Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

Plant Communications, Journal Year: 2024, Volume and Issue: 5(5), P. 100879 - 100879

Published: March 14, 2024

Spike architecture influences both grain weight and number per spike, which are the two major components of yield in bread wheat (Triticum aestivum L.). However, complex genome influence various environmental factors pose challenges mapping causal genes that affect spike traits. Here, we systematically identified involved trait formation by integrating information on genomic variation gene regulatory networks controlling young development wheat. We 170 loci responsible for variations length, spikelet through genome-wide association study meta-QTL analyses. constructed inflorescences at double ridge stage floret primordium stage, meristem predominant, respectively, transcriptome, histone modification, chromatin accessibility, eQTL, protein-protein interactome data. From these networks, 169 hub located 76 QTL regions whose polymorphisms significantly associated with The functions TaZF-B1, VRT-B2, TaSPL15-A/D establishment were verified. This provides valuable molecular resources understanding traits demonstrates combining genetic analysis developmental is a robust approach dissection

Language: Английский

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scPlant: A versatile framework for single-cell transcriptomic data analysis in plants

Plant Communications, Journal Year: 2023, Volume and Issue: 4(5), P. 100631 - 100631

Published: May 29, 2023

Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of growth, development, responses to external stimuli. However, single-cell transcriptomic data analysis plants not trivial, given that there currently no end-to-end solution integration various bioinformatics tools involves a large number required dependencies. Here, we present scPlant, versatile framework for exploring atlases with minimum input provided by users. The scPlant pipeline implemented numerous functions diverse analytical tasks, ranging from basic processing advanced demands such as cell-type annotation deconvolution, trajectory inference, cross-species integration, cell-type-specific gene regulatory network construction. In addition, variety visualization are bundled built-in Shiny application, enabling exploration on the fly.

Language: Английский

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The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution

Developmental Cell, Journal Year: 2023, Volume and Issue: 58(15), P. 1429 - 1444.e6

Published: June 15, 2023

Bryophytes represents a sister to the rest of land plants. Despite their evolutionary importance and relatively simple body plan, comprehensive understanding cell types transcriptional states that underpin temporal development bryophytes has not been achieved. Using time-resolved single-cell RNA sequencing, we define cellular taxonomy Marchantia polymorpha across asexual reproduction phases. We identify two maturation aging trajectories main plant M. at resolution: gradual tissues organs along tip-to-base axis midvein progressive decline meristem activities in tip chronological axis. Specifically, observe latter is temporally correlated with formation clonal propagules, suggesting an ancient strategy optimize allocation resources producing offspring. Our work thus provides insights into heterogeneity underpins bryophytes.

Language: Английский

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Progress in Rice Breeding Based on Genomic Research

Genes, Journal Year: 2024, Volume and Issue: 15(5), P. 564 - 564

Published: April 27, 2024

The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the genome will contribute to identification and utilization outstanding functional genes, enriching diversity genetic basis materials meeting diverse demands for various improvements. Here, we review significant contributions over last 25 years, discussing profound impact on sequencing, gene exploration, novel methods, provide valuable insights future practices.

Language: Английский

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Integrating physiological and multi-omics methods to elucidate heat stress tolerance for sustainable rice production

Physiology and Molecular Biology of Plants, Journal Year: 2024, Volume and Issue: 30(7), P. 1185 - 1208

Published: July 1, 2024

Language: Английский

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