scholarly journals Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4500 ◽  
Author(s):  
Liuxin Xiang ◽  
Chaowei Cai ◽  
Jieru Cheng ◽  
Lu Wang ◽  
Chaofeng Wu ◽  
...  
Keyword(s):  
Verticillium Wilt ◽  
Stress Responses ◽  
Response Term ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Rna Seq ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Stimulus Response ◽  
Segment Substitution

Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum, CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton.

scholarly journals Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 943
Author(s):  
Li ◽  
Cheng ◽  
Bai ◽  
Shi ◽  
Yu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Target Genes ◽  
Differentially Expressed ◽  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution ◽  
Extreme Materials

Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.

scholarly journals Combining Genome and Gene Co-expression Network Analyses for the Identification of Genes Potentially Regulating Salt Tolerance in Rice

2021 ◽  
Vol 12 ◽  
Author(s):  
Panita Chutimanukul ◽  
Triono Bagus Saputro ◽  
Puriphot Mahaprom ◽  
Kitiporn Plaimas ◽  
Luca Comai ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Stress Conditions ◽  
Clustering Coefficient ◽  
Differentially Expressed ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Network Analyses ◽  
Salinity Stress Tolerance ◽  
Segment Substitution

Salinity stress tolerance is a complex polygenic trait involving multi-molecular pathways. This study aims to demonstrate an effective transcriptomic approach for identifying genes regulating salt tolerance in rice. The chromosome segment substitution lines (CSSLs) of “Khao Dawk Mali 105 (KDML105)” rice containing various regions of DH212 between markers RM1003 and RM3362 displayed differential salt tolerance at the booting stage. CSSL16 and its nearly isogenic parent, KDML105, were used for transcriptome analysis. Differentially expressed genes in the leaves of seedlings, flag leaves, and second leaves of CSSL16 and KDML105 under normal and salt stress conditions were subjected to analyses based on gene co-expression network (GCN), on two-state co-expression with clustering coefficient (CC), and on weighted gene co-expression network (WGCN). GCN identified 57 genes, while 30 and 59 genes were identified using CC and WGCN, respectively. With the three methods, some of the identified genes overlapped, bringing the maximum number of predicted salt tolerance genes to 92. Among the 92 genes, nine genes, OsNodulin, OsBTBZ1, OsPSB28, OsERD, OsSub34, peroxidase precursor genes, and three expressed protein genes, displayed SNPs between CSSL16 and KDML105. The nine genes were differentially expressed in CSSL16 and KDML105 under normal and salt stress conditions. OsBTBZ1 and OsERD were identified by the three methods. These results suggest that the transcriptomic approach described here effectively identified the genes regulating salt tolerance in rice and support the identification of appropriate QTL for salt tolerance improvement.

scholarly journals Genome-wide quantitative trait loci mapping on Verticillium wilt resistance in 300 chromosome segment substitution lines from Gossypium hirsutum × Gossypium barbadense

2021 ◽  
Author(s):  
Md Harun or Rashid ◽  
Peng-tao Li ◽  
Ting-ting Chen ◽  
Koffi Kibalou Palanga ◽  
Wan-kui Gong ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Verticillium Wilt ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution

Abstract Cotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistance to VW. However, multiple attempts to improve the VW resistance of the most widely cultivated upland cottons have made little significant progress. The introduction of chromosome segment substitution lines (CSSLs) provide the practical solutions for merging the superior genes related with high yield and wide adaptation from Gossypium hirsutum and VW resistance and the excellent fiber quality from Gossypium barbadense. In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed from CCRI36 (G. hirsutum) and Hai1 (G. barbadense) to conduct quantitative trait locus (QTL) mapping of VW resistance, and a total of 40 QTL relevant to VW disease index (DI) were identified. Phenotypic data were obtained from a 2-year investigation in two fields with two replications per year. All the QTL were distributed on 21 chromosomes, with phenotypic variation of 1.05%–10.52%, and 21 stable QTL were consistent in at least two environments. Based on a meta-analysis, 34 novel QTL were identified, while 6 loci were consistent with previously identified QTL. Meanwhile, 70 QTL hotspot regions were detected, including 44 novel regions. This study concentrates on QTL identification and screening for hotspot regions related with VW in the 300 CSSLs, and the results lay a solid foundation not only for revealing the genetic and molecular mechanisms of VW resistance but also for further fine mapping, gene cloning and molecular designing in breeding programs for resistant cotton varieties.

scholarly journals Development and evaluation of Oryza glaberrima Steud. chromosome segment substitution lines (CSSLs) in the background of O. sativa L. cv. Koshihikari

2010 ◽  
Vol 60 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Rosalyn A. Shim ◽  
Enrique R. Angeles ◽  
Motoyuki Ashikari ◽  
Tomonori Takashi
Keyword(s):  
Chromosome Segment ◽  
Oryza Glaberrima ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution

scholarly journals Utilizing Chromosome Segment Substitution Lines (CSSLs) for Evaluation of Root Responses to Transient Moisture Stresses in Rice

2008 ◽  
Vol 11 (4) ◽  
pp. 457-465 ◽  
Author(s):  
Roel Rodriguez Suralta ◽  
Yoshiaki Inukai ◽  
Akira Yamauchi
Keyword(s):  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Root Responses ◽  
Segment Substitution

scholarly journals Identification and validation of QTLs for 100-seed weight using chromosome segment substitution lines in soybean

2018 ◽  
Vol 68 (4) ◽  
pp. 442-448 ◽  
Author(s):  
Dequan Liu ◽  
Yongliang Yan ◽  
Yasunari Fujita ◽  
Donghe Xu
Keyword(s):  
Seed Weight ◽  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution ◽  
100 Seed Weight

scholarly journals Identification and Characterization of Circular RNAs in Longissimus Dorsi Muscle Tissue from Two Goat Breeds using RNA-Seq

2021 ◽  
Author(s):  
Jiyuan Shen ◽  
Huimin Zhen ◽  
Lu Li ◽  
Yuting Zhang ◽  
Jiqing Wang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Fiber ◽  
Muscle Development ◽  
Production Performance ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Fiber Size

Abstract Background: Circular RNAs (circRNAs) are a class of non-coding RNA that play crucial roles in the development of skeletal muscle. However, little is known about the role of circRNAs in caprine skeletal muscle. In this study, the muscle fiber size and expression profiles of circRNAs were compared in Longissimus dorsi muscle of Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotypic differences in meat production performance, using hematoxylin and eosin staining and RNA-Seq, respectively.Results: The muscle fiber size in LC goats were larger than those in ZB goats (P < 0.05). A total of 10,875 circRNAs were identified and 214 of these were differentially expressed between the two caprine breeds. The authentication and expression levels of 20 circRNAs were confirmed using reverse transcriptase-polymerase chain reaction (RT-PCR) and DNA sequencing. The parent genes of differentially expressed circRNAs were mainly enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway. Some miRNAs reportedly associated with skeletal muscle development and intramuscular fat deposition would be targeted by several differentially expressed circRNAs and the most highly expressed circRNA (circ_001086).Conclusion: These results provide an improved understanding of the functions of circRNAs in skeletal muscle development of goats.

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