Yongming Chen

China Agricultural University | CAU · College of Agronomy and Biotechnology

Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in pangenomic era. We proposed a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes t...

Gene regulation is central to all aspects of organism growth, and understanding it from large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement still lacks. Her...

The dynamics of gene expression in crop grains has typically been investigated at the transcriptional level. However, this approach neglects translational regulation, a widespread mechanism that rapidly modulates gene expression to increase the plasticity of organisms. Here, we performed ribosome profiling and polysome profiling to obtain a compreh...

Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that...

Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization is currently elusive. Here, we profiled transcriptomes and DNA methylomes of two diploid wheat accessions (S l S l and AA) and their...

Bread wheat ( Triticum aestivum ) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional...

Long non-coding RNAs (lncRNAs) are key regulators of many biological processes, but our knowledge of lncRNAs associated with wheat (Triticum aestivum) grain development is limited. Here, to generate a comprehensive atlas of lncRNAs in wheat, we performed strand-specific RNA sequencing (ssRNA-seq) using wheat endosperm at 10 and 15 d after pollinati...

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progresses in studying on the wheat genome are substantially trailed behind those of other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput seq...

Dissecting genetic components in crop plants associated with heat stress (HS) sensing and adaptation will facilitate the design of modern crop varieties with improved thermotolerance. However, the molecular mechanisms underlying the ON/OFF switch controlling HS responses (HSRs) in wheat (Triticum aestivum) remain largely unknown. In this study, we...

Heat stress is a limiting factor in wheat production along with global warming. Development of heat-tolerant wheat varieties and generation of suitable pre-breeding materials are the major goals in current wheat breeding programs. Our understanding on the genetic basis of thermotolerance remains sparse. In this study, we genotyped a collection of 2...

To integrate the genomic information of the rice pan-genome, we performed comparative analyses and established a user-friendly Rice Gene Index (RGI, https://riceome.hzau.edu.cn) platform with 16 platinum standard reference genomes and supplementary transcriptome data. To logically organize and scientifically the index of 744,233 genes among rice ac...

Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshapes the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we propose a novel approach, IGTminer,...

Plants have evolved a two‐branched innate immune system to detect and cope with pathogen attack, which are initiated by cell‐surface and intracellular immune receptors leading to pattern‐triggered immunity (PTI) and effector‐triggered immunity (ETI), respectively. A core transducer including PAD4‐EDS1 node is proposed as the convergence point for a...

Along with increasing demands for high yield, elite processing quality and improved nutrient value in wheat, concerns have emerged around the effects of gluten in wheat‐based foods on human health. However, knowledge of the mechanisms regulating gluten accumulation remains largely unexplored. Here we report the identification and characterization o...

Leaf width (LW) is an important component of plant architecture that extensively affects light capture during photosynthesis and grain yield particularly under dense planting conditions. However, the genetic and molecular mechanisms regulating LW remain largely elusive in maize (Zea mays L.). In this study, qLW4a, one major quantitative trait locus...

In wheat (Triticum aestivum L.), breeding efforts have focused intensively on improving grain yield and quality. For quality, the content and composition of seed storage proteins (SSPs) determine the elasticity of wheat dough and flour processing quality. Moreover, starch levels in seeds are associated with yield. However, little is known about the...

Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of a Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 wheat accessions, including world-wide wheat landraces, cult...

Key message: This study dissected and validated a QTL cluster associated with thousand grain weight on chromosome 4B using multiple near-isogenic lines in common wheat. Grain size and weight are crucial components of wheat yield. Previously, we identified a QTL cluster for thousand grain weight (TGW) on chromosome 4B using the Nongda3338 (ND3338)/...

Key message This study precisely mapped and validated a major quantitative trait locus (QTL) on chromosome 4AL for thousand-grain weight in wheat using multiple near-isogenic lines. Abstract Thousand-grain weight (TGW) is an essential yield component. Following the previous identification of a major QTL for TGW within the interval of 15.7 cM (92.7...