Transcriptional profiling analysis of genic male sterile–fertile Capsicum annuum reveal candidate genes for pollen development and maturation by RNA-Seq technology

Abstract Background: Polygalacturonase (PG) belongs to a large family of hydrolases with important functions in cell separation during plant growth and development via the degradation of pectin. The specific expression of PG genes in anthers may be significant for male sterility research and hybrid wheat breeding, but it has not been characterized in wheat (Triticum aestivum L.). Results: We systematically studied the PG gene family using the latest published wheat reference genomic information. In total, 113 wheat PG genes were identified and renamed as TaPG01–113 based on their chromosomal positions. The PG genes are unequally distributed on 21 chromosomes and classified according to six categories from A–F. Analysis of the gene structures and conserved motifs demonstrated that the Class C and D TaPGs have relatively short gene sequences and a small number of introns. Class E TaPGs are the least conserved and lack conserved domain III. Polyploidy and segmental duplications in wheat were mainly responsible for the expansion of the wheat PG gene family. Predictions of cis-elements indicate that TaPGs have a wide range of functions, including the responses to light, hypothermia, anaerobic conditions, and hormonal stimulation, as well as being involved in meristematic tissue expression. RNA-seq showed that TaPGs have specific temporal and spatial expression characteristics. Twelve spike-specific TaPGs were screened using RNA-seq data and verified by qRT-PCR in the sterile and fertile anthers of thermo-sensitive male-sterile wheat. Four important candidate genes were identified as involved in the male fertility determination process. In fertile anthers, TaPG09 may be involved in the separation of pollen. TaPG87 and TaPG95 could play important roles in anther dehiscence. TaPG93 may be related to pollen development and pollen tube elongation. Conclusions: We analyzed the wheat PG gene family and identified four important TaPGs with differential expression levels in the wheat fertility conversion process. Our findings may facilitate functional investigations of the wheat PG gene family and provide new insights into the fertility conversion mechanism in male-sterile wheat.

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OsMYB80 Regulates Anther Development and Pollen Fertility by Targeting Multiple Biological Pathways

Plant and Cell Physiology ◽

10.1093/pcp/pcaa025 ◽

2020 ◽

Vol 61 (5) ◽

pp. 988-1004 ◽

Cited By ~ 3

Author(s):

Xiaoying Pan ◽

Wei Yan ◽

Zhenyi Chang ◽

Yingchao Xu ◽

Ming Luo ◽

...

Keyword(s):

Pollen Development ◽

Male Fertility ◽

Gene Networks ◽

Affinity Purification ◽

Anther Development ◽

Rna Seq ◽

Male Sterile ◽

New Information ◽

Gel Shift Assay

Abstract Pollen development is critical to the reproductive success of flowering plants, but how it is regulated is not well understood. Here, we isolated two allelic male-sterile mutants of OsMYB80 and investigated how OsMYB80 regulates male fertility in rice. OsMYB80 was barely expressed in tissues other than anthers, where it initiated the expression during meiosis, reached the peak at the tetrad-releasing stage and then quickly declined afterward. The osmyb80 mutants exhibited premature tapetum cell death, lack of Ubisch bodies, no exine and microspore degeneration. To understand how OsMYB80 regulates anther development, RNA-seq analysis was conducted to identify genes differentially regulated by OsMYB80 in rice anthers. In addition, DNA affinity purification sequencing (DAP-seq) analysis was performed to identify DNA fragments interacting with OsMYB80 in vitro. Overlap of the genes identified by RNA-seq and DAP-seq revealed 188 genes that were differentially regulated by OsMYB80 and also carried an OsMYB80-interacting DNA element in the promoter. Ten of these promoter elements were randomly selected for gel shift assay and yeast one-hybrid assay, and all showed OsMYB80 binding. The 10 promoters also showed OsMYB80-dependent induction when co-expressed in rice protoplast. Functional annotation of the 188 genes suggested that OsMYB80 regulates male fertility by directly targeting multiple biological processes. The identification of these genes significantly enriched the gene networks governing anther development and provided much new information for the understanding of pollen development and male fertility.

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Identification of candidate genes underlying genic male-sterile msc-1 locus via genome resequencing in Capsicum annuum L.

Theoretical and Applied Genetics ◽

10.1007/s00122-018-3119-1 ◽

2018 ◽

Vol 131 (9) ◽

pp. 1861-1872 ◽

Cited By ~ 9

Author(s):

Qing Cheng ◽

Peng Wang ◽

Jinqiu Liu ◽

Lang Wu ◽

Zongpeng Zhang ◽

...

Keyword(s):

Candidate Genes ◽

Capsicum Annuum ◽

Male Sterile ◽

Genome Resequencing ◽

Capsicum Annuum L

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Identification on mitogen-activated protein kinase signaling cascades by integrating protein interaction with transcriptional profiling analysis in cotton

Scientific Reports ◽

10.1038/s41598-018-26400-w ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 9

Author(s):

Xueying Zhang ◽

Xinyue Mi ◽

Chuan Chen ◽

Haitang Wang ◽

Wangzhen Guo

Keyword(s):

Protein Kinase ◽

Protein Interaction ◽

Transcriptional Profiling ◽

Mitogen Activated Protein Kinase ◽

Signaling Cascades ◽

Kinase Signaling ◽

Mitogen Activated Protein ◽

Protein Kinase Signaling ◽

Profiling Analysis

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Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽

10.3390/ani11051423 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1423

Author(s):

André Albuquerque ◽

Cristina Óvilo ◽

Yolanda Núñez ◽

Rita Benítez ◽

Adrián López-Garcia ◽

...

Keyword(s):

Candidate Genes ◽

Muscle Growth ◽

Rna Seq ◽

Next Generation Sequencing Technology ◽

Pig Breeds ◽

Nfkb Activation ◽

Main Gene ◽

Slow Type ◽

Longissimus Lumborum ◽

Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

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