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Volatile metabolome and transcriptome reveal fragrance release rhythm and molecular mechanisms of Rosa yangii

ZHOU Li-jun, HUANG Run-huan, LIU Ting-han, LIU Wei-chao, CHEN Yun-yi, LU Pei-feng, LUO Le, PAN Hui-tang, YU Chao, ZHANG Qi-xiang

2023, 22 (7): 2111-2125. DOI: 10.1016/j.jia.2023.06.015

Abstract （263） PDF in ScienceDirect

Rose is a highly significant ornamental plant with substantial edible and medicinal value, cultivated worldwide primarily for perfume production. Recently, Rosa yangii, a new species found in northwestern Yunnan, China, has drawn attention due to its strong sweet scented flowers. In this study, the floral components of R. yangii were extracted at different flowering stages using solid phase micro extraction (SPME) and analyzed through gas chromatography–mass spectrometry (GC–MS). A total of 131 volatile organic compounds (VOCs) were detected from R. yangii, including 69 odor compounds. The production and release of floral VOCs were the highest during the initial-open stage, making it the most suitable time for harvesting as a significant number of floral components were synthesized and preserved. The analysis of the odor activity values (OAV) highlighted several key aromatic ingredients of R. yangii, such as eugenol, methyleugenol, benzeneacetaldehyde and phenylethylalcohol, heptanal, decanal, (E)-2-hexen-1-yl acetate, caryophyllene, and others. Metabolome and time-order gene co-expression networks (TO-GCN) revealed that VOCs and benzenoids/phenylpropanoids, along with associated genes, played a pivotal role in the overall floral regulatory network of R. yangii. MYB and bHLH were identified as the essential regulatory factors governing the regulation of eugenol synthase (EGS) and isoeugenol synthase (IGS), consequently influencing the sweet scent of R. yangii. The findings of this study provide a scientific foundation for enhancing fragrance through molecular breeding of ornamental plants. Furthermore, the study facilitated the development and utilization of this new plant’s essential oil material in various industries, including food storage, aromatherapy, cosmetic, and perfumery.

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Transcriptomic analysis reveals the transcription factors involved in regulating the expression of EPSPS gene, which confers glyphosate resistance of goosegrass (Eleusine indica)

ZHANG Chun, YU Chao-jie, ZHANG Tai-jie, GUO Wen-lei, TIAN Xing-shan

2021, 20 (8): 2180-2194. DOI: 10.1016/S2095-3119(21)63682-1

Abstract （169） PDF in ScienceDirect

Glyphosate inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) and overexpression of the EPSPS gene is one of the molecular mechanisms conferring glyphosate resistance in weeds. A regulatory sequence of EPSPS gene was isolated previously, and an alteration in its 5´-untranslated region (UTR) pyrimidine (Py)-rich stretch element is involved in the regulation of EPSPS expression in glyphosate-resistant (GR) Eleusine indica. However, the transcription factors involved in this regulatory sequence remain to be elucidated. In this study, we investigated the regulatory network of EPSPS overexpression associated genes in a GR E. indica population by RNA-seq. The differentially expressed transcript analyses revealed that glyphosate treatment caused an increase in the expression of 2 752 unigenes and a decrease in the expression of 4 025 unigenes in the GR E. indica, compared to the glyphosate-susceptible (GS) E. indica. Among them, 1 373 unigenes were identified to be co-expressed with the EPSPS gene in GR E. indica. GO and KEGG pathway analyses showed that the up-regulated unigenes were mainly enriched in chloroplasts and associated with the shikimate biosynthesis pathway, chlorophy II and peroxisome metabolism processes. Notably, the expression of a Shikimate kinase which catalyzed the conversion of Shikimate to Shikimate 3-phosphate (S3P, a substrate of EPSPS), was also up-regulated. Eight transcription factors were identified as likely to be involved in the regulation of the EPSPS expression, and three of them (ARF2, ARF8 and BPC6) showed more binding sites because of a (CT)_n insertion of the 5´-UTR Py-rich stretch element in GR. However, the yeast one-hybrid assay illustrated that ARF8 and BPC6 could bind to the 5´-UTR Py-rich stretch element of wild type EPSPS, but could not bind to the mutated form. Our data suggests that the transcriptional regulation of EPSPS expression is complex and was significantly altered in GR E. indica. These discoveries provide new references for further study of the EPSPS overexpression mechanism that endows glyphosate resistance.

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High density genetic map and quantitative trait loci (QTLs) associated with petal number and flower diameter identified in tetraploid rose

YU Chao, WAN Hui-hua, Peter M. BOURKE, CHENG Bi-xuan, LUO Le, PAN Hui-tang, ZHANG Qi-xiang

2021, 20 (5): 1287-1301. DOI: 10.1016/S2095-3119(20)63416-5

Abstract （182） PDF in ScienceDirect

Rose is one of the most important ornamental and economic plants in the world. Modern rose cultivars are primarily tetraploid, and during meiosis, they may exhibit double reduction or preferential chromosome pairing. Therefore, the construction of a high density genetic map of tetraploid rose is both challenging and instructive. In this study, a tetraploid rose population was used to conduct a genetic analysis using genome sequencing. A total of 17 382 single nucleotide polymorphism (SNP) markers were selected from 2 308 042 detected SNPs. Combined with 440 previously developed simple sequence repeats (SSR) and amplified fragment length polymorphism (AFLP) markers, a marker dosage of 6 885 high quality markers was successfully assigned by GATK software in the tetraploid model. These markers were used in the construction of a high density genetic map, containing the expected seven linkage groups with 6 842 markers, a total map length of 1 158.9 cM, and an average inter-marker distance of 0.18 cM. Quantitative trait locus (QTL) analysis was subsequently performed to characterize the genetic architecture of petal number and flower diameter. One major QTL (qpnum-3-1) was detected for petal number in three consecutive years, which explained 20.18–22.11% of the variation in petal number. Four QTLs were detected for flower diameter; the main locus, qfdia-2-2, was identified in two consecutive years. Our results will benefit the molecular marker-assisted breeding of modern rose cultivars. In addition, this study provides a guide for the genetic and QTL analysis of autotetraploid plants using sequencing-based genotyping methods.

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Temporal dynamics of nutrient balance, plasma biochemical and immune traits, and liver function in transition dairy cows

SUN Bo-fei, CAO Yang-chun, CAI Chuan-jiang, YU Chao, LI Sheng-xiang, YAO Jun-hu

2020, 19 (3): 820-837. DOI: 10.1016/S2095-3119(20)63153-7

Abstract （102） PDF in ScienceDirect

The objective of this study was to analyze the dynamics of nutrient balance, physiological biomarkers and comprehensive indexes associated with metabolism and function of organs in transition cows. Fourteen transition cows were used for this research. Dietary intake was recorded daily, and samples of the diet, venous blood and milk were collected for measurements. The balance values of net energy for lactation (NE_L ), metabolizable protein (MP), and metabolizable glucose (MG) were calculated, and regression analysis and calculation of comprehensive indexes were performed. Accordingly, the prepartum cows presented positive balances of NEL , MP, and MG, while severe negative balances were found during the postpartum period. Dynamic changes of energy metabolism, nutrient mobilization, liver function, anti-oxidative status and immune response, as indicated by blood biomarkers and modified comprehensive indexes, were out of sync with the calculated balance values, but they were closely related to the day relative to calving. Compared with the 21 d prepartum, the plasma concentrations of non-esterified fatty acids (NEFA) and β-hydroxybutyric acid (BHBA) were significantly increased around and after calving (P<0.05), and similar variation tendency was observed for most of other parameters. The occurrence of parturition and the initiation of lactation were more responsible for the negative balances of nutrients in transition dairy cows. Although negative balances of NE_L , MP and MG were not observed using the assessment model, the nutritional strategies should be applied before calving, because metabolic adaptations had been validated during the prepartum period. In addition, it was plausible to conclude that the decline of hepatic metabolism, defense function and insulin sensitivity are critical causes of metabolic dysfunction.

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Identification of differentially-expressed genes of rice in overlapping responses to bacterial infection by Xanthomonas oryzae pv. oryzae and nitrogen deficiency

YU Chao, CHEN Hua-min, TIAN Fang, BI Yong-mei, Rothstein J Steven, Leach E Jan, HE Chen-yang

2015, 14 (5): 888-899. DOI: 10.1016/S2095-3119(14)60860-1

Abstract （2069） PDF in ScienceDirect

Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of high nitrogen (N) responsive diseases. Rice plants became more disease resistant with decreasing N suggesting that the crosstalk between disease resistance and N utilization pathways might exist. However, the co-regulatory components in such crosstalk have not been elucidated. Here, we comparatively analyzed the gene expression profiling of rice under Xoo inoculation, low N treatment, or a combination of both stresses, and identified the differentially-expressed genes (DEGs) in overlapping responses. These DEGs were involved in different biological processes, including innate immunity and nitrogen metabolism. The randomly-selected DEGs expression was validated by quantitative real-time PCR assays. Temporal expression of six genes from different functional categories suggested that N condition was the dominant factor when both stresses were present. These DEGs identified provide novel insights into the coordinated regulatory mechanism in biotic and abiotic stress responses in rice.

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