:italic> volumes based on: (i) chlorophyll fluorescence emerging from the thylakoid membrane, (ii) a CFP marker embedded in the envelope, and (iii) calculations from serial block‐face scanning electron microscopy (SBFSEM). The obtained data were corroborated by comparing wild‐type data with two mutant lines affected in the plastid division machinery known to produce small and large mesophyll chloroplasts, respectively. Furthermore, we also determined the volume of the much smaller guard cell plastids. Interestingly, their volume is not governed by the same components of the division machinery which defines mesophyll plastid size. Based on our three approaches, the average volume of a mature Col‐0 wild‐type mesophyll chloroplasts is 93 μm<jats:sup>3</jats:sup>. Wild‐type guard cell plastids are approximately 18 μm<jats:sup>3</jats:sup>. Lastly, our comparative analysis shows that the chlorophyll fluorescence analysis can accurately determine chloroplast volumes, providing an important tool to research groups without access to transgenic marker lines expressing genetically encoded fluorescence proteins or costly SBFSEM equipment.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Chloroplast biogenesis is critical for crop biomass and economic yield. However, chloroplast development is a very complicated process coordinated by cross‐communication between the nucleus and plastids, and the underlying mechanisms have not been fully revealed. To explore the regulatory machinery for chloroplast biogenesis, we conducted map‐based cloning of the <jats:italic>Grandpa</jats:italic> 1 (<jats:italic>Gpa1</jats:italic>) gene regulating chloroplast development in barley. The spontaneous mutation <jats:italic>gpa1.a</jats:italic> caused a variegation phenotype of the leaf, dwarfed growth, reduced grain yield, and increased tiller number. Genetic mapping anchored the <jats:italic>Gpa1</jats:italic> gene onto 2H within a gene cluster functionally related to photosynthesis or chloroplast differentiation. One gene (<jats:italic>HORVU.MOREX.r3.2HG0213170</jats:italic>) in the delimited region encodes a putative plastid terminal oxidase (PTOX) in thylakoid membranes, which is homologous to IMMUTANS (IM) of Arabidopsis. The IM gene is required for chloroplast biogenesis and maintenance of functional thylakoids in <jats:italic>Arabidopsis</jats:italic>. Using CRISPR technology and gene transformation, we functionally validated that the PTOX‐encoding gene, <jats:italic>HORVU.MOREX.r3.2HG0213170</jats:italic>, is the causal gene of <jats:italic>Gpa1</jats:italic>. Gene expression and chemical analysis revealed that the carotenoid biosynthesis pathway is suppressed by the <jats:italic>gpa1</jats:italic> mutation, rendering mutants vulnerable to photobleaching. Our results showed that the overtillering associated with the <jats:italic>gpa1</jats:italic> mutation was caused by the lower accumulation of carotenoid‐derived strigolactones (SLs) in the mutant. The cloning of <jats:italic>Gpa1</jats:italic> not only improves our understanding of the molecular mechanisms underlying chloroplast biosynthesis but also indicates that the PTOX activity is conserved between monocots and dicots for the establishment of the photosynthesis factory.</jats:p>