scholarly journals iTRAQ-Based Proteomic Analysis of Ogura-CMS Cabbage and Its Maintainer Line

2018 ◽  
Vol 19 (10) ◽  
pp. 3180 ◽  
Author(s):  
Fengqing Han ◽  
Xiaoli Zhang ◽  
Limei Yang ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
...  
Keyword(s):  
Oxidative Phosphorylation ◽  
Male Sterility ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Pcr Analysis ◽  
Hybrid Seed Production ◽  
Protein Species ◽  
Absolute Quantitation ◽  
Maintainer Line ◽  
Cms Line

Ogura cytoplasmic male sterility (CMS) contributes considerably to hybrid seed production in Brassica crops. To detect the key protein species and pathways involved in Ogura-CMS, we analysed the proteome of the cabbage Ogura-CMS line CMS01-20 and its corresponding maintainer line F01-20 using the isobaric tags for the relative and absolute quantitation (iTRAQ) approach. In total, 162 differential abundance protein species (DAPs) were identified between the two lines, of which 92 were down-accumulated and 70 were up-accumulated in CMS01-20. For energy metabolism in the mitochondrion, eight DAPs involved in oxidative phosphorylation were down-accumulated in CMS01-20, whereas in the tricarboxylic acid (TCA) cycle, five DAPs were up-accumulated, which may compensate for the decreased respiration capacity and may be associated with the elevated O2 consumption rate in Ogura-CMS plants. Other key protein species and pathways involved in pollen wall assembly and programmed cell death (PCD) were also identified as being male-sterility related. Transcriptome profiling revealed 3247 differentially expressed genes between the CMS line and the fertile line. In a conjoint analysis of the proteome and transcriptome data, 30 and 9 protein species/genes showed the same and opposite accumulation patterns, respectively. Nine noteworthy genes involved in sporopollenin synthesis, callose wall degeneration, and oxidative phosphorylation were presumably associated with the processes leading to male sterility, and their expression levels were validated by qRT-PCR analysis. This study will improve our understanding of the protein species involved in pollen development and the molecular mechanisms underlying Ogura-CMS.

scholarly journals Comparative Transcriptome Analysis of the Anthers from the Cytoplasmic Male-Sterile Pepper Line HZ1A and Its Maintainer Line HZ1B

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 580
Author(s):  
Zhixing Nie ◽  
Jianying Chen ◽  
Yunpeng Song ◽  
Hongfei Fu ◽  
Hong Wang ◽  
...  
Keyword(s):  
Male Sterility ◽  
Molecular Mechanisms ◽  
Male Sterile ◽  
Maintainer Line ◽  
Breeding Programs ◽  
Kegg Pathways ◽  
Kegg Analysis ◽  
Cms Line ◽  
Phenylpropanoid Biosynthesis ◽  
Go Terms

Cytoplasmic male-sterility (CMS) is important for the utilization of crop heterosis and study of the molecular mechanisms involved in CMS could improve breeding programs. In the present study, anthers of the pepper CMS line HZ1A and its maintainer line HZ1B were collected from stages S1, S2, and S3 for transcriptome sequencing. A total of 47.95 million clean reads were obtained, and the reads were assembled into 31,603 unigenes. We obtained 42 (27 up-regulated and 15 down-regulated), 691 (346 up-regulated and 345 down-regulated), and 709 (281 up-regulated and 428 down-regulated) differentially expressed genes (DEGs) in stages S1, S2, and S3, respectively. Through Gene Ontology (GO) analysis, the DEGs were found to be composed of 46 functional groups. Two GO terms involved in photosynthesis, photosynthesis (GO:0015986) and photosystem I (GO:0009522), may be related to CMS. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, oxidative phosphorylation (ko00190) and phenylpropanoid biosynthesis (ko00940) were significantly enriched in the S1 and S2 stages, respectively. Through the analysis of 104 lipid metabolism-related DEGs, four significantly enriched KEGG pathways may help to regulate male sterility during anther development. The mitochondrial genes orf470 and atp6 were identified as candidate genes of male sterility for the CMS line HZ1A. Overall, the results will provide insights into the molecular mechanisms of pepper CMS.

Transcriptome analysis implicates involvement of long noncoding RNAs in cytoplasmic male sterility and fertility restoration in cotton

2019 ◽  
Author(s):  
Bingbing Zhang ◽  
Xuexian Zhang ◽  
Meng Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
...  
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Molecular Mechanisms ◽  
Fertility Restoration ◽  
Noncoding Rnas ◽  
Anther Development ◽  
Long Noncoding Rnas ◽  
Pcr Analysis ◽  
Hybrid Seed Production ◽  
Restorer Of Fertility

Abstract Background Hybrid cotton has greatly contributed to global increase in cotton productivity. The cytoplasmic male sterility (CMS)/restorer-of-fertility system is an important tool to exploit heterosis because it is convenient for commercial hybrid seed production. The importance of long noncoding RNAs (lncRNAs) in plant development is recognized, few analyses of lncRNAs during anther development of three-line hybrid cotton (CMS-D2 line A, maintainer line B, restorer-of-fertility line R) have been reported. Results Here, we performed transcriptome sequencing during anther development in Upland cotton carrying cytoplasmic male sterile Gossypium harknessii (D2) cytoplasm. Totally 80,695 lncRNAs were identified, in which 43,347 and 44,739 lncRNAs were differentially expressed in A–B and A–R comparisons, respectively. These lncRNAs represent functional candidates involved in CMS and fertility restoration. Gene ontology enrichment analysis indicated that cellular hormone metabolic processes and oxidation–reduction reaction processes might be involved in CMS, and cellular component morphogenesis and small molecular biosynthetic processes might participate in fertility restoration. Analysis of the putative relationship between lncRNAs and miRNAs revealed that 63 lncRNAs were identified as putative precursors of 35 miRNAs, and qRT-PCR analysis showed a similar expression pattern to that of RNA-sequencing data. Furthermore, construction of lncRNA regulatory networks indicated that several miRNA–lncRNA–mRNA networks might be involved in CMS and fertility restoration. Conclusion Our findings provide systematic identification of lncRNAs during anther development and lays a solid foundation for future investigation of the regulatory molecular mechanisms and utilization in ­­breeding of hybrid cotton.

scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

scholarly journals Candidate Gene Selection for Cytoplasmic Male Sterility in Pepper (Capsicum annuum L.) through Whole Mitochondrial Genome Sequencing

2019 ◽  
Vol 20 (3) ◽  
pp. 578 ◽  
Author(s):  
Peng Wang ◽  
Qiaohua Lu ◽  
Yixin Ai ◽  
Yihao Wang ◽  
Tiantian Li ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Cytoplasmic Male Sterility ◽  
Candidate Gene ◽  
Male Sterility ◽  
Gene Selection ◽  
Transmembrane Domain ◽  
Genome Structure ◽  
Potential Candidate ◽  
Hybrid Seed Production ◽  
Cms Line

Cytoplasmic male sterility (CMS), which is controlled by mitochondrial genes, is an important trait for commercial hybrid seed production. So far, genes controlling this trait are still not clear in pepper. In this study, complete mitochondrial genomes were sequenced and assembled for the CMS line 138A and its maintainer line 138B. The genome size of 138A is 504,210 bp, which is 8618 bp shorter than that of 138B. Meanwhile, more than 214 and 215 open reading frames longer than 100 amino acids (aas) were identified in 138A and 138B, respectively. Mitochondrial genome structure of 138A was quite different from that of 138B, indicating the existence of recombination and rearrangement events. Based on the mitochondrial genome sequence and structure variations, mitochondrion of 138A and FS4401, a Korean origin CMS line, may have inherited from a common female ancestor, but their CMS traits did originate separately. Candidate gene selection was performed according to the published characteristics of the CMS genes, including the presence SNPs and InDels, located in unique regions, their chimeric structure, co-transcription, and transmembrane domain. A total of 35 ORFs were considered as potential candidate genes and 14 of these were selected, with orf300a and 0rf314a as strong candidates. A new marker, orf300a, was developed which did co-segregate with the CMS trait.

scholarly journals Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shi-Fei Sang ◽  
De-Sheng Mei ◽  
Jia Liu ◽  
Qamar U. Zaman ◽  
Hai-Yan Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Mitochondrial Genome ◽  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Parental Species ◽  
Sequencing Technology ◽  
Genome Composition ◽  
Maintainer Line ◽  
Organelle Genomes ◽  
Cms Line

Abstract Background Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a prerequisite for a better understanding of the origin and molecular mechanism of this CMS. With the development of genome sequencing technology, organelle genomes of Nsa CMS line and its maintainer line were sequenced by pyro-sequencing technology, and comparative analysis of the organelle genomes was carried out to characterize the organelle genome composition of Nsa CMS as well as to identify the candidate Nsa CMS-associated genes. Results Nsa CMS mitochondrial genome showed a higher collinearity with that of S. arvensis than B. napus, indicating that Nsa CMS mitochondrial genome was mainly derived from S. arvensis. However, mitochondrial genome recombination of parental lines was clearly detected. In contrast, the chloroplast genome of Nsa CMS was highly collinear with its B. napus parent, without any evidence of recombination of the two parental chloroplast genomes or integration from S. arvensis. There were 16 open reading frames (ORFs) specifically existed in Nsa CMS mitochondrial genome, which could not be identified in the maintainer line. Among them, three ORFs (orf224, orf309, orf346) possessing chimeric and transmembrane structure are most likely to be the candidate CMS genes. Sequences of all three candidate CMS genes in Nsa CMS line were found to be 100% identical with those from S. arvensis mitochondrial genome. Phylogenetic and homologous analysis showed that all the mitochondrial genes were highly conserved during evolution. Conclusions Nsa CMS contains a recombined mitochondrial genome of its two parental species with the majority form S. arvensis. Three candidate Nsa CMS genes were identified and proven to be derived from S. arvensis other than recombination of its two parental species. Further functional study of the candidate genes will help to identify the gene responsible for the CMS and the underlying molecular mechanism.

scholarly journals Knockout of SlMS10 Gene (Solyc02g079810) Encoding bHLH Transcription Factor Using CRISPR/Cas9 System Confers Male Sterility Phenotype in Tomato

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1189
Author(s):  
Yu Jin Jung ◽  
Dong Hyun Kim ◽  
Hyo Ju Lee ◽  
Ki Hong Nam ◽  
Sangsu Bae ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Male Sterility ◽  
Mutant Line ◽  
Pcr Analysis ◽  
Bhlh Transcription Factor ◽  
Hybrid Seed Production ◽  
Sequencing Analysis ◽  
Alternative Approach ◽  
Deep Sequencing Analysis ◽  
Male Sterility Phenotype

The utilization of male sterility into hybrid seed production reduces its cost and ensures high purity of tomato varieties because it does not produce pollen and has exserted stigmas. Here, we report on the generation of gene edited lines into male sterility phenotype by knockout of SlMS10 gene (Solyc02g079810) encoding the bHLH transcription factor that regulates meiosis and cell death of the tapetum during microsporogenesis in the tomato. Twenty-eight gene edited lines out of 60 transgenic plants were selected. Of these, eleven different mutation types at the target site of the SlMS10 gene were selected through deep sequencing analysis. These mutations were confirmed to be transmitted to subsequent generations. The null lines without the transferred DNA (T-DNA) were obtained by segregation in the T1 and T2 generations. In addition, we showed that the cr-ms10-1-4 mutant line exhibited dysfunctional meiosis and abnormal tapetum during flower development, resulting in no pollen production. RT-PCR analysis showed that the most genes associated with pollen and tapetum development in tomatoes had lower expression in the cr-ms10-1-4 mutant line compared to wild type. We demonstrate that modification of the SlMS10 gene via CRISPR/Cas9-mediated genome editing results in male sterility of tomato plants. Our results suggest an alternative approach to generating male sterility in crops.

scholarly journals iTRAQ-Based Comparative Proteomic Analysis Provides Insights into Molecular Mechanisms of Salt Tolerance in Sugar Beet (Beta vulgaris L.)

2018 ◽  
Vol 19 (12) ◽  
pp. 3866 ◽  
Author(s):  
Guo-Qiang Wu ◽  
Jin-Long Wang ◽  
Rui-Jun Feng ◽  
Shan-Jia Li ◽  
Chun-Mei Wang
Keyword(s):  
Salt Tolerance ◽  
Sugar Beet ◽  
Beta Vulgaris ◽  
Molecular Mechanisms ◽  
Stress Factors ◽  
Pcr Analysis ◽  
Absolute Quantitation ◽  
Abiotic Stress Factors ◽  
Starting Point ◽  
Isobaric Tags

Salinity is one of the major abiotic stress factors that limit plant growth and crop yield worldwide. To understand the molecular mechanisms and screen the key proteins in response of sugar beet (Beta vulgaris L.) to salt, in the present study, the proteomics of roots and shoots in three-week-old sugar beet plants exposed to 50 mM NaCl for 72 h was investigated by isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technology. The results showed that 105 and 30 differentially expressed proteins (DEPs) were identified in roots and shoots of salt-treated plants compared with untreated plants, respectively. There were 46 proteins up-regulated and 59 proteins down-regulated in roots; and 13 up-regulated proteins and 17 down-regulated proteins found in shoots, respectively. These DEPs were mainly involved in carbohydrate metabolism, energy metabolism, lipid metabolism, biosynthesis of secondary metabolites, transcription, translation, protein folding, sorting, and degradation as well as transport. It is worth emphasizing that some novel salt-responsive proteins were identified, such as PFK5, MDH, KAT2, ACAD10, CYP51, F3H, TAL, SRPR, ZOG, V-H+-ATPase, V-H+-PPase, PIPs, TIPs, and tubulin α-2/β-1 chain. qRT-PCR analysis showed that six of the selected proteins, including BvPIP1-4, BvVP and BvVAP in root and BvTAL, BvURO-D1, and BvZOG in shoot, displayed good correlation between the expression levels of protein and mRNA. These novel proteins provide a good starting point for further research into their functions using genetic or other approaches. These findings should significantly improve the understanding of the molecular mechanisms involved in salt tolerance of sugar beet plants.

scholarly journals Morfologi Bunga dan Korelasinya terhadap Kemampuan Menyerbuk Silang Galur Mandul Jantan Padi

2014 ◽  
Vol 33 (2) ◽  
pp. 109
Author(s):  
Indrastuti A. Rumanti ◽  
B. S. Purwoko ◽  
Iswari S. Dewi ◽  
Hajrial Aswidinnoor ◽  
Satoto Satoto
Keyword(s):  
Seed Set ◽  
Block Design ◽  
Hybrid Seed Production ◽  
Male Sterile ◽  
Maintainer Line ◽  
Field Station ◽  
Cms Line ◽  
Randomized Complete Block Design ◽  
Flowering Behaviour ◽  
Stigma Exsertion

Good male sterile lines should have high and stable sterility, as well as have good characters of flowers that enhances the outcrossing ability. Research was conducted at Sukamandi field station during DS of 2010 to study the character and flowering behaviour and their genetic variability among the new CMS lines. Five new CMS lines were tested in the field in three replicates of randomized complete block design. The results showed that CMS derived from the Wild Abortive, Kalinga and Gambiaca all were early flowering. The new CMS lines have better flower characters than that of IR58025A, including the following: bigger stigma, higher stigma exsertion percentage, wider degree of glume opening, and longer duration of glume opening. Better flowering behaviour enhanced the ability of outcrossing, and resulted in seed set obtained from CMS lines, up to 25.90%; the traditional IR58025A CMS line produced seed set of only 2.98%. The significant positive correlation was found between seed set with stigma width (r = 0.44*), with stigma exsertion (r = 0.54*); and with degree of glume opening of male sterile lines (r = 0.42*); also with filament length (r = 0.47*) and degree of glume opening of maintainer line (r = 0.57**). Those characters are important for the seed set of CMS lines in the hybrid seed production.

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