Dataset Information

Identification and Expression of miRNAs Related to Female Flower Induction in Walnut (Juglans regia L.).

ABSTRACT: Flower induction is an essential stage in walnut (Juglans regia L.) trees, directly affecting yield, yield stability, fruit quality and commodity value. The objective of this study was to identify miRNAs related to female flower induction via high-throughput sequencing and bioinformatics analysis. A total of 123 miRNAs were identified including 51 known miRNAs and 72 novel miRNAs. Differential expression was observed in 19 of the known miRNAs and 34 of the novel miRNAs. Twelve miRNAs were confirmed by RT-qPCR. A total of 1339 target genes were predicted for the differentially expressed miRNAs. The functions of 616 of those target genes had been previously annotated. The target genes of the differentially expressed miRNAs included: (i) floral homeotic protein APETALA 2 (AP2) and ethylene-responsive transcription factor RAP2-7 which were targeted by jre-miRn69; (ii) squamosa promoter-binding protein 1 (SPB1) and various SPLs (squamosa promoter-binding-like protein) which were targeted by jre-miR157a-5p; (iii) various hormone response factors which were targeted by jre-miR160a-5p (ARF18) and jre-miR167a-5p (ARF8) and (iv) transcription factor SCL6 which was targeted by jre-miR171b-3p, jre-miRn46 and jre-miRn49. The KEGG pathway analysis of the target genes indicated that the differentially expressed miRNAs were mainly enriched to ubiquitin mediated proteolysis, RNA degradation and various carbohydrate metabolism pathways. Many miRNAs were detected in J. regia during female flower induction. Some miRNAs (jre-miR157a-5p, jre-miR160a-5p, jre-miR167a-5p, miR171b-3p jre-miRn69 and jre-miRn49) were involved in female flower induction. The results of this experiment will contribute valuable information for further research about the function of miRNAs in flower induction of J. regia and other fruit trees.

SUBMITTER: Zhou L

PROVIDER: S-EPMC6099546 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Identification and Expression of miRNAs Related to Female Flower Induction in Walnut (<i>Juglans regia</i> L.).

Zhou Li L Quan Shaowen S Xu Hang H Ma Li L Niu Jianxin J

Molecules (Basel, Switzerland) 20180517 5

Flower induction is an essential stage in walnut (<i>Juglans regia</i> L.) trees, directly affecting yield, yield stability, fruit quality and commodity value. The objective of this study was to identify miRNAs related to female flower induction via high-throughput sequencing and bioinformatics analysis. A total of 123 miRNAs were identified including 51 known miRNAs and 72 novel miRNAs. Differential expression was observed in 19 of the known miRNAs and 34 of the novel miRNAs. Twelve miRNAs were ...[more]

PMID: 29772800

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Project description:The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

Project description:The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21-18 kyr BP) and LIG (130-116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut.

Dataset Information

Identification and Expression of miRNAs Related to Female Flower Induction in Walnut (Juglans regia L.).

Publications

Identification and Expression of miRNAs Related to Female Flower Induction in Walnut (<i>Juglans regia</i> L.).

Similar Datasets

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