Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

Zhang, Lei; Yu, Yan; Shi, Tianye; Kou, Meng; Sun, Jian; Xu, Tao; Li, Qiang; Wu, Shaoyuan; Cao, Qinghe; Hou, Wenqian; Li, Zongyun

doi:10.1038/s41438-020-0314-4

Cited by 40 publications

(40 citation statements)

References 65 publications

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“…Sequencing data analysis was performed according to our previous studies [25,26]. High-quality clean reads for each sample were obtained from raw RNA-seq data by removing adaptor sequences and ambiguous nucleotides using Trimmomatic (version 0.34) [27] and then were mapped to the eggplant genome HQ-1315 [28] using STAR (version 2.7.1a) under the 2-pass mapping mode [29].…”

Section: Transcriptome Sequence Processing and Analysismentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Zhang

Sun

et al. 2021

Genes

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Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.

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Section: Transcriptome Sequence Processing and Analysismentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Zhang

Sun

et al. 2021

Genes

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“…The anthocyanin synthesis in plants could also be regulated by visible light or be light independent. For instance, the roots of some potatoes (Liu et al, 2016;Vincenzo et al, 2014), sweet potatoes (Mano et al, 2007;Zhang et al, 2020), and carrots (Xu et al, 2019), the flesh of some apples (Chagné et al, 2013;Espley et al, 2007), kiwifruits (Wang et al, 2019), and plums (Niu et al, 2017) can accumulate abundant amounts of anthocyanins via the regulation of MYB transcription factors during their growth underground, or above the ground in the dark. After photosynthesis was interrupted, the anthocyanin synthesis was inhibited in turnip (Schneider & Stimson, 1971), corn (Kim et al, 2006), and Arabidopsis (Jeong et al, 2010).…”

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confidence: 99%

Visible light regulates anthocyanin synthesis via malate dehydrogenases and the ethylene signaling pathway in plum (Prunus salicina L.)

Zhang

Cui

Niu

et al. 2021

Physiologia Plantarum

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Light regulates anthocyanins synthesis in plants. Upon exposure to visible light, the inhibition of photosynthetic electron transfer significantly lowered the contents of anthocyanins and the expression levels of key genes involved in anthocyanins synthesis in plum fruit peel. Meanwhile, the expression levels of PsmMDH2 (encoding the malate dehydrogenase in mitochondria) and PschMDH (encoding the malate dehydrogenase in chloroplasts) decreased significantly. The contents of anthocyanins and the levels of the key genes involved in anthocyanin synthesis decreased significantly with the treatment of 1-MCP (an inhibitor of ethylene perception) but were enhanced by the exogenous application of ethylene. The ethylene treatment could also recover the anthocyanin synthesis capacity lowered by the photosynthetic electron transfer inhibition. Silencing PsmMDH2 and PschMDH significantly lowered the contents of anthocyanins in plum fruit. At low temperature, visible light irradiation induced anthocyanin accumulation in Arabidopsis leaves. However, the mmdh, chmdh, and etr1-1 mutants had significantly lower anthocyanins content and expressions of the key genes involved in anthocyanins synthesis compared to wild type. Overall, the present study demonstrates that both photosynthesis and respiration were involved in the regulation of anthocyanin synthesis in visible light. The visible light regulates anthocyanin synthesis by controlling the malate metabolism via MDHs and the ethylene signaling pathway. 1 | INTRODUCTION Anthocyanins are a group of water-soluble flavonoids and exist in various tissues of plants and make them appear red, blue, and purple colors. Anthocyanins can attenuate light to protect plants from photoinhibition/photodamage (Li et al.

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“…(Zhang et al. , 2020 ), and traits devised alternative ways to integrate phenotyping, transcriptomic, and GWA data to prioritize candidate genes. These studies demonstrated that combined approaches, when applied on large datasets in some cases already available in the literature, may effectively advance our understanding of the molecular mechanisms underlying complex traits and provide candidate genes to prioritize for validation and breeding.…”

Section: Discussionmentioning

confidence: 99%

A forward genetics approach integrating genome‐wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays)

et al. 2021

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SUMMARY The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29 573 gene models in RILs and to derive 373 769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript–trait correlations. Then, leaf traits were associated with SNPs in a genome‐wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript–trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co‐expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize.

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Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

Cited by 40 publications

References 65 publications

Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Visible light regulates anthocyanin synthesis via malate dehydrogenases and the ethylene signaling pathway in plum (Prunus salicina L.)

A forward genetics approach integrating genome‐wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays)

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