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  • 1
    Online Resource
    Online Resource
    Combined small RNA and gene expression analysis revealed roles of miRNAs in maize response to rice black-streaked dwarf virus infection
    Springer Science and Business Media LLC ; 2018
    In:  Scientific Reports Vol. 8, No. 1 ( 2018-09-10)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-09-10)
    Abstract: Maize rough dwarf disease, caused by rice black-streaked dwarf virus (RBSDV), is a devastating disease in maize ( Zea mays L.). MicroRNAs (miRNAs) are known to play critical roles in regulation of plant growth, development, and adaptation to abiotic and biotic stresses. To elucidate the roles of miRNAs in the regulation of maize in response to RBSDV, we employed high-throughput sequencing technology to analyze the miRNAome and transcriptome following RBSDV infection. A total of 76 known miRNAs, 226 potential novel miRNAs and 351 target genes were identified. Our dataset showed that the expression patterns of 81 miRNAs changed dramatically in response to RBSDV infection. Transcriptome analysis showed that 453 genes were differentially expressed after RBSDV infection. GO, COG and KEGG analysis results demonstrated that genes involved with photosynthesis and metabolism were significantly enriched. In addition, twelve miRNA-mRNA interaction pairs were identified, and six of them were likely to play significant roles in maize response to RBSDV. This study provided valuable information for understanding the molecular mechanism of maize disease resistance, and could be useful in method development to protect maize against RBSDV.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-018-31919-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2615211-3
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  • 2
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    Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds
    Springer Science and Business Media LLC ; 2020
    In:  BMC Plant Biology Vol. 20, No. 1 ( 2020-12)
    Details
    In: BMC Plant Biology, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2020-12)
    Abstract: MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut- A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth . Results A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus . A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs. Conclusions Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus .
    Type of Medium: Online Resource
    ISSN: 1471-2229
    URL: Article
    DOI: 10.1186/s12870-020-02426-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2059868-3
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  • 3
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    Whole‐genome resequencing‐based QTL ‐seq identified AhTc1 gene encoding a R2R3‐ MYB transcription factor controlling peanut purple testa colour
    Wiley ; 2020
    In:  Plant Biotechnology Journal Vol. 18, No. 1 ( 2020-01), p. 96-105
    Details
    In: Plant Biotechnology Journal, Wiley, Vol. 18, No. 1 ( 2020-01), p. 96-105
    Abstract: Peanut ( Arachis hypogaea . L) is an important oil crop worldwide. The common testa colours of peanut varieties are pink or red. But the peanut varieties with dark purple testa have been focused in recent years due to the potential high levels of anthocyanin, an added nutritional value of antioxidant. However, the genetic mechanism regulating testa colour of peanut is unknown. In this study, we found that the purple testa was decided by the female parent and controlled by a single major gene named AhTc1 . To identify the candidate gene controlling peanut purple testa, whole‐genome resequencing‐based approach ( QTL ‐seq) was applied, and a total of 260.9 Gb of data were generated from the parental and bulked lines. SNP index analysis indicated that AhTc1 located in a 4.7 Mb region in chromosome A10, which was confirmed by bulked segregant RNA sequencing ( BSR ) analysis in three segregation populations derived from the crosses between pink and purple testa varieties. Allele‐specific markers were developed and demonstrated that the marker pT esta1089 was closely linked with purple testa. Further, AhTc1 encoding a R2R3‐ MYB gene was positional cloned. The expression of AhTc1 was significantly up‐regulated in the purple testa parent YH 29. Overexpression of AhTc1 in transgenic tobacco plants led to purple colour of leaves, flowers, pods and seeds. In conclusion, AhTc1 , encoding a R2R3‐ MYB transcription factor and conferring peanut purple testa, was identified, which will be useful for peanut molecular breeding selection for cultivars with purple testa colour for potential increased nutritional value to consumers.
    Type of Medium: Online Resource
    ISSN: 1467-7644 , 1467-7652
    URL: Issue
    URL: Article
    DOI: 10.1111/pbi.v18.1
    DOI: 10.1111/pbi.13175
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2136367-5
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  • 4
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    Transcriptome Analysis and Gene Expression Profiling of the Peanut Small Seed Mutant Identified Genes Involved in Seed Size Control
    MDPI AG ; 2022
    In:  International Journal of Molecular Sciences Vol. 23, No. 17 ( 2022-08-27), p. 9726-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 23, No. 17 ( 2022-08-27), p. 9726-
    Abstract: Seed size is a key factor affecting crop yield and a major agronomic trait concerned in peanut (Arachis hypogaea L.) breeding. However, little is known about the regulation mechanism of peanut seed size. In the present study, a peanut small seed mutant1 (ssm1) was identified through irradiating peanut cultivar Luhua11 (LH11) using 60Coγ ray. Since the globular embryo stage, the embryo size of ssm1 was significantly smaller than that of LH11. The dry seed weight of ssm1 was only 39.69% of the wild type LH14. The seeds were wrinkled with darker seed coat. The oil content of ssm1 seeds were also decreased significantly. Seeds of ssm1 and LH11 were sampled 10, 20, and 40 days after pegging (DAP) and were used for RNA-seq. The results revealed that genes involved in plant hormones and several transcription factors related to seed development were differentially expressed at all three stages, especially at DAP10 and DAP20. Genes of fatty acid biosynthesis and late embryogenesis abundant protein were significantly decreased to compare with LH11. Interestingly, the gene profiling data suggested that PKp2 and/or LEC1 could be the key candidate genes leading to the small seed phenotype of the mutant. Our results provide valuable clues for further understanding the mechanisms underlying seed size control in peanut.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms23179726
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2019364-6
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  • 5
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    Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant
    Springer Science and Business Media LLC ; 2020
    In:  BMC Genomics Vol. 21, No. 1 ( 2020-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2020-12)
    Abstract: Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. Results In this study, a semi-dwarf peanut mutant was identified from 60 Co γ-ray induced mutant population and designated as semi-dwarf mutant 2 ( sdm2 ). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. Conclusions A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-020-6614-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2041499-7
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  • 6
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    Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness
    Springer Science and Business Media LLC ; 2013
    In:  BMC Genomics Vol. 14, No. 1 ( 2013-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2013-12)
    Abstract: After the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried in soil. It is interesting to study the mechanisms of gynophore development and pod formation in peanut. Results In this study, transcriptome analysis of peanut gynophore was performed using Illumina HiSeq™ 2000 to understand the mechanisms of geocarpy. More than 13 million short sequences were assembled into 72527 unigenes with average size of 394 bp. A large number of genes that were not identified previously in peanut EST projects were identified in this study, including most genes involved in plant circadian rhythm, intra-cellular transportation, plant spliceosome, eukaryotes basal transcription factors, genes encoding ribosomal proteins, brassinosteriod biosynthesis, light-harvesting chlorophyll protein complex, phenylpropanoid biosynthesis and TCA cycle. RNA-seq based gene expression profiling results showed that before and after gynophore soil penetration, the transcriptional level of a large number of genes changed significantly. Genes encoding key enzymes for hormone metabolism, signaling, photosynthesis, light signaling, cell division and growth, carbon and nitrogen metabolism as well as genes involved in stress responses were high lighted. Conclusions Transcriptome analysis of peanut gynophore generated a large number of unigenes which provide useful information for gene cloning and expression study. Digital gene expression study suggested that gynophores experience global changes and reprogram from light to dark grown condition to resume embryo and fruit development.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/1471-2164-14-517
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
    detail.hit.zdb_id: 2041499-7
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  • 7
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    Genome-wide identification of Thellungiella salsuginea microRNAs with putative roles in the salt stress response
    Springer Science and Business Media LLC ; 2013
    In:  BMC Plant Biology Vol. 13, No. 1 ( 2013-12)
    Details
    In: BMC Plant Biology, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2013-12)
    Abstract: MicroRNAs are key regulators of plant growth and development with important roles in environmental adaptation. The microRNAs from the halophyte species Thellungiella salsuginea (salt cress), which exhibits extreme salt stress tolerance, remain to be investigated. The sequenced genome of T. salsuginea and the availability of high-throughput sequencing technology enabled us to discover the conserved and novel miRNAs in this plant species. It is interesting to identify the microRNAs from T. salsuginea genome wide and study their roles in salt stress response. Results In this study, two T. salsuginea small RNA libraries were constructed and sequenced using Solexa technology. We identified 109 miRNAs that had previously been reported in other plant species. A total of 137 novel miRNA candidates were identified, among which the miR* sequence of 26 miRNAs was detected. In addition, 143 and 425 target mRNAs were predicted for the previously identified and Thellungiella- specific miRNAs, respectively. A quarter of these putative targets encode transcription factors. Furthermore, numerous signaling factor encoding genes, defense-related genes, and transporter encoding genes were amongst the identified targets, some of which were shown to be important for salt tolerance. Cleavage sites of seven target genes were validated by 5’ RACE, and some of the miRNAs were confirmed by qRT-PCR analysis. The expression levels of 26 known miRNAs in the roots and leaves of plants subjected to NaCl treatment were determined by Affymetrix microarray analysis. The expression of most tested miRNA families was up- or down-regulated upon NaCl treatment. Differential response patterns between the leaves and roots were observed for these miRNAs. Conclusions Our results indicated that diverse set of miRNAs of T. salsuginea were responsive to salt stress and could play an important role in the salt stress response .
    Type of Medium: Online Resource
    ISSN: 1471-2229
    URL: Article
    DOI: 10.1186/1471-2229-13-180
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
    detail.hit.zdb_id: 2059868-3
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  • 8
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    BSA‑seq and genetic mapping reveals AhRt2 as a candidate gene responsible for red testa of peanut
    Springer Science and Business Media LLC ; 2022
    In:  Theoretical and Applied Genetics Vol. 135, No. 5 ( 2022-05), p. 1529-1540
    Details
    In: Theoretical and Applied Genetics, Springer Science and Business Media LLC, Vol. 135, No. 5 ( 2022-05), p. 1529-1540
    Type of Medium: Online Resource
    ISSN: 0040-5752 , 1432-2242
    URL: Article
    DOI: 10.1007/s00122-022-04051-w
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1478966-8
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  • 9
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    Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may)
    Springer Science and Business Media LLC ; 2015
    In:  BMC Genomics Vol. 16, No. 1 ( 2015-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2015-12)
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-014-1204-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2041499-7
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  • 10
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    Coordination between MIDASIN 1 -mediated ribosome biogenesis and auxin modulates plant development
    Oxford University Press (OUP) ; 2021
    In:  Journal of Experimental Botany Vol. 72, No. 7 ( 2021-03-29), p. 2501-2513
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 72, No. 7 ( 2021-03-29), p. 2501-2513
    Abstract: Ribosomes are required for plant growth and development, and ribosome biogenesis-deficient mutants generally display auxin-related phenotypes. Although the relationship between ribosome dysfunction and auxin is known, many aspects of this subject remain to be understood. We previously reported that MIDASIN 1 (MDN1) is an essential pre-60S ribosome biogenesis factor (RBF) in Arabidopsis. In this study, we further characterized the aberrant auxin-related phenotypes of mdn1-1, a weak mutant allele of MDN1. Auxin response is disturbed in both shoots and roots of mdn1-1, as indicated by the DR5:GUS reporter. By combining transcriptome profiling analysis and reporter gene detection, we found that expression of genes involved in auxin biosynthesis, transport, and signaling is changed in mdn1-1. Furthermore, MDN1 deficiency affects the post-transcriptional regulation and protein distribution of PIN-FORMED 2 (PIN2, an auxin efflux facilitator) in mdn1-1 roots. These results indicate that MDN1 is required for maintaining the auxin system. More interestingly, MDN1 is an auxin-responsive gene, and its promoter can be targeted by multiple AUXIN RESPONSE FACTORs (ARFs), including ARF7 and ARF19, in vitro. Indeed, in arf7 arf19, the auxin sensitivity of MDN1 expression is significantly reduced. Together, our results reveal a coordination mechanism between auxin and MDN1-dependent ribosome biogenesis for regulating plant development.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erab025
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1466717-4
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