scholarly journals Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the MiR156, MiR5488 and MiR399 Are Involved in the Regulation of Male Sterility in PTGMS Rice

2021 ◽  
Vol 22 (5) ◽  
pp. 2260
Author(s):  
Yujun Sun ◽  
Xinguo Xiong ◽  
Qian Wang ◽  
Lan Zhu ◽  
Lei Wang ◽  
...  
Keyword(s):  
Male Sterility ◽  
Small Rna ◽  
Male Fertility ◽  
Target Genes ◽  
Hybrid Rice ◽  
Basic Material ◽  
Integrated Analysis ◽  
Male Sterile ◽  
Degradome Sequencing ◽  
Ptgms Rice

A photoperiod- and thermo-sensitive genic male sterile (PTGMS) line is the basic material for two-hybrid rice and is an important genetic breeding resource. Peiai64S (PA64S) is an important germplasm resource of PTGMS rice, and it has been applied to two-line hybrid rice systems in China. Pollen fertility in PA64S is regulated by the temperature and photoperiod, but the mechanism of the fertility transition is unclear. In this study, we obtained the male fertile plant PA64S(F) and the male sterile plant PA64S(S) by controlling different temperatures under long light conditions and used the male fertile and sterile plants to investigate the role of microRNAs (miRNAs) in regulating male fertility in rice. We performed the small RNA library sequencing of anthers from PA64S(S) and PA64S(F). A total of 196 miRNAs were identified—166 known miRNAs among 27 miRNA families and 30 novel miRNAs. In the transcriptome analysis, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes revealed significant enrichment in the synthesis and metabolism of fatty acids and some secondary metabolism pathways such as fatty acid metabolism and phenylalanine metabolism. With a comprehensive analysis of miRNA, transcriptome, and degradome sequencing, we identified that 13 pairs of miRNA/target genes regulated male fertility in rice by responding to temperature change, among which the miR156, miR5488, and miR399 affect the male fertility of PA64S by influencing SPLs, the lignin synthesis of anther walls, and the flavonoid metabolism pathway. The results provide a new understanding of PTGMS rice, which will help us better understand the potential regulatory mechanisms of male sterility in the future.

scholarly journals Integrated Analysis of MicroRNA and Target Genes in Brachypodium distachyon Infected by Magnaporthe oryzae by Small RNA and Degradome Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Weiye Peng ◽  
Na Song ◽  
Wei Li ◽  
Mingxiong Yan ◽  
Chenting Huang ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Small Rna ◽  
Target Genes ◽  
Brachypodium Distachyon ◽  
Grass Species ◽  
Integrated Analysis ◽  
Post Inoculation ◽  
New Approach ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas

Rice blast caused by Magnaporthe oryzae is one of the most important diseases that seriously threaten rice production. Brachypodium distachyon is a grass species closely related to grain crops, such as rice, barley, and wheat, and has become a new model plant of Gramineae. In this study, 15 small RNA samples were sequenced to examine the dynamic changes in microRNA (miRNA) expression in B. distachyon infected by M. oryzae at 0, 24, and 48 h after inoculation. We identified 432 conserved miRNAs and 288 predicted candidate miRNAs in B. distachyon. Additionally, there were 7 and 19 differentially expressed miRNAs at 24 and 48 h post-inoculation, respectively. Furthermore, using degradome sequencing, we identified 2,126 genes as targets for 308 miRNAs; using quantitative real-time PCR (qRT-PCR), we validated five miRNA/target regulatory units involved in B. distachyon–M. oryzae interactions. Moreover, using co-transformation technology, we demonstrated that BdNAC21 was negatively regulated by miR164c. This study provides a new approach for identifying resistance genes in B. distachyon by mining the miRNA regulatory network of host–pathogen interactions.

scholarly journals Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

2019 ◽  
Author(s):  
Paulina Glazinska ◽  
Milena Kulasek ◽  
Wojciech Glinkowski ◽  
Waldemar Wojciechowski ◽  
Jan Kosiński
Keyword(s):  
Information Processing ◽  
Small Rna ◽  
Target Genes ◽  
Signal Transduction Pathway ◽  
Lupinus Luteus ◽  
Integrated Analysis ◽  
Degradome Sequencing ◽  
Kegg Pathways ◽  
Legume Crop ◽  
Yellow Lupine

Abstract Background Yellow lupine (Lupinus luteus L., Taper c.) is an important legume crop. However, its flower development and pod formation are often affected by excessive abscission. Organ detachment occurs within the abscission zone (AZ) and in L. luteus primarily affects flowers formed at the top of the inflorescence. The top flowers’ fate appears determined before anthesis. The organ development and abscission mechanisms utilize a complex molecular network, not yet not fully understood, especially as to the role of miRNAs and siRNAs. We aimed at identifying differentially expressed (DE) small ncRNAs in lupine by comparing small RNA-seq libraries generated from developing upper and lower raceme flowers, and flower pedicels with active and inactive AZs. Their target genes were also identified using transcriptome and degradome sequencing. Results Within all the libraries, 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development, 30 miRNAs displayed DE in the upper and 29 in the lower parts of the raceme. In comparisons between upper and lower raceme flowers, a total of 46 DE miRNAs were identified. miR393 and miR160 were related to the upper and miR396 to the lower flowers and pedicels of non-abscising flowers. In flower pedicels we identified 34 DE miRNAs, with miR167 being the most abundant of all. Most siRNAs seem to play a marginal role in the processes studied herein, with the exception of tasiR-ARFs, which were DE in the developing flowers. The target genes of these miRNAs were predominantly categorized into the following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ‘Metabolism’ (15,856), ‘Genetic information processing’ (5,267), and ‘Environmental information processing’ (1,517). Over 700 putative targets were categorized as belonging to the ‘Plant Hormone Signal Transduction pathway’. 26,230 target genes exhibited Gene Ontology (GO) terms: 23,092 genes were categorized into the ‘Cellular component’, 23,501 into the ‘Molecular function’, and 22,939 into the ’Biological process’. Conclusion Our results indicate that miRNAs and siRNAs in yellow lupine may influence the development of flowers and, consequently, their fate by repressing their target genes, particularly those associated with the homeostasis of phytohormones, mainly auxins.

scholarly journals Heat-Responsive miRNAs Participate in the Regulation of Male Fertility Stability in Soybean CMS-Based F1 under High Temperature Stress

2021 ◽  
Vol 22 (5) ◽  
pp. 2446
Author(s):  
Xianlong Ding ◽  
Jinfeng Guo ◽  
Qiqi Zhang ◽  
Lifeng Yu ◽  
Tuanjie Zhao ◽  
...  
Keyword(s):  
High Temperature ◽  
Male Sterility ◽  
Male Fertility ◽  
Target Genes ◽  
High Temperature Stress ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
New Members ◽  
Squamosa Promoter Binding Protein ◽  
Ppr Proteins

MicroRNAs (miRNAs), a class of noncoding small RNAs (sRNAs), are widely involved in the response to high temperature (HT) stress at both the seedling and flowering stages. To dissect the roles of miRNAs in regulating male fertility in soybean cytoplasmic male sterility (CMS)-based F1 under HT, sRNA sequencing was performed using flower buds from HT-tolerant and HT-sensitive CMS-based F1 combinations (NF1 and YF1, respectively). A total of 554 known miRNAs, 59 new members of known miRNAs, 712 novel miRNAs, and 1145 target genes of 580 differentially expressed miRNAs (DEMs) were identified under normal temperature and HT conditions. Further integrated analysis of sRNA and transcriptome sequencing found that 21 DEMs and 15 differentially expressed target genes, such as gma-miR397a/Laccase 2, gma-miR399a/Inorganic phosphate transporter 1-4, and gma-miR4413a/PPR proteins, mitochondrial-like, were negatively regulated under HT stress. Furthermore, all members of the gma-miR156 family were suppressed by HT stress in both NF1 and YF1, but were highly expressed in YF1 under HT condition. The negative correlation between gma-miR156b and its target gene squamosa promoter-binding protein-like 2b was confirmed by expression analysis, and overexpression of gma-miR156b in Arabidopsis led to male sterility under HT stress. With these results, we proposed that miRNAs play an important role in the regulation of male fertility stability in soybean CMS-based F1 under HT stress.

scholarly journals The Dynamics of Gynodioecy in Plantago lanceolatu L. II. Mode of Action and Frequencies of Restorer Alleles

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1317-1328
Author(s):  
Anita A de Haan ◽  
Hans P Koelewijn ◽  
Maria P J Hundscheid ◽  
Jos M M Van Damme
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Allele Frequency ◽  
Mode Of Action ◽  
Male Fertility ◽  
Fertility Restoration ◽  
Plantago Lanceolata ◽  
Allele Frequencies ◽  
Male Sterile ◽  
Male Fertility Restoration

Male fertility in Plantago lanceolata is controlled by the interaction of cytoplasmic and nuclear genes. Different cytoplasmic male sterility (CMS) types can be either male sterile or hermaphrodite, depending on the presence of nuclear restorer alleles. In three CMS types of P. lanceolata (CMSI, CMSIIa, and CMSIIb) the number of loci involved in male fertility restoration was determined. In each CMS type, male fertility was restored by multiple genes with either dominant or recessive action and capable either of restoring male fertility independently or in interaction with each other (epistasis). Restorer allele frequencies for CMSI, CMSIIa and CMSIIb were determined by crossing hermaphrodites with “standard” male steriles. Segregation of male steriles vs. non-male steriles was used to estimate overall restorer allele frequency. The frequency of restorer alleles was different for the CMS types: restorer alleles for CMSI were less frequent than for CMSIIa and CMSIIb. On the basis of the frequencies of male steriles and the CMS types an “expected” restorer allele frequency could be calculated. The correlation between estimated and expected restorer allele frequency was significant.

Small RNA, transcriptome, and degradome sequencing to identify salinity stress responsive miRNAs and target genes in Dunaliella salina

2018 ◽  
Vol 31 (2) ◽  
pp. 1175-1183 ◽  
Author(s):  
Xiangnan Gao ◽  
Yuting Cong ◽  
Jinrong Yue ◽  
Zhenyu Xing ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Small Rna ◽  
Dunaliella Salina ◽  
Target Genes ◽  
Degradome Sequencing

scholarly journals Construction of a male sterility system for hybrid rice breeding and seed production using a nuclear male sterility gene

2016 ◽  
Vol 113 (49) ◽  
pp. 14145-14150 ◽  
Author(s):  
Zhenyi Chang ◽  
Zhufeng Chen ◽  
Na Wang ◽  
Gang Xie ◽  
Jiawei Lu ◽  
...  
Keyword(s):  
Male Sterility ◽  
Seed Production ◽  
Environmental Conditions ◽  
Hybrid Rice ◽  
Rice Breeding ◽  
Male Sterile ◽  
Red Fluorescence ◽  
Cytoplasmic Male Sterile ◽  
Cross Pollination ◽  
Self Pollination

The breeding and large-scale adoption of hybrid seeds is an important achievement in agriculture. Rice hybrid seed production uses cytoplasmic male sterile lines or photoperiod/thermo-sensitive genic male sterile lines (PTGMS) as female parent. Cytoplasmic male sterile lines are propagated via cross-pollination by corresponding maintainer lines, whereas PTGMS lines are propagated via self-pollination under environmental conditions restoring male fertility. Despite huge successes, both systems have their intrinsic drawbacks. Here, we constructed a rice male sterility system using a nuclear gene named Oryza sativa No Pollen 1 (OsNP1). OsNP1 encodes a putative glucose–methanol–choline oxidoreductase regulating tapetum degeneration and pollen exine formation; it is specifically expressed in the tapetum and miscrospores. The osnp1 mutant plant displays normal vegetative growth but complete male sterility insensitive to environmental conditions. OsNP1 was coupled with an α-amylase gene to devitalize transgenic pollen and the red fluorescence protein (DsRed) gene to mark transgenic seed and transformed into the osnp1 mutant. Self-pollination of the transgenic plant carrying a single hemizygous transgene produced nontransgenic male sterile and transgenic fertile seeds in 1:1 ratio that can be sorted out based on the red fluorescence coded by DsRed. Cross-pollination of the fertile transgenic plants to the nontransgenic male sterile plants propagated the male sterile seeds of high purity. The male sterile line was crossed with ∼1,200 individual rice germplasms available. Approximately 85% of the F1s outperformed their parents in per plant yield, and 10% out-yielded the best local cultivars, indicating that the technology is promising in hybrid rice breeding and production.

scholarly journals Identification of Ms2, a Novel Locus Controlling Male-fertility Restoration of Cytoplasmic Male-sterility in Onion (Allium Cepa L.), and Development of Tightly Linked Molecular Markers

2021 ◽  
Author(s):  
Nari Yu ◽  
Sunggil Kim
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Allium Cepa ◽  
Male Fertility ◽  
Bulked Segregant Analysis ◽  
Fertility Restoration ◽  
Chromosome 2 ◽  
Rna Seq ◽  
Male Sterile ◽  
Male Fertility Restoration

Abstract Cytoplasmic male-sterility (CMS) has been exclusively used to produce F1 hybrid seeds of onion (Allium cepa L.). A single nuclear locus, Ms, is known to restore male-fertility of CMS in onions. Unstable male-sterile onions producing a small amount of pollen grains have been identified in a previous study. When such unstable male-sterile onions were crossed with stable male-sterile onions containing CMS-T cytoplasm, male-fertility was completely restored, although genotypes of the Ms locus were homozygous recessive. Inheritance patterns indicated that male-fertility restoration was controlled by a single locus designated as Ms2. A combined approach of bulked segregant analysis and RNA-seq was used to identify candidate genes for the Ms2 locus. High resolution melting (HRM) markers were developed based on single nucleotide polymorphisms (SNPs) detected by RNA-Seq. Comparative mapping of the Ms2 locus showed that Ms2 was positioned at the end of chromosome 2 with a distance of approximately 70 cM away from the Ms locus. Although 38 contigs containing reliable SNPs were analyzed using recombinants selected from 1,344 individuals, no contig showed perfect linkage to Ms2. Interestingly, transcription levels of orf725, a CMS-associated gene in onions, were significantly reduced in male-fertile individuals of segregating populations. However, no significant change in its transcription level was observed in individuals of a segregating population with male-fertility phenotypes determined by the Ms locus, suggesting that male-fertility restoration mechanism of Ms2 might be different from that of the Ms locus.

scholarly journals Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem of Pinus massoniana via Small RNA and Degradome Sequencing

2021 ◽  
Vol 22 (18) ◽  
pp. 10154
Author(s):  
Tengfei Shen ◽  
Mengxuan Xu ◽  
Haoran Qi ◽  
Yuanheng Feng ◽  
Zhangqi Yang ◽  
...  
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Higher Plants ◽  
Raw Materials ◽  
Pinus Massoniana ◽  
Wood Formation ◽  
Mineral Elements ◽  
Small Rna Sequencing ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas

Xylem is required for the growth and development of higher plants to provide water and mineral elements. The thickening of the xylem secondary cell wall (SCW) not only improves plant survival, but also provides raw materials for industrial production. Numerous studies have found that transcription factors and non-coding RNAs regulate the process of SCW thickening. Pinus massoniana is an important woody tree species in China and is widely used to produce materials for construction, furniture, and packaging. However, the target genes of microRNAs (miRNAs) in the developing xylem of P. massoniana are not known. In this study, a total of 25 conserved miRNAs and 173 novel miRNAs were identified via small RNA sequencing, and 58 differentially expressed miRNAs were identified between the developing xylem (PM_X) and protoplasts isolated from the developing xylem (PM_XP); 26 of these miRNAs were significantly up-regulated in PM_XP compared with PM_X, and 32 were significantly down-regulated. A total of 153 target genes of 20 conserved miRNAs and 712 target genes of 113 novel miRNAs were verified by degradome sequencing. There may be conserved miRNA-mRNA modules (miRNA-MYB, miRNA-ARF, and miRNA-LAC) involved in softwood and hardwood formation. The results of qRT-PCR-based parallel validation were in relatively high agreement. This study explored the potential regulatory network of miRNAs in the developing xylem of P. massoniana and provides new insights into wood formation in coniferous species.

scholarly journals Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, mRNA, and degradome sequencing

2020 ◽  
Author(s):  
Xiao-Meng Liu ◽  
Shui-Yuan Cheng ◽  
Jia-Bao Ye ◽  
Ze-Xiong Chen ◽  
Yong-Ling Liao ◽  
...  
Keyword(s):  
Small Rna ◽  
Ginkgo Biloba ◽  
Sexual Differentiation ◽  
Target Genes ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Multiple Perspectives ◽  
Juvenile Period ◽  
Degradome Sequencing ◽  
Screening And Identification

Abstract Background: Ginkgo biloba, a typical dioecious plant, is a traditional medicinal plant widely planted. However, it has a long juvenile period, which severely affected the breeding and cultivation of superior ginkgo varieties.Results: In order to clarify the complex mechanism of sexual differentiation in G. biloba strobili. Here, a total of 3,293 miRNAs were identified in buds and strobili of G. biloba, including 1,085 conserved miRNAs and 2,208 novel miRNAs using the three sequencing approaches of transcriptome, small RNA, and degradome. Comparative transcriptome analysis screened 4,346 and 7,087 differentially expressed genes (DEGs) in MB _vs_ FB and MS _vs_ OS, respectively. A total of 6,032 target genes were predicted for differentially expressed miRNA. The combined analysis of both small RNA and transcriptome datasets identified 51 miRNA-mRNA interaction pairs that may be involved in the process of G. biloba strobili sexual differentiation, of which 15 pairs were verified in the analysis of degradome sequencing. Conclusions: The comprehensive analysis of the small RNA, RNA and degradome sequencing data in this study provided candidate genes and clarified the regulatory mechanism of sexual differentiation of G. biloba strobili from multiple perspectives.

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