RiceAntherNet: a gene co‐expression network for identifying anther and pollen development genes

Lin, Hong; Yu, Jing; Pearce, Simon P.; Zhang, Dabing; Wilson, Zoe A.

doi:10.1111/tpj.13744

Cited by 34 publications

(25 citation statements)

References 89 publications

(155 reference statements)

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“…Ba, bacula; CW, cell wall; dML, degraded middle layer; dT, degraded tapetum; E, Epidermis; En, endothecium; Msp, microspores; Ne, nexine; Pb, probacula; Pe, primexine; SP, sporopollenin; T, tapetal layer; Te, tectum; WT, wild type. Aya et al, 2009;Fu et al, 2014;Ko et al, 2014;Lin et al, 2017). Tapetum persistent mutants, such as ptc1 (Li et al, 2011) and eat1 (Ji et al, 2013;Niu et al, 2013), also have a tapetum resistant to degradation.…”

Section: Ptc2 Is Required For Tapetal Pcdmentioning

confidence: 99%

PERSISTENT TAPETAL CELL2 Is Required for Normal Tapetal Programmed Cell Death and Pollen Wall Patterning

Uzair

Schreiber

et al. 2019

Plant Physiol.

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The timely programmed cell death (PCD) of the tapetum, the innermost somatic anther cell layer in flowering plants, is critical for pollen development, including the deposition and patterning of the pollen wall. Although several genes involved in tapetal PCD and pollen wall development have been characterized, the underlying regulatory mechanism remains elusive. Here we report that PERSISTENT TAPETAL CELL2 (PTC2), which encodes an AT-hook nuclear localized protein in rice (Oryza sativa), is required for normal tapetal PCD and pollen wall development. The mutant ptc2 showed persistent tapetal cells and abnormal pollen wall patterning including absent nexine, collapsed bacula, and disordered tectum. The defective tapetal PCD phenotype of ptc2 was similar to that of a PCD delayed mutant, ptc1, in rice, while the abnormal pollen wall patterning resembled that of a pollen wall defective mutant, Transposable Element Silencing Via AT-Hook, in Arabidopsis (Arabidopsis thaliana). Levels of anther cutin monomers in ptc2 anthers were significantly reduced, as was expression of a series of lipid biosynthetic genes. PTC2 transcript and protein were shown to be present in the anther after meiosis, consistent with the observed phenotype. Based on these data, we propose a model explaining how PTC2 affects anther and pollen development. The characterization of PTC2 in tapetal PCD and pollen wall patterning expands our understanding of the regulatory network of male reproductive development in rice and will aid future breeding approaches.

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Section: Ptc2 Is Required For Tapetal Pcdmentioning

confidence: 99%

PERSISTENT TAPETAL CELL2 Is Required for Normal Tapetal Programmed Cell Death and Pollen Wall Patterning

Uzair

Schreiber

et al. 2019

Plant Physiol.

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“…Comparison of sorghum and rice anther transcriptome. Lin and co-workers 82 identified differentially expressed genes (DEGs) in several male sterile mutants of rice and divided them into three clades based on stage specific expression. Clade 2, 1, and 3 represent premeiotic to tetrad, tetrad and microspore, and pollen-related genes, respectively.…”

Section: Methodsmentioning

confidence: 99%

Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum

Dhaka

Krishnan

Kandpal

et al. 2020

Sci Rep

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Sorghum is a self-pollinated crop with multiple economic uses as cereal, forage, and biofuel feedstock. Hybrid breeding is a cornerstone for sorghum improvement strategies that currently relies on cytoplasmic male sterile lines. To engineer genic male sterility, it is imperative to examine the genetic components regulating anther/pollen development in sorghum. To this end, we have performed transcriptomic analysis from three temporal stages of developing anthers that correspond to meiotic, microspore and mature pollen stages. A total of 5286 genes were differentially regulated among the three anther stages with 890 of them exhibiting anther-preferential expression. Differentially expressed genes could be clubbed into seven distinct developmental trajectories using K-means clustering. Pathway mapping revealed that genes involved in cell cycle, DNA repair, regulation of transcription, brassinosteroid and auxin biosynthesis/signalling exhibit peak expression in meiotic anthers, while those regulating abiotic stress, carbohydrate metabolism, and transport were enriched in microspore stage. Conversely, genes associated with protein degradation, post-translational modifications, cell wall biosynthesis/modifications, abscisic acid, ethylene, cytokinin and jasmonic acid biosynthesis/ signalling were highly expressed in mature pollen stage. High concurrence in transcriptional dynamics and cis-regulatory elements of differentially expressed genes in rice and sorghum confirmed conserved developmental pathways regulating anther development across species. Comprehensive literature survey in conjunction with orthology analysis and anther-preferential accumulation enabled shortlisting of 21 prospective candidates for in-depth characterization and engineering male fertility in sorghum. Sorghum, grown widely for food, feed, and forage, is a gluten-free substitute for staple grains, and a promising feedstock for biofuels 1. It exhibits huge phenotypic and morphological diversity in key agronomic traits including photoperiod sensitivity, biomass, grain yield, disease resistance, abiotic stress tolerance etc., with considerable scope for genetic enhancement of cultivated sorghum. However, sorghum is a self-pollinated crop with 75 to 95% rate of self-pollination observed under natural conditions with outcrossing rates varying with panicle type, distance between plants, wind direction, etc 2,3. Therefore, overcoming reproductive constraints is a major challenge to utilize sorghum diversity for breeding programs. Plant breeders have been using cytoplasmic (CMS) and nuclear male sterility (NMS) systems to take advantage of hybrid vigour in many self-pollinated crop species 4. While CMS, caused by specific nuclear and mitochondrial genetic interactions, is maternally inherited; NMS results due to defects in nuclear genes usually inherited as a recessive trait 5. Studies in rice suggest that hybrids produced through NMS give higher yields and germplasm utilization efficiency with better genetic stability under diverse environmental condit...

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“…Another microarray-based GCE network was reconstructed in A. thaliana anther by using 10,797 genes expressed in anther/ flora, and transcriptional landscape of GMS mutant was included in the stable examination of this newly constructed network [51]. In rice, microarrays from WT anther tissue across stages 2-14 and nine GMS lines were integrated to reconstruct a big GCE network containing more than 9000 genes and 0.4 million pairs of coexpression relationships [52].…”

Section: Gene Co-expression Analysismentioning

confidence: 99%

Plant Comparative Transcriptomics Reveals Functional Mechanisms and Gene Regulatory Networks Involved in Anther Development and Male Sterility

Wan¹,

Li²

2019

Transcriptome Analysis

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Gene transcription and transcriptional regulation are crucial biological processes in all cellular life. Through the next-generation sequencing (NGS) technology, transcriptome data from different tissues and developmental stages can be easily obtained, which provides us a powerful tool to reveal the transcriptional landscape of investigated tissue(s) at special developmental stage(s). Anther development is an important process not only for sexual plant reproduction but also for genic male sterility (GMS) used in agriculture production. Plant comparative transcriptomics has been widely used to uncover molecular mechanism of GMS. Here, we focused on researches of anther developmental process and plant GMS genes by using comparative transcriptomics method. In detail, the contents include the following: (1) we described the commonly used flowchart in comparative transcriptomics; (2) we summarized the comparative strategies used to analyze transcriptome data; (3) we presented a case study on a maize GMS gene, ZmMs33; (4) we described the methods and results previously reported on gene co-expression and gene regulatory networks; (5) we presented the workflow of a case study on gene regulatory network reconstruction. The further development of comparative transcriptomics will provide us more powerful theoretical and application tools to investigate molecular mechanism underlying anther development and plant male sterility.

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RiceAntherNet: a gene co‐expression network for identifying anther and pollen development genes

Cited by 34 publications

References 89 publications

PERSISTENT TAPETAL CELL2 Is Required for Normal Tapetal Programmed Cell Death and Pollen Wall Patterning

PERSISTENT TAPETAL CELL2 Is Required for Normal Tapetal Programmed Cell Death and Pollen Wall Patterning

Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum

Plant Comparative Transcriptomics Reveals Functional Mechanisms and Gene Regulatory Networks Involved in Anther Development and Male Sterility

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